SILAC + light channel

[drstiltz]

Hi All,

I'm working on this project where I add light and heavy-labeled peptides together, mix them and run on an Orbitrap, using LC-DIA.

Interestingly, when I create my own peptide library using only heavy peptides on Fragpipe, and use this library for my DIA-NN searches, DIA-NN finds my heavy-labeled peptides, but not he light peptides. Interestingly, when I use a regular library, I only get the light peptide hits, but never the heavy peptides. When I used the SILAC settings of DIA-NN, I'm only getting the light peptides again. I get a tsv file with heavy peptides but the intensity values are all empty.

Would there be a way to quantify both the light and the heavy channel?

[vdemichev]

Hi,

For DIA-NN, the input library should not have any differential labels, i.e. DIA-NN always adds labels in silico when instructed to do so using the --channels command. If you only have a heavy library, you can (i) specify the light channel as a negative mass label with the --channels command or (ii) use some script to adjust the masses in the library to make it a light one.

When I used the SILAC settings of DIA-NN, I'm only getting the light peptides again.

How does the log look like?

Best, Vadim

[drstiltz]

Hi Vadim,

I use these parameters for my SILAC search when I use a regular library: --fixed-mod SILAC,0.0,KR,label --channels SILAC,L,KR,0:0; SILAC,H,KR,6.020129:10.008269 --original-mods --strip-unknown-mods --peak-translation

seems like this worked for my Orbitrap files, but sadly when we get data from our Bruker SCP-Tof, it seems like I don't get intensities of my heavy peptides.

[Uploading report.log.txt…]()

[drstiltz]

here is my log:

DIA-NN 1.9 (Data-Independent Acquisition by Neural Networks) Compiled on Jun 8 2024 20:00:31 Current date and time: Tue Sep 3 09:48:39 2024 CPU: GenuineIntel Intel(R) Xeon(R) CPU E5-2690 v4 @ 2.60GHz SIMD instructions: AVX AVX2 FMA SSE4.1 SSE4.2 Logical CPU cores: 16 diann.exe --f Y:\TimsTOF-SCP\Data\240711_HK2_LIBRARY\HK2_LIBRARY_GN1_1_30168.d --f Y:\TimsTOF-SCP\Data\240711_HK2_LIBRARY\HK2_LIBRARY_RC2_1_30145.d --f Y:\TimsTOF-SCP\Data\240711_HK2_LIBRARY\HK2_LIBRARY_RC3_1_30146.d --f Y:\TimsTOF-SCP\Data\240711_HK2_LIBRARY\HK2_LIBRARY_RC4_1_30147.d --f Y:\TimsTOF-SCP\Data\240711_HK2_LIBRARY\HK2_LIBRARY_RC5_1_30148.d --f Y:\TimsTOF-SCP\Data\240711_HK2_LIBRARY\HK2_LIBRARY_RC6_1_30149.d --f Y:\TimsTOF-SCP\Data\240711_HK2_LIBRARY\HK2_LIBRARY_RC7_1_30150.d --f Y:\TimsTOF-SCP\Data\240711_HK2_LIBRARY\HK2_LIBRARY_RC8_1_30151.d --f Y:\TimsTOF-SCP\Data\240711_HK2_LIBRARY\HK2_LIBRARY_RC9_1_30152.d --f Y:\TimsTOF-SCP\Data\240711_HK2_LIBRARY\HK2_LIBRARY_RC10_1_30153.d --f Y:\TimsTOF-SCP\Data\240711_HK2_LIBRARY\HK2_LIBRARY_RC11_1_30154.d --f Y:\TimsTOF-SCP\Data\240711_HK2_LIBRARY\HK2_LIBRARY_RC12_1_30155.d --f Y:\TimsTOF-SCP\Data\240711_HK2_LIBRARY\HK2_LIBRARY_RC13_1_30156.d --f Y:\TimsTOF-SCP\Data\240711_HK2_LIBRARY\HK2_LIBRARY_RC14_1_30157.d --f Y:\TimsTOF-SCP\Data\240711_HK2_LIBRARY\HK2_LIBRARY_RC15_1_30158.d --f Y:\TimsTOF-SCP\Data\240711_HK2_LIBRARY\HK2_LIBRARY_RC16_1_30159.d --f Y:\TimsTOF-SCP\Data\240711_HK2_LIBRARY\HK2_LIBRARY_RC17_1_30160.d --f Y:\TimsTOF-SCP\Data\240711_HK2_LIBRARY\HK2_LIBRARY_RC18_1_30161.d --f Y:\TimsTOF-SCP\Data\240711_HK2_LIBRARY\HK2_LIBRARY_RC19_1_30162.d --f Y:\TimsTOF-SCP\Data\240711_HK2_LIBRARY\HK2_LIBRARY_RC20_1_30163.d --f Y:\TimsTOF-SCP\Data\240711_HK2_LIBRARY\HK2_LIBRARY_RC21_1_30164.d --f Y:\TimsTOF-SCP\Data\240711_HK2_LIBRARY\HK2_LIBRARY_RC22_1_30165.d --f Y:\TimsTOF-SCP\Data\240711_HK2_LIBRARY\HK2_LIBRARY_RC23_1_30166.d --f Y:\TimsTOF-SCP\Data\240711_HK2_LIBRARY\HK2_LIBRARY_RC24_1_30167.d --f \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2--A1_RF1_1_30634.d --f \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-A2_RA2_1_30639.d --f \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-A3_RF8_1_30708.d --f \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-A4_GF7_1_30713.d --f \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-B1_RF2_1_30644.d --f \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-B2_RA3_1_30649.d --f \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-B3_RF9_1_30722.d --f \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-B4_RA10_1_30727.d --f 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\smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-SILAC-A1_RC1_1_30631.d --f \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-SILAC-A2_RH1_1_30636.d --f \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-SILAC-A3_RC8_1_30705.d --f \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-SILAC-A4_RH8_1_30710.d --f \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-SILAC-B1_RC2_1_30641.d --f \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-SILAC-B2_RH2_1_30646.d --f \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-SILAC-B3_RC9_1_30719.d --f \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-SILAC-B4_RH9_1_30724.d --f \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-SILAC-C1_RC3_1_30651.d --f \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-SILAC-C2_RH3_1_30656.d --f \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-SILAC-C3_RC10_1_30729.d --lib D:\HK2_library\HK2_3\library_HK2_light.tsv --threads 16 --verbose 1 --out D:\HK2_library\forskyline2\report.tsv --qvalue 0.01 --matrices --out-lib D:\HK2_library\forskyline2\report.tsv --gen-spec-lib --unimod4 --mass-acc 15 --mass-acc-ms1 20 --reanalyse --relaxed-prot-inf --rt-profiling

WARNING: unrecognised option [--A1_RF1_1_30634.d] WARNING: unrecognised option [--A1_RE1_1_30633.d] Thread number set to 16 Output will be filtered at 0.01 FDR Precursor/protein x samples expression level matrices will be saved along with the main report A spectral library will be generated Cysteine carbamidomethylation enabled as a fixed modification A spectral library will be created from the DIA runs and used to reanalyse them; .quant files will only be saved to disk during the first step Heuristic protein grouping will be used, to reduce the number of protein groups obtained; this mode is recommended for benchmarking protein ID numbers, GO/pathway and system-scale analyses The spectral library (if generated) will retain the original spectra but will include empirically-aligned RTs WARNING: skipping \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2 - invalid raw MS data format WARNING: skipping \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-NUC - invalid raw MS data format Mass accuracy will be fixed to 1.5e-05 (MS2) and 2e-05 (MS1) WARNING: protein inference is enabled but no FASTA provided - is this intended?

97 files will be processed [0:00] Loading spectral library D:\HK2_library\HK2_3\library_HK2_light.tsv [0:01] Spectral library loaded: 4312 protein isoforms, 4312 protein groups and 22897 precursors in 20499 elution groups. [0:01] Initialising library [0:01] Saving the library to D:\HK2_library\HK2_3\library_HK2_light.tsv.skyline.speclib

First pass: generating a spectral library from DIA data

[0:01] File #1/97 [0:01] Loading run Y:\TimsTOF-SCP\Data\240711_HK2_LIBRARY\HK2_LIBRARY_GN1_1_30168.d For most Slice/DIA-PASEF datasets it is better to manually fix both the MS1 and MS2 mass accuracies to values in the range 10-15 ppm. ERROR: either the dia-PASEF file is damaged or a .dia file produced by an older DIA-NN version has been loaded: performance might be suboptimal, regenerate the .dia file using this DIA-NN version WARNING: incorrectly recorded isolation window margins [0:18] 0 library precursors are potentially detectable [0:18] Processing... [0:18] Removing low confidence identifications [0:18] Removing interfering precursors [0:18] Too few confident identifications, neural networks will not be used [0:18] Number of IDs at 0.01 FDR: 0 [0:18] Calculating protein q-values [0:18] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [0:18] Quantification [0:18] Quantification information saved to Y:\TimsTOF-SCP\Data\240711_HK2_LIBRARY\HK2_LIBRARY_GN1_1_30168.d.quant

[0:18] File #2/97 [0:18] Loading run Y:\TimsTOF-SCP\Data\240711_HK2_LIBRARY\HK2_LIBRARY_RC2_1_30145.d ERROR: either the dia-PASEF file is damaged or a .dia file produced by an older DIA-NN version has been loaded: performance might be suboptimal, regenerate the .dia file using this DIA-NN version WARNING: incorrectly recorded isolation window margins [0:36] 0 library precursors are potentially detectable [0:36] Processing... [0:36] Removing low confidence identifications [0:36] Removing interfering precursors [0:36] Too few confident identifications, neural networks will not be used [0:36] Number of IDs at 0.01 FDR: 0 [0:36] Calculating protein q-values [0:36] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [0:36] Quantification [0:36] Quantification information saved to Y:\TimsTOF-SCP\Data\240711_HK2_LIBRARY\HK2_LIBRARY_RC2_1_30145.d.quant

[0:36] File #3/97 [0:36] Loading run Y:\TimsTOF-SCP\Data\240711_HK2_LIBRARY\HK2_LIBRARY_RC3_1_30146.d ERROR: either the dia-PASEF file is damaged or a .dia file produced by an older DIA-NN version has been loaded: performance might be suboptimal, regenerate the .dia file using this DIA-NN version WARNING: incorrectly recorded isolation window margins [0:42] 0 library precursors are potentially detectable [0:42] Processing... [0:42] Removing low confidence identifications [0:42] Removing interfering precursors [0:42] Too few confident identifications, neural networks will not be used [0:42] Number of IDs at 0.01 FDR: 0 [0:42] Calculating protein q-values [0:42] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [0:42] Quantification [0:42] Quantification information saved to Y:\TimsTOF-SCP\Data\240711_HK2_LIBRARY\HK2_LIBRARY_RC3_1_30146.d.quant

[0:42] File #4/97 [0:42] Loading run Y:\TimsTOF-SCP\Data\240711_HK2_LIBRARY\HK2_LIBRARY_RC4_1_30147.d ERROR: either the dia-PASEF file is damaged or a .dia file produced by an older DIA-NN version has been loaded: performance might be suboptimal, regenerate the .dia file using this DIA-NN version WARNING: incorrectly recorded isolation window margins [0:59] 0 library precursors are potentially detectable [0:59] Processing... [0:59] Removing low confidence identifications [0:59] Removing interfering precursors [0:59] Too few confident identifications, neural networks will not be used [0:59] Number of IDs at 0.01 FDR: 0 [0:59] Calculating protein q-values [0:59] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [0:59] Quantification [0:59] Quantification information saved to Y:\TimsTOF-SCP\Data\240711_HK2_LIBRARY\HK2_LIBRARY_RC4_1_30147.d.quant

[0:59] File #5/97 [0:59] Loading run Y:\TimsTOF-SCP\Data\240711_HK2_LIBRARY\HK2_LIBRARY_RC5_1_30148.d ERROR: either the dia-PASEF file is damaged or a .dia file produced by an older DIA-NN version has been loaded: performance might be suboptimal, regenerate the .dia file using this DIA-NN version WARNING: incorrectly recorded isolation window margins [1:16] 0 library precursors are potentially detectable [1:16] Processing... [1:16] Removing low confidence identifications [1:16] Removing interfering precursors [1:16] Too few confident identifications, neural networks will not be used [1:16] Number of IDs at 0.01 FDR: 0 [1:16] Calculating protein q-values [1:16] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [1:16] Quantification [1:16] Quantification information saved to Y:\TimsTOF-SCP\Data\240711_HK2_LIBRARY\HK2_LIBRARY_RC5_1_30148.d.quant

[1:16] File #6/97 [1:16] Loading run Y:\TimsTOF-SCP\Data\240711_HK2_LIBRARY\HK2_LIBRARY_RC6_1_30149.d ERROR: either the dia-PASEF file is damaged or a .dia file produced by an older DIA-NN version has been loaded: performance might be suboptimal, regenerate the .dia file using this DIA-NN version WARNING: incorrectly recorded isolation window margins [1:30] 0 library precursors are potentially detectable [1:30] Processing... [1:30] Removing low confidence identifications [1:30] Removing interfering precursors [1:30] Too few confident identifications, neural networks will not be used [1:30] Number of IDs at 0.01 FDR: 0 [1:30] Calculating protein q-values [1:30] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [1:30] Quantification [1:30] Quantification information saved to Y:\TimsTOF-SCP\Data\240711_HK2_LIBRARY\HK2_LIBRARY_RC6_1_30149.d.quant

[1:30] File #7/97 [1:30] Loading run Y:\TimsTOF-SCP\Data\240711_HK2_LIBRARY\HK2_LIBRARY_RC7_1_30150.d ERROR: either the dia-PASEF file is damaged or a .dia file produced by an older DIA-NN version has been loaded: performance might be suboptimal, regenerate the .dia file using this DIA-NN version WARNING: incorrectly recorded isolation window margins [1:47] 0 library precursors are potentially detectable [1:47] Processing... [1:47] Removing low confidence identifications [1:47] Removing interfering precursors [1:47] Too few confident identifications, neural networks will not be used [1:47] Number of IDs at 0.01 FDR: 0 [1:47] Calculating protein q-values [1:47] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [1:47] Quantification [1:48] Quantification information saved to Y:\TimsTOF-SCP\Data\240711_HK2_LIBRARY\HK2_LIBRARY_RC7_1_30150.d.quant

[1:48] File #8/97 [1:48] Loading run Y:\TimsTOF-SCP\Data\240711_HK2_LIBRARY\HK2_LIBRARY_RC8_1_30151.d ERROR: either the dia-PASEF file is damaged or a .dia file produced by an older DIA-NN version has been loaded: performance might be suboptimal, regenerate the .dia file using this DIA-NN version WARNING: incorrectly recorded isolation window margins [2:02] 0 library precursors are potentially detectable [2:02] Processing... [2:02] Removing low confidence identifications [2:02] Removing interfering precursors [2:02] Too few confident identifications, neural networks will not be used [2:02] Number of IDs at 0.01 FDR: 0 [2:02] Calculating protein q-values [2:02] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [2:02] Quantification [2:02] Quantification information saved to Y:\TimsTOF-SCP\Data\240711_HK2_LIBRARY\HK2_LIBRARY_RC8_1_30151.d.quant

[2:02] File #9/97 [2:02] Loading run Y:\TimsTOF-SCP\Data\240711_HK2_LIBRARY\HK2_LIBRARY_RC9_1_30152.d ERROR: either the dia-PASEF file is damaged or a .dia file produced by an older DIA-NN version has been loaded: performance might be suboptimal, regenerate the .dia file using this DIA-NN version WARNING: incorrectly recorded isolation window margins [2:16] 0 library precursors are potentially detectable [2:16] Processing... [2:16] Removing low confidence identifications [2:16] Removing interfering precursors [2:16] Too few confident identifications, neural networks will not be used [2:16] Number of IDs at 0.01 FDR: 0 [2:16] Calculating protein q-values [2:16] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [2:16] Quantification [2:16] Quantification information saved to Y:\TimsTOF-SCP\Data\240711_HK2_LIBRARY\HK2_LIBRARY_RC9_1_30152.d.quant

[2:16] File #10/97 [2:16] Loading run Y:\TimsTOF-SCP\Data\240711_HK2_LIBRARY\HK2_LIBRARY_RC10_1_30153.d ERROR: either the dia-PASEF file is damaged or a .dia file produced by an older DIA-NN version has been loaded: performance might be suboptimal, regenerate the .dia file using this DIA-NN version WARNING: incorrectly recorded isolation window margins [2:30] 0 library precursors are potentially detectable [2:30] Processing... [2:30] Removing low confidence identifications [2:30] Removing interfering precursors [2:30] Too few confident identifications, neural networks will not be used [2:30] Number of IDs at 0.01 FDR: 0 [2:30] Calculating protein q-values [2:30] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [2:30] Quantification [2:30] Quantification information saved to Y:\TimsTOF-SCP\Data\240711_HK2_LIBRARY\HK2_LIBRARY_RC10_1_30153.d.quant

[2:30] File #11/97 [2:30] Loading run Y:\TimsTOF-SCP\Data\240711_HK2_LIBRARY\HK2_LIBRARY_RC11_1_30154.d ERROR: either the dia-PASEF file is damaged or a .dia file produced by an older DIA-NN version has been loaded: performance might be suboptimal, regenerate the .dia file using this DIA-NN version WARNING: incorrectly recorded isolation window margins [2:46] 0 library precursors are potentially detectable [2:46] Processing... [2:46] Removing low confidence identifications [2:46] Removing interfering precursors [2:46] Too few confident identifications, neural networks will not be used [2:46] Number of IDs at 0.01 FDR: 0 [2:46] Calculating protein q-values [2:46] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [2:46] Quantification [2:46] Quantification information saved to Y:\TimsTOF-SCP\Data\240711_HK2_LIBRARY\HK2_LIBRARY_RC11_1_30154.d.quant

[2:46] File #12/97 [2:46] Loading run Y:\TimsTOF-SCP\Data\240711_HK2_LIBRARY\HK2_LIBRARY_RC12_1_30155.d ERROR: either the dia-PASEF file is damaged or a .dia file produced by an older DIA-NN version has been loaded: performance might be suboptimal, regenerate the .dia file using this DIA-NN version WARNING: incorrectly recorded isolation window margins [3:00] 0 library precursors are potentially detectable [3:00] Processing... [3:00] Removing low confidence identifications [3:00] Removing interfering precursors [3:00] Too few confident identifications, neural networks will not be used [3:00] Number of IDs at 0.01 FDR: 0 [3:00] Calculating protein q-values [3:00] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [3:00] Quantification [3:00] Quantification information saved to Y:\TimsTOF-SCP\Data\240711_HK2_LIBRARY\HK2_LIBRARY_RC12_1_30155.d.quant

[3:00] File #13/97 [3:00] Loading run Y:\TimsTOF-SCP\Data\240711_HK2_LIBRARY\HK2_LIBRARY_RC13_1_30156.d ERROR: either the dia-PASEF file is damaged or a .dia file produced by an older DIA-NN version has been loaded: performance might be suboptimal, regenerate the .dia file using this DIA-NN version WARNING: incorrectly recorded isolation window margins [3:15] 0 library precursors are potentially detectable [3:15] Processing... [3:15] Removing low confidence identifications [3:15] Removing interfering precursors [3:15] Too few confident identifications, neural networks will not be used [3:15] Number of IDs at 0.01 FDR: 0 [3:15] Calculating protein q-values [3:15] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [3:15] Quantification [3:15] Quantification information saved to Y:\TimsTOF-SCP\Data\240711_HK2_LIBRARY\HK2_LIBRARY_RC13_1_30156.d.quant

[3:15] File #14/97 [3:15] Loading run Y:\TimsTOF-SCP\Data\240711_HK2_LIBRARY\HK2_LIBRARY_RC14_1_30157.d ERROR: either the dia-PASEF file is damaged or a .dia file produced by an older DIA-NN version has been loaded: performance might be suboptimal, regenerate the .dia file using this DIA-NN version WARNING: incorrectly recorded isolation window margins [3:29] 0 library precursors are potentially detectable [3:29] Processing... [3:29] Removing low confidence identifications [3:29] Removing interfering precursors [3:29] Too few confident identifications, neural networks will not be used [3:29] Number of IDs at 0.01 FDR: 0 [3:29] Calculating protein q-values [3:29] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [3:29] Quantification [3:29] Quantification information saved to Y:\TimsTOF-SCP\Data\240711_HK2_LIBRARY\HK2_LIBRARY_RC14_1_30157.d.quant

[3:29] File #15/97 [3:29] Loading run Y:\TimsTOF-SCP\Data\240711_HK2_LIBRARY\HK2_LIBRARY_RC15_1_30158.d ERROR: either the dia-PASEF file is damaged or a .dia file produced by an older DIA-NN version has been loaded: performance might be suboptimal, regenerate the .dia file using this DIA-NN version WARNING: incorrectly recorded isolation window margins [3:43] 0 library precursors are potentially detectable [3:43] Processing... [3:43] Removing low confidence identifications [3:43] Removing interfering precursors [3:43] Too few confident identifications, neural networks will not be used [3:43] Number of IDs at 0.01 FDR: 0 [3:43] Calculating protein q-values [3:43] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [3:43] Quantification [3:43] Quantification information saved to Y:\TimsTOF-SCP\Data\240711_HK2_LIBRARY\HK2_LIBRARY_RC15_1_30158.d.quant

[3:43] File #16/97 [3:43] Loading run Y:\TimsTOF-SCP\Data\240711_HK2_LIBRARY\HK2_LIBRARY_RC16_1_30159.d ERROR: either the dia-PASEF file is damaged or a .dia file produced by an older DIA-NN version has been loaded: performance might be suboptimal, regenerate the .dia file using this DIA-NN version WARNING: incorrectly recorded isolation window margins [3:59] 0 library precursors are potentially detectable [3:59] Processing... [3:59] Removing low confidence identifications [3:59] Removing interfering precursors [3:59] Too few confident identifications, neural networks will not be used [3:59] Number of IDs at 0.01 FDR: 0 [3:59] Calculating protein q-values [3:59] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [3:59] Quantification [4:00] Quantification information saved to Y:\TimsTOF-SCP\Data\240711_HK2_LIBRARY\HK2_LIBRARY_RC16_1_30159.d.quant

[4:00] File #17/97 [4:00] Loading run Y:\TimsTOF-SCP\Data\240711_HK2_LIBRARY\HK2_LIBRARY_RC17_1_30160.d ERROR: either the dia-PASEF file is damaged or a .dia file produced by an older DIA-NN version has been loaded: performance might be suboptimal, regenerate the .dia file using this DIA-NN version WARNING: incorrectly recorded isolation window margins [4:14] 0 library precursors are potentially detectable [4:14] Processing... [4:14] Removing low confidence identifications [4:14] Removing interfering precursors [4:14] Too few confident identifications, neural networks will not be used [4:14] Number of IDs at 0.01 FDR: 0 [4:14] Calculating protein q-values [4:14] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [4:14] Quantification [4:14] Quantification information saved to Y:\TimsTOF-SCP\Data\240711_HK2_LIBRARY\HK2_LIBRARY_RC17_1_30160.d.quant

[4:14] File #18/97 [4:14] Loading run Y:\TimsTOF-SCP\Data\240711_HK2_LIBRARY\HK2_LIBRARY_RC18_1_30161.d ERROR: either the dia-PASEF file is damaged or a .dia file produced by an older DIA-NN version has been loaded: performance might be suboptimal, regenerate the .dia file using this DIA-NN version WARNING: incorrectly recorded isolation window margins [4:27] 0 library precursors are potentially detectable [4:27] Processing... [4:27] Removing low confidence identifications [4:27] Removing interfering precursors [4:27] Too few confident identifications, neural networks will not be used [4:27] Number of IDs at 0.01 FDR: 0 [4:27] Calculating protein q-values [4:27] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [4:27] Quantification [4:27] Quantification information saved to Y:\TimsTOF-SCP\Data\240711_HK2_LIBRARY\HK2_LIBRARY_RC18_1_30161.d.quant

[4:27] File #19/97 [4:27] Loading run Y:\TimsTOF-SCP\Data\240711_HK2_LIBRARY\HK2_LIBRARY_RC19_1_30162.d ERROR: either the dia-PASEF file is damaged or a .dia file produced by an older DIA-NN version has been loaded: performance might be suboptimal, regenerate the .dia file using this DIA-NN version WARNING: incorrectly recorded isolation window margins [4:40] 0 library precursors are potentially detectable [4:40] Processing... [4:40] Removing low confidence identifications [4:40] Removing interfering precursors [4:40] Too few confident identifications, neural networks will not be used [4:40] Number of IDs at 0.01 FDR: 0 [4:40] Calculating protein q-values [4:40] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [4:40] Quantification [4:40] Quantification information saved to Y:\TimsTOF-SCP\Data\240711_HK2_LIBRARY\HK2_LIBRARY_RC19_1_30162.d.quant

[4:40] File #20/97 [4:40] Loading run Y:\TimsTOF-SCP\Data\240711_HK2_LIBRARY\HK2_LIBRARY_RC20_1_30163.d ERROR: either the dia-PASEF file is damaged or a .dia file produced by an older DIA-NN version has been loaded: performance might be suboptimal, regenerate the .dia file using this DIA-NN version WARNING: incorrectly recorded isolation window margins [4:55] 0 library precursors are potentially detectable [4:55] Processing... [4:55] Removing low confidence identifications [4:55] Removing interfering precursors [4:55] Too few confident identifications, neural networks will not be used [4:55] Number of IDs at 0.01 FDR: 0 [4:55] Calculating protein q-values [4:55] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [4:55] Quantification [4:55] Quantification information saved to Y:\TimsTOF-SCP\Data\240711_HK2_LIBRARY\HK2_LIBRARY_RC20_1_30163.d.quant

[4:55] File #21/97 [4:55] Loading run Y:\TimsTOF-SCP\Data\240711_HK2_LIBRARY\HK2_LIBRARY_RC21_1_30164.d ERROR: either the dia-PASEF file is damaged or a .dia file produced by an older DIA-NN version has been loaded: performance might be suboptimal, regenerate the .dia file using this DIA-NN version WARNING: incorrectly recorded isolation window margins [5:09] 0 library precursors are potentially detectable [5:09] Processing... [5:09] Removing low confidence identifications [5:09] Removing interfering precursors [5:09] Too few confident identifications, neural networks will not be used [5:09] Number of IDs at 0.01 FDR: 0 [5:09] Calculating protein q-values [5:09] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [5:09] Quantification [5:09] Quantification information saved to Y:\TimsTOF-SCP\Data\240711_HK2_LIBRARY\HK2_LIBRARY_RC21_1_30164.d.quant

[5:09] File #22/97 [5:09] Loading run Y:\TimsTOF-SCP\Data\240711_HK2_LIBRARY\HK2_LIBRARY_RC22_1_30165.d ERROR: either the dia-PASEF file is damaged or a .dia file produced by an older DIA-NN version has been loaded: performance might be suboptimal, regenerate the .dia file using this DIA-NN version WARNING: incorrectly recorded isolation window margins [5:23] 0 library precursors are potentially detectable [5:23] Processing... [5:23] Removing low confidence identifications [5:23] Removing interfering precursors [5:23] Too few confident identifications, neural networks will not be used [5:23] Number of IDs at 0.01 FDR: 0 [5:23] Calculating protein q-values [5:23] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [5:23] Quantification [5:23] Quantification information saved to Y:\TimsTOF-SCP\Data\240711_HK2_LIBRARY\HK2_LIBRARY_RC22_1_30165.d.quant

[5:23] File #23/97 [5:23] Loading run Y:\TimsTOF-SCP\Data\240711_HK2_LIBRARY\HK2_LIBRARY_RC23_1_30166.d ERROR: either the dia-PASEF file is damaged or a .dia file produced by an older DIA-NN version has been loaded: performance might be suboptimal, regenerate the .dia file using this DIA-NN version WARNING: incorrectly recorded isolation window margins [5:38] 0 library precursors are potentially detectable [5:38] Processing... [5:38] Removing low confidence identifications [5:38] Removing interfering precursors [5:38] Too few confident identifications, neural networks will not be used [5:38] Number of IDs at 0.01 FDR: 0 [5:38] Calculating protein q-values [5:38] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [5:38] Quantification [5:38] Quantification information saved to Y:\TimsTOF-SCP\Data\240711_HK2_LIBRARY\HK2_LIBRARY_RC23_1_30166.d.quant

[5:38] File #24/97 [5:38] Loading run Y:\TimsTOF-SCP\Data\240711_HK2_LIBRARY\HK2_LIBRARY_RC24_1_30167.d ERROR: either the dia-PASEF file is damaged or a .dia file produced by an older DIA-NN version has been loaded: performance might be suboptimal, regenerate the .dia file using this DIA-NN version WARNING: incorrectly recorded isolation window margins [5:53] 0 library precursors are potentially detectable [5:53] Processing... [5:53] Removing low confidence identifications [5:53] Removing interfering precursors [5:53] Too few confident identifications, neural networks will not be used [5:53] Number of IDs at 0.01 FDR: 0 [5:53] Calculating protein q-values [5:53] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [5:53] Quantification [5:53] Quantification information saved to Y:\TimsTOF-SCP\Data\240711_HK2_LIBRARY\HK2_LIBRARY_RC24_1_30167.d.quant

[5:53] File #25/97 [5:53] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-A2_RA2_1_30639.d [6:18] 22897 library precursors are potentially detectable [6:18] Processing... [6:29] Cannot perform mass calibration, too few confidently identified precursors [6:29] Cannot perform MS1 mass calibration, too few confidently identified precursors [6:40] RT window set to 6.41409 [6:40] Peak width: 0 [6:40] Scan window radius set to 5 [6:40] Cannot perform mass calibration, too few confidently identified precursors [6:40] Cannot perform MS1 mass calibration, too few confidently identified precursors [7:28] Removing low confidence identifications [7:28] Removing interfering precursors [7:28] Too few confident identifications, neural networks will not be used [7:28] Number of IDs at 0.01 FDR: 2 [7:28] Calculating protein q-values [7:28] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [7:28] Quantification [7:28] Quantification information saved to \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-A2_RA2_1_30639.d.quant

[7:28] File #26/97 [7:28] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-A3_RF8_1_30708.d [8:01] 22897 library precursors are potentially detectable [8:01] Processing... [8:06] RT window set to 0.556117 [8:06] Recommended MS1 mass accuracy setting: 9.75262 ppm [8:13] Removing low confidence identifications [8:13] Removing interfering precursors [8:13] Training neural networks: 9705 targets, 5278 decoys [8:14] Number of IDs at 0.01 FDR: 5882 [8:14] Calculating protein q-values [8:14] Number of protein isoforms identified at 1% FDR: 1526 (precursor-level), 1434 (protein-level) (inference performed using proteotypic peptides only) [8:14] Quantification [8:15] Quantification information saved to \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-A3_RF8_1_30708.d.quant

[8:15] File #27/97 [8:15] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-A4_GF7_1_30713.d [8:48] 22897 library precursors are potentially detectable [8:48] Processing... [8:53] RT window set to 0.48683 [8:53] Recommended MS1 mass accuracy setting: 10.188 ppm [8:59] Removing low confidence identifications [9:00] Removing interfering precursors [9:00] Training neural networks: 9603 targets, 5206 decoys [9:00] Number of IDs at 0.01 FDR: 5803 [9:00] Calculating protein q-values [9:00] Number of protein isoforms identified at 1% FDR: 1499 (precursor-level), 1397 (protein-level) (inference performed using proteotypic peptides only) [9:00] Quantification [9:01] Quantification information saved to \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-A4_GF7_1_30713.d.quant

[9:01] File #28/97 [9:01] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-B1_RF2_1_30644.d [9:30] 22897 library precursors are potentially detectable [9:30] Processing... [9:36] RT window set to 0.418704 [9:36] Recommended MS1 mass accuracy setting: 9.972 ppm [9:44] Removing low confidence identifications [9:44] Removing interfering precursors [9:44] Training neural networks: 7817 targets, 4160 decoys [9:44] Number of IDs at 0.01 FDR: 4073 [9:44] Calculating protein q-values [9:44] Number of protein isoforms identified at 1% FDR: 1115 (precursor-level), 1007 (protein-level) (inference performed using proteotypic peptides only) [9:44] Quantification [9:45] Quantification information saved to \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-B1_RF2_1_30644.d.quant

[9:45] File #29/97 [9:45] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-B2_RA3_1_30649.d [10:11] 22897 library precursors are potentially detectable [10:11] Processing... [10:22] Cannot perform mass calibration, too few confidently identified precursors [10:22] Cannot perform MS1 mass calibration, too few confidently identified precursors [10:34] RT window set to 6.08023 [10:34] Cannot perform mass calibration, too few confidently identified precursors [10:34] Cannot perform MS1 mass calibration, too few confidently identified precursors [11:24] Removing low confidence identifications [11:24] Removing interfering precursors [11:24] Too few confident identifications, neural networks will not be used [11:24] Number of IDs at 0.01 FDR: 0 [11:24] Calculating protein q-values [11:24] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [11:24] Quantification [11:24] Quantification information saved to \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-B2_RA3_1_30649.d.quant

[11:24] File #30/97 [11:24] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-B3_RF9_1_30722.d [11:51] 22897 library precursors are potentially detectable [11:51] Processing... [11:57] RT window set to 0.438984 [11:57] Recommended MS1 mass accuracy setting: 10.5814 ppm [12:05] Removing low confidence identifications [12:05] Removing interfering precursors [12:05] Training neural networks: 7792 targets, 4131 decoys [12:05] Number of IDs at 0.01 FDR: 4125 [12:05] Calculating protein q-values [12:05] Number of protein isoforms identified at 1% FDR: 1118 (precursor-level), 1027 (protein-level) (inference performed using proteotypic peptides only) [12:05] Quantification [12:06] Quantification information saved to \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-B3_RF9_1_30722.d.quant

[12:06] File #31/97 [12:06] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-B4_RA10_1_30727.d [12:30] 22897 library precursors are potentially detectable [12:30] Processing... [12:35] RT window set to 0.440391 [12:35] Recommended MS1 mass accuracy setting: 11.0389 ppm [12:42] Removing low confidence identifications [12:42] Removing interfering precursors [12:42] Training neural networks: 8461 targets, 4572 decoys [12:43] Number of IDs at 0.01 FDR: 4632 [12:43] Calculating protein q-values [12:43] Number of protein isoforms identified at 1% FDR: 1213 (precursor-level), 1180 (protein-level) (inference performed using proteotypic peptides only) [12:43] Quantification [12:44] Quantification information saved to \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-B4_RA10_1_30727.d.quant

[12:44] File #32/97 [12:44] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-C1_RF3_1_30654.d [13:08] 22897 library precursors are potentially detectable [13:08] Processing... [13:19] RT window set to 0.370536 [13:19] Recommended MS1 mass accuracy setting: 10.4569 ppm [13:28] Removing low confidence identifications [13:28] Removing interfering precursors [13:28] Training neural networks: 6413 targets, 3417 decoys [13:28] Number of IDs at 0.01 FDR: 2941 [13:28] Calculating protein q-values [13:28] Number of protein isoforms identified at 1% FDR: 826 (precursor-level), 753 (protein-level) (inference performed using proteotypic peptides only) [13:28] Quantification [13:29] Quantification information saved to \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-C1_RF3_1_30654.d.quant

[13:29] File #33/97 [13:29] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-C2_RA4_1_30659.d [13:57] 22897 library precursors are potentially detectable [13:57] Processing... [14:08] Cannot perform mass calibration, too few confidently identified precursors [14:08] Cannot perform MS1 mass calibration, too few confidently identified precursors [14:19] RT window set to 6.02443 [14:19] Cannot perform mass calibration, too few confidently identified precursors [14:19] Cannot perform MS1 mass calibration, too few confidently identified precursors [15:08] Removing low confidence identifications [15:08] Removing interfering precursors [15:08] Too few confident identifications, neural networks will not be used [15:08] Number of IDs at 0.01 FDR: 0 [15:08] Calculating protein q-values [15:08] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [15:08] Quantification [15:09] Quantification information saved to \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-C2_RA4_1_30659.d.quant

[15:09] File #34/97 [15:09] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-C3_RF10_1_30732.d [15:37] 22897 library precursors are potentially detectable [15:37] Processing... [15:47] RT window set to 0.392181 [15:47] Recommended MS1 mass accuracy setting: 10.71 ppm [15:57] Removing low confidence identifications [15:57] Removing interfering precursors [15:57] Training neural networks: 6583 targets, 3511 decoys [15:57] Number of IDs at 0.01 FDR: 3210 [15:57] Calculating protein q-values [15:57] Number of protein isoforms identified at 1% FDR: 905 (precursor-level), 844 (protein-level) (inference performed using proteotypic peptides only) [15:57] Quantification [15:58] Quantification information saved to \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-C3_RF10_1_30732.d.quant

[15:58] File #35/97 [15:58] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-C4_RA11_1_30737.d [16:31] 22897 library precursors are potentially detectable [16:31] Processing... [16:39] RT window set to 0.430866 [16:40] Recommended MS1 mass accuracy setting: 10.3497 ppm [16:48] Removing low confidence identifications [16:48] Removing interfering precursors [16:48] Training neural networks: 7313 targets, 3904 decoys [16:49] Number of IDs at 0.01 FDR: 3666 [16:49] Calculating protein q-values [16:49] Number of protein isoforms identified at 1% FDR: 1000 (precursor-level), 946 (protein-level) (inference performed using proteotypic peptides only) [16:49] Quantification [16:49] Quantification information saved to \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-C4_RA11_1_30737.d.quant

[16:49] File #36/97 [16:49] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-D1_RF4_1_30664.d [16:56] 22897 library precursors are potentially detectable [16:56] Processing... [17:01] RT window set to 0.954488 [17:01] Recommended MS1 mass accuracy setting: 11.4538 ppm [17:10] Removing low confidence identifications [17:10] Removing interfering precursors [17:11] Training neural networks: 16857 targets, 17284 decoys [17:12] Number of IDs at 0.01 FDR: 3 [17:12] Calculating protein q-values [17:12] Number of protein isoforms identified at 1% FDR: 2 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [17:12] Quantification [17:12] Quantification information saved to \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-D1_RF4_1_30664.d.quant

[17:12] File #37/97 [17:12] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-D2_GF5_1_30669.d [17:36] 22897 library precursors are potentially detectable [17:36] Processing... [17:48] Cannot perform mass calibration, too few confidently identified precursors [17:48] Cannot perform MS1 mass calibration, too few confidently identified precursors [17:59] RT window set to 5.50325 [17:59] Cannot perform mass calibration, too few confidently identified precursors [17:59] Cannot perform MS1 mass calibration, too few confidently identified precursors [18:48] Removing low confidence identifications [18:48] Removing interfering precursors [18:48] Too few confident identifications, neural networks will not be used [18:48] Number of IDs at 0.01 FDR: 0 [18:48] Calculating protein q-values [18:48] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [18:48] Quantification [18:48] Quantification information saved to \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-D2_GF5_1_30669.d.quant

[18:48] File #38/97 [18:48] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-D3_RF11_1_30742.d [19:16] 22897 library precursors are potentially detectable [19:16] Processing... [19:30] RT window set to 0.374478 [19:30] Recommended MS1 mass accuracy setting: 10.8901 ppm [19:40] Removing low confidence identifications [19:40] Removing interfering precursors [19:40] Training neural networks: 4995 targets, 2630 decoys [19:41] Number of IDs at 0.01 FDR: 2116 [19:41] Calculating protein q-values [19:41] Number of protein isoforms identified at 1% FDR: 651 (precursor-level), 573 (protein-level) (inference performed using proteotypic peptides only) [19:41] Quantification [19:42] Quantification information saved to \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-D3_RF11_1_30742.d.quant

[19:42] File #39/97 [19:42] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-D4_RA12_1_30747.d [20:04] 22897 library precursors are potentially detectable [20:04] Processing... [20:18] RT window set to 0.374099 [20:18] Recommended MS1 mass accuracy setting: 11.5127 ppm [20:29] Removing low confidence identifications [20:29] Removing interfering precursors [20:29] Training neural networks: 4871 targets, 2563 decoys [20:29] Number of IDs at 0.01 FDR: 1874 [20:29] Calculating protein q-values [20:29] Number of protein isoforms identified at 1% FDR: 576 (precursor-level), 418 (protein-level) (inference performed using proteotypic peptides only) [20:29] Quantification [20:30] Quantification information saved to \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-D4_RA12_1_30747.d.quant

[20:30] File #40/97 [20:30] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-E1_RF5_1_30678.d [20:53] 22897 library precursors are potentially detectable [20:53] Processing... [21:14] RT window set to 0.54642 [21:14] Recommended MS1 mass accuracy setting: 9.17458 ppm [21:25] Removing low confidence identifications [21:25] Removing interfering precursors [21:25] Training neural networks: 4465 targets, 3762 decoys [21:25] Number of IDs at 0.01 FDR: 381 [21:25] Calculating protein q-values [21:25] Number of protein isoforms identified at 1% FDR: 132 (precursor-level), 102 (protein-level) (inference performed using proteotypic peptides only) [21:25] Quantification [21:26] Quantification information saved to \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-E1_RF5_1_30678.d.quant

[21:26] File #41/97 [21:26] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-E2_RA6_1_30683.d [21:50] 22897 library precursors are potentially detectable [21:50] Processing... [22:01] Cannot perform mass calibration, too few confidently identified precursors [22:01] Cannot perform MS1 mass calibration, too few confidently identified precursors [22:12] RT window set to 4.67789 [22:12] Cannot perform mass calibration, too few confidently identified precursors [22:12] Cannot perform MS1 mass calibration, too few confidently identified precursors [22:57] Removing low confidence identifications [22:57] Removing interfering precursors [22:57] Too few confident identifications, neural networks will not be used [22:57] Number of IDs at 0.01 FDR: 0 [22:57] Calculating protein q-values [22:57] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [22:57] Quantification [22:57] Quantification information saved to \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-E2_RA6_1_30683.d.quant

[22:57] File #42/97 [22:57] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-E3_RA17_1_30752.d [23:18] 22897 library precursors are potentially detectable [23:18] Processing... [23:39] RT window set to 6.02086 [23:39] Cannot perform MS1 mass calibration, too few confidently identified precursors [23:39] Recommended MS1 mass accuracy setting: 12.3661 ppm [24:24] Removing low confidence identifications [24:24] Removing interfering precursors [24:24] Training neural networks: 18603 targets, 18943 decoys [24:25] Number of IDs at 0.01 FDR: 0 [24:25] Too low number of IDs with NNs: reverting to the linear classifier [24:25] Number of IDs at 0.01 FDR: 0 [24:25] Calculating protein q-values [24:25] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 2 (protein-level) (inference performed using proteotypic peptides only) [24:25] Quantification [24:25] Quantification information saved to \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-E3_RA17_1_30752.d.quant

[24:26] File #43/97 [24:26] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-E4_GF9_1_30757.d [24:47] 22897 library precursors are potentially detectable [24:47] Processing... [24:57] Cannot perform mass calibration, too few confidently identified precursors [24:57] Cannot perform MS1 mass calibration, too few confidently identified precursors [25:07] RT window set to 10.9565 [25:07] Cannot perform mass calibration, too few confidently identified precursors [25:07] Cannot perform MS1 mass calibration, too few confidently identified precursors [25:55] Removing low confidence identifications [25:55] Removing interfering precursors [25:55] Too few confident identifications, neural networks will not be used [25:55] Number of IDs at 0.01 FDR: 0 [25:55] Calculating protein q-values [25:55] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [25:55] Quantification [25:55] Quantification information saved to \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-E4_GF9_1_30757.d.quant

[25:55] File #44/97 [25:55] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-F1_RF6_1_30688.d [26:17] 22897 library precursors are potentially detectable [26:17] Processing... [26:27] Cannot perform mass calibration, too few confidently identified precursors [26:27] Cannot perform MS1 mass calibration, too few confidently identified precursors [26:38] RT window set to 4.85309 [26:38] Cannot perform mass calibration, too few confidently identified precursors [26:38] Cannot perform MS1 mass calibration, too few confidently identified precursors [27:16] Removing low confidence identifications [27:16] Removing interfering precursors [27:16] Too few confident identifications, neural networks will not be used [27:16] Number of IDs at 0.01 FDR: 1 [27:16] Calculating protein q-values [27:16] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [27:16] Quantification [27:16] Quantification information saved to \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-F1_RF6_1_30688.d.quant

[27:17] File #45/97 [27:17] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-F2_RA7_1_30693.d [27:42] 22897 library precursors are potentially detectable [27:42] Processing... [27:53] Cannot perform mass calibration, too few confidently identified precursors [27:53] Cannot perform MS1 mass calibration, too few confidently identified precursors [28:04] RT window set to 5.77637 [28:04] Cannot perform mass calibration, too few confidently identified precursors [28:04] Cannot perform MS1 mass calibration, too few confidently identified precursors [28:54] Removing low confidence identifications [28:54] Removing interfering precursors [28:54] Too few confident identifications, neural networks will not be used [28:54] Number of IDs at 0.01 FDR: 0 [28:54] Calculating protein q-values [28:54] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [28:54] Quantification [28:54] Quantification information saved to \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-F2_RA7_1_30693.d.quant

[28:55] File #46/97 [28:55] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-F3_RB7_1_30766.d [29:17] 22897 library precursors are potentially detectable [29:17] Processing... [29:27] Cannot perform mass calibration, too few confidently identified precursors [29:27] Cannot perform MS1 mass calibration, too few confidently identified precursors [29:37] RT window set to 10.9319 [29:37] Cannot perform mass calibration, too few confidently identified precursors [29:37] Cannot perform MS1 mass calibration, too few confidently identified precursors [30:26] Removing low confidence identifications [30:26] Removing interfering precursors [30:26] Too few confident identifications, neural networks will not be used [30:26] Number of IDs at 0.01 FDR: 3 [30:26] Calculating protein q-values [30:26] Number of protein isoforms identified at 1% FDR: 1 (precursor-level), 1 (protein-level) (inference performed using proteotypic peptides only) [30:26] Quantification [30:26] Quantification information saved to \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-F3_RB7_1_30766.d.quant

[30:26] File #47/97 [30:26] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-F4_RB12_1_30771.d [30:47] 22897 library precursors are potentially detectable [30:47] Processing... [31:04] RT window set to 0.474609 [31:04] Recommended MS1 mass accuracy setting: 11.55 ppm [31:14] Removing low confidence identifications [31:14] Removing interfering precursors [31:14] Training neural networks: 4515 targets, 3645 decoys [31:15] Number of IDs at 0.01 FDR: 421 [31:15] Calculating protein q-values [31:15] Number of protein isoforms identified at 1% FDR: 131 (precursor-level), 106 (protein-level) (inference performed using proteotypic peptides only) [31:15] Quantification [31:15] Quantification information saved to \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-F4_RB12_1_30771.d.quant

[31:15] File #48/97 [31:15] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-G1_RF7_1_30698.d [31:36] 22897 library precursors are potentially detectable [31:36] Processing... [31:47] Cannot perform mass calibration, too few confidently identified precursors [31:47] Cannot perform MS1 mass calibration, too few confidently identified precursors [31:58] RT window set to 6.13902 [31:58] Cannot perform mass calibration, too few confidently identified precursors [31:58] Cannot perform MS1 mass calibration, too few confidently identified precursors [32:45] Removing low confidence identifications [32:45] Removing interfering precursors [32:45] Too few confident identifications, neural networks will not be used [32:45] Number of IDs at 0.01 FDR: 3 [32:45] Calculating protein q-values [32:45] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [32:45] Quantification [32:45] Quantification information saved to \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-G1_RF7_1_30698.d.quant

[32:45] File #49/97 [32:45] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-G2_RA8_1_30703.d [33:11] 22897 library precursors are potentially detectable [33:11] Processing... [33:23] Cannot perform mass calibration, too few confidently identified precursors [33:23] Cannot perform MS1 mass calibration, too few confidently identified precursors [33:34] RT window set to 4.39254 [33:34] Cannot perform mass calibration, too few confidently identified precursors [33:34] Cannot perform MS1 mass calibration, too few confidently identified precursors [34:16] Removing low confidence identifications [34:16] Removing interfering precursors [34:16] Too few confident identifications, neural networks will not be used [34:16] Number of IDs at 0.01 FDR: 0 [34:16] Calculating protein q-values [34:16] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [34:16] Quantification [34:16] Quantification information saved to \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-G2_RA8_1_30703.d.quant

[34:16] File #50/97 [34:16] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-G3_RF10_1_30776.d [34:37] 22897 library precursors are potentially detectable [34:37] Processing... [34:58] RT window set to 0.694931 [34:58] Recommended MS1 mass accuracy setting: 10.7463 ppm [35:09] Removing low confidence identifications [35:09] Removing interfering precursors [35:09] Training neural networks: 3738 targets, 3114 decoys [35:10] Number of IDs at 0.01 FDR: 344 [35:10] Calculating protein q-values [35:10] Number of protein isoforms identified at 1% FDR: 105 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [35:10] Quantification [35:10] Quantification information saved to \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-G3_RF10_1_30776.d.quant

[35:10] File #51/97 [35:10] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-G4_RJ11_1_30781.d [35:30] 22897 library precursors are potentially detectable [35:30] Processing... [35:49] RT window set to 0.813496 [35:49] Recommended MS1 mass accuracy setting: 10.5538 ppm [36:01] Removing low confidence identifications [36:01] Removing interfering precursors [36:01] Training neural networks: 5195 targets, 4442 decoys [36:02] Number of IDs at 0.01 FDR: 508 [36:02] Calculating protein q-values [36:02] Number of protein isoforms identified at 1% FDR: 170 (precursor-level), 100 (protein-level) (inference performed using proteotypic peptides only) [36:02] Quantification [36:02] Quantification information saved to \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-G4_RJ11_1_30781.d.quant

[36:02] File #52/97 [36:02] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-H1_RJ16_1_30786.d [36:25] 22897 library precursors are potentially detectable [36:25] Processing... [36:36] Cannot perform mass calibration, too few confidently identified precursors [36:36] Cannot perform MS1 mass calibration, too few confidently identified precursors [36:47] RT window set to 4.62165 [36:47] Cannot perform mass calibration, too few confidently identified precursors [36:47] Cannot perform MS1 mass calibration, too few confidently identified precursors [37:31] Removing low confidence identifications [37:31] Removing interfering precursors [37:31] Too few confident identifications, neural networks will not be used [37:31] Number of IDs at 0.01 FDR: 0 [37:31] Calculating protein q-values [37:31] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [37:31] Quantification [37:31] Quantification information saved to \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-H1_RJ16_1_30786.d.quant

[37:32] File #53/97 [37:32] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-H2_RJ21_1_30791.d [37:53] 22897 library precursors are potentially detectable [37:53] Processing... [38:03] Cannot perform mass calibration, too few confidently identified precursors [38:03] Cannot perform MS1 mass calibration, too few confidently identified precursors [38:13] RT window set to 11.9884 [38:13] Cannot perform mass calibration, too few confidently identified precursors [38:13] Cannot perform MS1 mass calibration, too few confidently identified precursors [39:02] Removing low confidence identifications [39:02] Removing interfering precursors [39:02] Training neural networks: 5514 targets, 5508 decoys [39:03] Number of IDs at 0.01 FDR: 0 [39:03] Too low number of IDs with NNs: reverting to the linear classifier [39:03] Number of IDs at 0.01 FDR: 0 [39:03] Calculating protein q-values [39:03] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [39:03] Quantification [39:03] Quantification information saved to \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-H2_RJ21_1_30791.d.quant

[39:03] File #54/97 [39:03] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-H3_RK2_1_30796.d [39:25] 22897 library precursors are potentially detectable [39:25] Processing... [39:35] Cannot perform mass calibration, too few confidently identified precursors [39:35] Cannot perform MS1 mass calibration, too few confidently identified precursors [39:46] RT window set to 11.9408 [39:46] Cannot perform mass calibration, too few confidently identified precursors [39:46] Cannot perform MS1 mass calibration, too few confidently identified precursors [40:36] Removing low confidence identifications [40:36] Removing interfering precursors [40:36] Too few confident identifications, neural networks will not be used [40:36] Number of IDs at 0.01 FDR: 0 [40:36] Calculating protein q-values [40:36] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [40:36] Quantification [40:36] Quantification information saved to \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-H3_RK2_1_30796.d.quant

[40:36] File #55/97 [40:36] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-H4_GF11_1_30801.d [40:59] 22897 library precursors are potentially detectable [40:59] Processing... [41:09] Cannot perform mass calibration, too few confidently identified precursors [41:09] Cannot perform MS1 mass calibration, too few confidently identified precursors [41:20] RT window set to 10.1167 [41:20] Cannot perform mass calibration, too few confidently identified precursors [41:20] Cannot perform MS1 mass calibration, too few confidently identified precursors [42:07] Removing low confidence identifications [42:07] Removing interfering precursors [42:07] Too few confident identifications, neural networks will not be used [42:07] Number of IDs at 0.01 FDR: 0 [42:07] Calculating protein q-values [42:07] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [42:07] Quantification [42:07] Quantification information saved to \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-H4_GF11_1_30801.d.quant

[42:07] File #56/97 [42:07] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-NUC-A2_RJ1_1_30638.d [42:29] 22897 library precursors are potentially detectable [42:29] Processing... [42:44] RT window set to 0.358073 [42:44] Recommended MS1 mass accuracy setting: 12.0733 ppm [42:53] Removing low confidence identifications [42:53] Removing interfering precursors [42:53] Training neural networks: 3102 targets, 1607 decoys [42:54] Number of IDs at 0.01 FDR: 1100 [42:54] Calculating protein q-values [42:54] Number of protein isoforms identified at 1% FDR: 337 (precursor-level), 323 (protein-level) (inference performed using proteotypic peptides only) [42:54] Quantification [42:54] Quantification information saved to \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-NUC-A2_RJ1_1_30638.d.quant

[42:54] File #57/97 [42:54] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-NUC-A3_RE8_1_30707.d [43:15] 22897 library precursors are potentially detectable [43:15] Processing... [43:29] RT window set to 0.408289 [43:29] Recommended MS1 mass accuracy setting: 11.4407 ppm [43:40] Removing low confidence identifications [43:40] Removing interfering precursors [43:40] Training neural networks: 3930 targets, 2072 decoys [43:41] Number of IDs at 0.01 FDR: 1559 [43:41] Calculating protein q-values [43:41] Number of protein isoforms identified at 1% FDR: 446 (precursor-level), 402 (protein-level) (inference performed using proteotypic peptides only) [43:41] Quantification [43:41] Quantification information saved to \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-NUC-A3_RE8_1_30707.d.quant

[43:41] File #58/97 [43:41] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-NUC-A4_RJ8_1_30712.d [44:01] 22897 library precursors are potentially detectable [44:01] Processing... [44:16] RT window set to 0.39824 [44:16] Recommended MS1 mass accuracy setting: 11.5597 ppm [44:26] Removing low confidence identifications [44:26] Removing interfering precursors [44:26] Training neural networks: 3079 targets, 1605 decoys [44:26] Number of IDs at 0.01 FDR: 1108 [44:26] Calculating protein q-values [44:26] Number of protein isoforms identified at 1% FDR: 346 (precursor-level), 265 (protein-level) (inference performed using proteotypic peptides only) [44:26] Quantification [44:26] Quantification information saved to \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-NUC-A4_RJ8_1_30712.d.quant

[44:26] File #59/97 [44:26] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-NUC-B1_RE2_1_30643.d [44:48] 22897 library precursors are potentially detectable [44:48] Processing... [45:09] RT window set to 0.448799 [45:09] Recommended MS1 mass accuracy setting: 13.3429 ppm [45:19] Removing low confidence identifications [45:19] Removing interfering precursors [45:19] Training neural networks: 3871 targets, 3154 decoys [45:19] Number of IDs at 0.01 FDR: 541 [45:19] Calculating protein q-values [45:19] Number of protein isoforms identified at 1% FDR: 182 (precursor-level), 122 (protein-level) (inference performed using proteotypic peptides only) [45:19] Quantification [45:19] Quantification information saved to \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-NUC-B1_RE2_1_30643.d.quant

[45:20] File #60/97 [45:20] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-NUC-B2_RJ2_1_30648.d [45:46] 22897 library precursors are potentially detectable [45:46] Processing... [46:06] RT window set to 0.566133 [46:06] Recommended MS1 mass accuracy setting: 11.0749 ppm [46:17] Removing low confidence identifications [46:17] Removing interfering precursors [46:17] Training neural networks: 4298 targets, 3514 decoys [46:18] Number of IDs at 0.01 FDR: 545 [46:18] Calculating protein q-values [46:18] Number of protein isoforms identified at 1% FDR: 201 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [46:18] Quantification [46:18] Quantification information saved to \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-NUC-B2_RJ2_1_30648.d.quant

[46:18] File #61/97 [46:18] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-NUC-B3_RE9_1_30721.d [46:40] 22897 library precursors are potentially detectable [46:40] Processing... [47:02] RT window set to 0.5123 [47:02] Recommended MS1 mass accuracy setting: 12.0062 ppm [47:13] Removing low confidence identifications [47:13] Removing interfering precursors [47:13] Training neural networks: 5161 targets, 4382 decoys [47:13] Number of IDs at 0.01 FDR: 667 [47:13] Calculating protein q-values [47:13] Number of protein isoforms identified at 1% FDR: 223 (precursor-level), 169 (protein-level) (inference performed using proteotypic peptides only) [47:13] Quantification [47:14] Quantification information saved to \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-NUC-B3_RE9_1_30721.d.quant

[47:14] File #62/97 [47:14] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-NUC-B4_RJ9_1_30726.d [47:38] 22897 library precursors are potentially detectable [47:38] Processing... [48:00] RT window set to 0.366963 [48:00] Recommended MS1 mass accuracy setting: 9.12707 ppm [48:08] Removing low confidence identifications [48:08] Removing interfering precursors [48:08] Training neural networks: 5157 targets, 4124 decoys [48:09] Number of IDs at 0.01 FDR: 658 [48:09] Calculating protein q-values [48:09] Number of protein isoforms identified at 1% FDR: 214 (precursor-level), 118 (protein-level) (inference performed using proteotypic peptides only) [48:09] Quantification [48:09] Quantification information saved to \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-NUC-B4_RJ9_1_30726.d.quant

[48:09] File #63/97 [48:09] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-NUC-C1_RE3_1_30653.d [48:31] 22897 library precursors are potentially detectable [48:31] Processing... [48:53] RT window set to 4.53832 [48:53] Recommended MS1 mass accuracy setting: 9.48981 ppm [49:30] Removing low confidence identifications [49:30] Removing interfering precursors [49:31] Training neural networks: 19142 targets, 19373 decoys [49:32] Number of IDs at 0.01 FDR: 180 [49:32] Calculating protein q-values [49:32] Number of protein isoforms identified at 1% FDR: 66 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [49:32] Quantification [49:32] Quantification information saved to \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-NUC-C1_RE3_1_30653.d.quant

[49:32] File #64/97 [49:32] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-NUC-C2_RJ3_1_30658.d [49:55] 22897 library precursors are potentially detectable [49:55] Processing... [50:14] RT window set to 4.40178 [50:14] Recommended MS1 mass accuracy setting: 12.1886 ppm [50:51] Removing low confidence identifications [50:51] Removing interfering precursors [50:51] Training neural networks: 18790 targets, 19083 decoys [50:52] Number of IDs at 0.01 FDR: 118 [50:52] Calculating protein q-values [50:52] Number of protein isoforms identified at 1% FDR: 48 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [50:52] Quantification [50:52] Quantification information saved to \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-NUC-C2_RJ3_1_30658.d.quant

[50:52] File #65/97 [50:52] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-NUC-C3_RE10_1_30731.d [51:15] 22897 library precursors are potentially detectable [51:15] Processing... [51:36] RT window set to 1.25809 [51:36] Recommended MS1 mass accuracy setting: 10.3737 ppm [51:53] Removing low confidence identifications [51:53] Removing interfering precursors [51:53] Training neural networks: 4642 targets, 4066 decoys [51:54] Number of IDs at 0.01 FDR: 328 [51:54] Calculating protein q-values [51:54] Number of protein isoforms identified at 1% FDR: 123 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [51:54] Quantification [51:54] Quantification information saved to \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-NUC-C3_RE10_1_30731.d.quant

[51:54] File #66/97 [51:54] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-NUC-C4_RJ10_1_30736.d [52:16] 22897 library precursors are potentially detectable [52:16] Processing... [52:36] RT window set to 2.02469 [52:36] Recommended MS1 mass accuracy setting: 12.3249 ppm [52:59] Removing low confidence identifications [52:59] Removing interfering precursors [52:59] Training neural networks: 4470 targets, 3891 decoys [52:59] Number of IDs at 0.01 FDR: 272 [52:59] Calculating protein q-values [52:59] Number of protein isoforms identified at 1% FDR: 100 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [52:59] Quantification [53:00] Quantification information saved to \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-NUC-C4_RJ10_1_30736.d.quant

[53:00] File #67/97 [53:00] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-NUC-D1_RE4_1_30663.d [53:21] 22897 library precursors are potentially detectable [53:21] Processing... [53:32] Cannot perform mass calibration, too few confidently identified precursors [53:32] Cannot perform MS1 mass calibration, too few confidently identified precursors [53:43] RT window set to 6.38092 [53:43] Cannot perform mass calibration, too few confidently identified precursors [53:43] Cannot perform MS1 mass calibration, too few confidently identified precursors [54:26] Removing low confidence identifications [54:26] Removing interfering precursors [54:26] Training neural networks: 18536 targets, 18850 decoys [54:27] Number of IDs at 0.01 FDR: 0 [54:27] Too low number of IDs with NNs: reverting to the linear classifier [54:27] Number of IDs at 0.01 FDR: 0 [54:27] Calculating protein q-values [54:27] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [54:27] Quantification [54:28] Quantification information saved to \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-NUC-D1_RE4_1_30663.d.quant

[54:28] File #68/97 [54:28] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-NUC-D2_RJ4_1_30668.d [54:50] 22897 library precursors are potentially detectable [54:50] Processing... [55:01] Cannot perform mass calibration, too few confidently identified precursors [55:01] Cannot perform MS1 mass calibration, too few confidently identified precursors [55:11] RT window set to 6.24502 [55:11] Cannot perform mass calibration, too few confidently identified precursors [55:11] Cannot perform MS1 mass calibration, too few confidently identified precursors [55:54] Removing low confidence identifications [55:54] Removing interfering precursors [55:54] Training neural networks: 18569 targets, 18922 decoys [55:55] Number of IDs at 0.01 FDR: 0 [55:55] Too low number of IDs with NNs: reverting to the linear classifier [55:55] Number of IDs at 0.01 FDR: 0 [55:55] Calculating protein q-values [55:55] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [55:55] Quantification [55:56] Quantification information saved to \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-NUC-D2_RJ4_1_30668.d.quant

[55:56] File #69/97 [55:56] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-NUC-D3_RE11_1_30741.d [56:21] 22897 library precursors are potentially detectable [56:21] Processing... [56:32] Cannot perform mass calibration, too few confidently identified precursors [56:32] Cannot perform MS1 mass calibration, too few confidently identified precursors [56:43] RT window set to 7.66995 [56:43] Cannot perform mass calibration, too few confidently identified precursors [56:43] Cannot perform MS1 mass calibration, too few confidently identified precursors [57:32] Removing low confidence identifications [57:32] Removing interfering precursors [57:32] Training neural networks: 17457 targets, 18257 decoys [57:33] Number of IDs at 0.01 FDR: 0 [57:33] Too low number of IDs with NNs: reverting to the linear classifier [57:33] Number of IDs at 0.01 FDR: 0 [57:33] Calculating protein q-values [57:33] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [57:33] Quantification [57:34] Quantification information saved to \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-NUC-D3_RE11_1_30741.d.quant

[57:34] File #70/97 [57:34] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-NUC-D4_RJ11_1_30746.d [57:58] 22897 library precursors are potentially detectable [57:58] Processing... [58:13] RT window set to 0.40079 [58:13] Recommended MS1 mass accuracy setting: 10.9261 ppm [58:24] Removing low confidence identifications [58:24] Removing interfering precursors [58:24] Training neural networks: 2735 targets, 1442 decoys [58:24] Number of IDs at 0.01 FDR: 1062 [58:24] Calculating protein q-values [58:24] Number of protein isoforms identified at 1% FDR: 343 (precursor-level), 277 (protein-level) (inference performed using proteotypic peptides only) [58:24] Quantification [58:25] Quantification information saved to \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-NUC-D4_RJ11_1_30746.d.quant

[58:25] File #71/97 [58:25] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-NUC-E1_RE5_1_30677.d [58:58] 22897 library precursors are potentially detectable [58:58] Processing... [59:08] Cannot perform mass calibration, too few confidently identified precursors [59:08] Cannot perform MS1 mass calibration, too few confidently identified precursors [59:19] RT window set to 6.43067 [59:19] Cannot perform mass calibration, too few confidently identified precursors [59:19] Cannot perform MS1 mass calibration, too few confidently identified precursors [60:06] Removing low confidence identifications [60:06] Removing interfering precursors [60:06] Too few confident identifications, neural networks will not be used [60:06] Number of IDs at 0.01 FDR: 2 [60:06] Calculating protein q-values [60:06] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [60:06] Quantification [60:06] Quantification information saved to \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-NUC-E1_RE5_1_30677.d.quant

[60:06] File #72/97 [60:06] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-NUC-E2_RJ5_1_30682.d [60:26] 22897 library precursors are potentially detectable [60:26] Processing... [60:37] Cannot perform mass calibration, too few confidently identified precursors [60:37] Cannot perform MS1 mass calibration, too few confidently identified precursors [60:49] RT window set to 7.362 [60:49] Cannot perform mass calibration, too few confidently identified precursors [60:49] Cannot perform MS1 mass calibration, too few confidently identified precursors [61:37] Removing low confidence identifications [61:37] Removing interfering precursors [61:37] Too few confident identifications, neural networks will not be used [61:37] Number of IDs at 0.01 FDR: 3 [61:37] Number of IDs at 0.01 FDR: 0 [61:37] Calculating protein q-values [61:37] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [61:37] Quantification [61:37] Quantification information saved to \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-NUC-E2_RJ5_1_30682.d.quant

[61:37] File #73/97 [61:37] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-NUC-E3_RA16_1_30751.d [62:00] 22897 library precursors are potentially detectable [62:00] Processing... [62:10] Cannot perform mass calibration, too few confidently identified precursors [62:10] Cannot perform MS1 mass calibration, too few confidently identified precursors [62:21] RT window set to 7.39224 [62:21] Cannot perform mass calibration, too few confidently identified precursors [62:21] Cannot perform MS1 mass calibration, too few confidently identified precursors [63:09] Removing low confidence identifications [63:09] Removing interfering precursors [63:09] Training neural networks: 18689 targets, 18968 decoys [63:11] Number of IDs at 0.01 FDR: 0 [63:11] Too low number of IDs with NNs: reverting to the linear classifier [63:11] Number of IDs at 0.01 FDR: 0 [63:11] Calculating protein q-values [63:11] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [63:11] Quantification [63:11] Quantification information saved to \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-NUC-E3_RA16_1_30751.d.quant

[63:11] File #74/97 [63:11] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-NUC-E4_RA21_1_30756.d [63:30] 22897 library precursors are potentially detectable [63:30] Processing... [63:40] Cannot perform mass calibration, too few confidently identified precursors [63:40] Cannot perform MS1 mass calibration, too few confidently identified precursors [63:50] RT window set to 13.5886 [63:50] Cannot perform mass calibration, too few confidently identified precursors [63:50] Cannot perform MS1 mass calibration, too few confidently identified precursors [64:39] Removing low confidence identifications [64:39] Removing interfering precursors [64:39] Too few confident identifications, neural networks will not be used [64:39] Number of IDs at 0.01 FDR: 0 [64:39] Number of IDs at 0.01 FDR: 1 [64:39] Number of IDs at 0.01 FDR: 0 [64:39] Calculating protein q-values [64:39] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [64:39] Quantification [64:39] Quantification information saved to \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-NUC-E4_RA21_1_30756.d.quant

[64:39] File #75/97 [64:39] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-NUC-F1_RE6_1_30687.d [65:03] 22897 library precursors are potentially detectable [65:03] Processing... [65:14] Cannot perform mass calibration, too few confidently identified precursors [65:14] Cannot perform MS1 mass calibration, too few confidently identified precursors [65:24] RT window set to 7.17114 [65:24] Cannot perform mass calibration, too few confidently identified precursors [65:24] Cannot perform MS1 mass calibration, too few confidently identified precursors [66:12] Removing low confidence identifications [66:12] Removing interfering precursors [66:12] Too few confident identifications, neural networks will not be used [66:12] Number of IDs at 0.01 FDR: 3 [66:12] Calculating protein q-values [66:12] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [66:12] Quantification [66:12] Quantification information saved to \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-NUC-F1_RE6_1_30687.d.quant

[66:12] File #76/97 [66:12] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-NUC-F2_RJ6_1_30692.d [66:37] 22897 library precursors are potentially detectable [66:37] Processing... [66:47] Cannot perform mass calibration, too few confidently identified precursors [66:47] Cannot perform MS1 mass calibration, too few confidently identified precursors [66:58] RT window set to 5.7725 [66:58] Cannot perform mass calibration, too few confidently identified precursors [66:58] Cannot perform MS1 mass calibration, too few confidently identified precursors [67:40] Removing low confidence identifications [67:40] Removing interfering precursors [67:40] Too few confident identifications, neural networks will not be used [67:40] Number of IDs at 0.01 FDR: 4 [67:40] Calculating protein q-values [67:40] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [67:40] Quantification [67:40] Quantification information saved to \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-NUC-F2_RJ6_1_30692.d.quant

[67:40] File #77/97 [67:40] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-NUC-F3_RB6_1_30765.d [68:00] 22897 library precursors are potentially detectable [68:00] Processing... [68:10] Cannot perform mass calibration, too few confidently identified precursors [68:10] Cannot perform MS1 mass calibration, too few confidently identified precursors [68:20] RT window set to 8.63002 [68:20] Cannot perform mass calibration, too few confidently identified precursors [68:20] Cannot perform MS1 mass calibration, too few confidently identified precursors [69:06] Removing low confidence identifications [69:06] Removing interfering precursors [69:06] Training neural networks: 19370 targets, 19550 decoys [69:07] Number of IDs at 0.01 FDR: 0 [69:07] Too low number of IDs with NNs: reverting to the linear classifier [69:07] Number of IDs at 0.01 FDR: 2 [69:07] Calculating protein q-values [69:07] Number of protein isoforms identified at 1% FDR: 1 (precursor-level), 1 (protein-level) (inference performed using proteotypic peptides only) [69:07] Quantification [69:08] Quantification information saved to \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-NUC-F3_RB6_1_30765.d.quant

[69:08] File #78/97 [69:08] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-NUC-F4_RB11_1_30770.d [69:30] 22897 library precursors are potentially detectable [69:30] Processing... [69:47] RT window set to 0.30339 [69:47] Recommended MS1 mass accuracy setting: 9.96038 ppm [69:55] Removing low confidence identifications [69:55] Removing interfering precursors [69:55] Training neural networks: 2364 targets, 1222 decoys [69:56] Number of IDs at 0.01 FDR: 749 [69:56] Calculating protein q-values [69:56] Number of protein isoforms identified at 1% FDR: 253 (precursor-level), 196 (protein-level) (inference performed using proteotypic peptides only) [69:56] Quantification [69:56] Quantification information saved to \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-NUC-F4_RB11_1_30770.d.quant

[69:56] File #79/97 [69:56] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-NUC-G1_RE7_1_30697.d [70:17] 22897 library precursors are potentially detectable [70:17] Processing... [70:28] Cannot perform mass calibration, too few confidently identified precursors [70:28] Cannot perform MS1 mass calibration, too few confidently identified precursors [70:39] RT window set to 6.55862 [70:39] Cannot perform mass calibration, too few confidently identified precursors [70:39] Cannot perform MS1 mass calibration, too few confidently identified precursors [71:27] Removing low confidence identifications [71:27] Removing interfering precursors [71:27] Too few confident identifications, neural networks will not be used [71:27] Number of IDs at 0.01 FDR: 0 [71:27] Calculating protein q-values [71:27] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [71:27] Quantification [71:27] Quantification information saved to \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-NUC-G1_RE7_1_30697.d.quant

[71:27] File #80/97 [71:27] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-NUC-G2_RJ7_1_30702.d [71:49] 22897 library precursors are potentially detectable [71:49] Processing... [72:00] Cannot perform mass calibration, too few confidently identified precursors [72:00] Cannot perform MS1 mass calibration, too few confidently identified precursors [72:10] RT window set to 6.36101 [72:10] Cannot perform mass calibration, too few confidently identified precursors [72:10] Cannot perform MS1 mass calibration, too few confidently identified precursors [72:55] Removing low confidence identifications [72:55] Removing interfering precursors [72:55] Too few confident identifications, neural networks will not be used [72:55] Number of IDs at 0.01 FDR: 4 [72:55] Calculating protein q-values [72:55] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [72:55] Quantification [72:56] Quantification information saved to \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-NUC-G2_RJ7_1_30702.d.quant

[72:56] File #81/97 [72:56] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-NUC-G3_RE10_1_30775.d [73:19] 22897 library precursors are potentially detectable [73:19] Processing... [73:30] Cannot perform mass calibration, too few confidently identified precursors [73:30] Cannot perform MS1 mass calibration, too few confidently identified precursors [73:41] RT window set to 6.06283 [73:41] Cannot perform mass calibration, too few confidently identified precursors [73:41] Cannot perform MS1 mass calibration, too few confidently identified precursors [74:30] Removing low confidence identifications [74:30] Removing interfering precursors [74:30] Too few confident identifications, neural networks will not be used [74:30] Number of IDs at 0.01 FDR: 0 [74:30] Calculating protein q-values [74:30] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [74:30] Quantification [74:31] Quantification information saved to \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-NUC-G3_RE10_1_30775.d.quant

[74:31] File #82/97 [74:31] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-NUC-G4_RJ10_1_30780.d [74:52] 22897 library precursors are potentially detectable [74:52] Processing... [75:02] Cannot perform mass calibration, too few confidently identified precursors [75:02] Cannot perform MS1 mass calibration, too few confidently identified precursors [75:12] RT window set to 9.23116 [75:12] Cannot perform mass calibration, too few confidently identified precursors [75:12] Cannot perform MS1 mass calibration, too few confidently identified precursors [75:58] Removing low confidence identifications [75:58] Removing interfering precursors [75:58] Too few confident identifications, neural networks will not be used [75:58] Number of IDs at 0.01 FDR: 3 [75:58] Calculating protein q-values [75:58] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [75:58] Quantification [75:58] Quantification information saved to \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-NUC-G4_RJ10_1_30780.d.quant

[75:58] File #83/97 [75:58] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-NUC-H1_RJ15_1_30785.d [76:18] 22897 library precursors are potentially detectable [76:18] Processing... [76:29] Cannot perform mass calibration, too few confidently identified precursors [76:29] Cannot perform MS1 mass calibration, too few confidently identified precursors [76:40] RT window set to 6.22358 [76:40] Cannot perform mass calibration, too few confidently identified precursors [76:40] Cannot perform MS1 mass calibration, too few confidently identified precursors [77:24] Removing low confidence identifications [77:24] Removing interfering precursors [77:24] Too few confident identifications, neural networks will not be used [77:24] Number of IDs at 0.01 FDR: 4 [77:24] Calculating protein q-values [77:24] Number of protein isoforms identified at 1% FDR: 1 (precursor-level), 1 (protein-level) (inference performed using proteotypic peptides only) [77:24] Quantification [77:24] Quantification information saved to \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-NUC-H1_RJ15_1_30785.d.quant

[77:24] File #84/97 [77:24] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-NUC-H2_RJ20_1_30790.d [77:47] 22897 library precursors are potentially detectable [77:47] Processing... [77:57] Cannot perform mass calibration, too few confidently identified precursors [77:57] Cannot perform MS1 mass calibration, too few confidently identified precursors [78:07] RT window set to 10.4643 [78:07] Cannot perform mass calibration, too few confidently identified precursors [78:07] Cannot perform MS1 mass calibration, too few confidently identified precursors [78:56] Removing low confidence identifications [78:56] Removing interfering precursors [78:56] Too few confident identifications, neural networks will not be used [78:56] Number of IDs at 0.01 FDR: 0 [78:56] Calculating protein q-values [78:56] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [78:56] Quantification [78:57] Quantification information saved to \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-NUC-H2_RJ20_1_30790.d.quant

[78:57] File #85/97 [78:57] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-NUC-H3_RK1_1_30795.d [79:24] 22897 library precursors are potentially detectable [79:24] Processing... [79:35] Cannot perform mass calibration, too few confidently identified precursors [79:35] Cannot perform MS1 mass calibration, too few confidently identified precursors [79:45] RT window set to 11.54 [79:45] Cannot perform mass calibration, too few confidently identified precursors [79:45] Cannot perform MS1 mass calibration, too few confidently identified precursors [80:34] Removing low confidence identifications [80:34] Removing interfering precursors [80:34] Too few confident identifications, neural networks will not be used [80:34] Number of IDs at 0.01 FDR: 0 [80:34] Calculating protein q-values [80:34] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [80:34] Quantification [80:34] Quantification information saved to \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-NUC-H3_RK1_1_30795.d.quant

[80:34] File #86/97 [80:34] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-NUC-H4_RK6_1_30800.d [81:01] 22897 library precursors are potentially detectable [81:01] Processing... [81:12] Cannot perform mass calibration, too few confidently identified precursors [81:12] Cannot perform MS1 mass calibration, too few confidently identified precursors [81:22] RT window set to 11.3935 [81:22] Cannot perform mass calibration, too few confidently identified precursors [81:22] Cannot perform MS1 mass calibration, too few confidently identified precursors [82:10] Removing low confidence identifications [82:10] Removing interfering precursors [82:10] Too few confident identifications, neural networks will not be used [82:10] Number of IDs at 0.01 FDR: 0 [82:10] Calculating protein q-values [82:10] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [82:10] Quantification [82:10] Quantification information saved to \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-NUC-H4_RK6_1_30800.d.quant

[82:10] File #87/97 [82:10] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-SILAC-A1_RC1_1_30631.d [82:47] 22897 library precursors are potentially detectable [82:47] Processing... [82:50] RT window set to 0.449751 [82:50] Recommended MS1 mass accuracy setting: 9.88209 ppm [82:56] Removing low confidence identifications [82:56] Removing interfering precursors [82:56] Training neural networks: 11193 targets, 6111 decoys [82:56] Number of IDs at 0.01 FDR: 7717 [82:56] Calculating protein q-values [82:57] Number of protein isoforms identified at 1% FDR: 1770 (precursor-level), 1679 (protein-level) (inference performed using proteotypic peptides only) [82:57] Quantification [82:58] Quantification information saved to \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-SILAC-A1_RC1_1_30631.d.quant

[82:58] File #88/97 [82:58] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-SILAC-A2_RH1_1_30636.d [83:38] 22897 library precursors are potentially detectable [83:38] Processing... [83:42] RT window set to 0.436499 [83:42] Recommended MS1 mass accuracy setting: 10.1656 ppm [83:47] Removing low confidence identifications [83:47] Removing interfering precursors [83:47] Training neural networks: 11042 targets, 6038 decoys [83:48] Number of IDs at 0.01 FDR: 7211 [83:48] Calculating protein q-values [83:48] Number of protein isoforms identified at 1% FDR: 1742 (precursor-level), 1625 (protein-level) (inference performed using proteotypic peptides only) [83:48] Quantification [83:49] Quantification information saved to \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-SILAC-A2_RH1_1_30636.d.quant

[83:49] File #89/97 [83:49] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-SILAC-A3_RC8_1_30705.d [84:28] 22897 library precursors are potentially detectable [84:28] Processing... [84:32] RT window set to 0.428915 [84:32] Recommended MS1 mass accuracy setting: 10.6615 ppm [84:37] Removing low confidence identifications [84:37] Removing interfering precursors [84:37] Training neural networks: 10790 targets, 5836 decoys [84:38] Number of IDs at 0.01 FDR: 7313 [84:38] Calculating protein q-values [84:38] Number of protein isoforms identified at 1% FDR: 1794 (precursor-level), 1712 (protein-level) (inference performed using proteotypic peptides only) [84:38] Quantification [84:39] Quantification information saved to \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-SILAC-A3_RC8_1_30705.d.quant

[84:39] File #90/97 [84:39] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-SILAC-A4_RH8_1_30710.d [85:12] 22897 library precursors are potentially detectable [85:12] Processing... [85:17] RT window set to 0.439061 [85:17] Recommended MS1 mass accuracy setting: 9.97784 ppm [85:23] Removing low confidence identifications [85:24] Removing interfering precursors [85:24] Training neural networks: 10513 targets, 5720 decoys [85:24] Number of IDs at 0.01 FDR: 6908 [85:24] Calculating protein q-values [85:24] Number of protein isoforms identified at 1% FDR: 1713 (precursor-level), 1635 (protein-level) (inference performed using proteotypic peptides only) [85:24] Quantification [85:25] Quantification information saved to \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-SILAC-A4_RH8_1_30710.d.quant

[85:25] File #91/97 [85:25] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-SILAC-B1_RC2_1_30641.d [85:57] 22897 library precursors are potentially detectable [85:57] Processing... [86:02] RT window set to 0.424706 [86:02] Recommended MS1 mass accuracy setting: 9.94619 ppm [86:07] Removing low confidence identifications [86:07] Removing interfering precursors [86:07] Training neural networks: 9741 targets, 5259 decoys [86:08] Number of IDs at 0.01 FDR: 5947 [86:08] Calculating protein q-values [86:08] Number of protein isoforms identified at 1% FDR: 1482 (precursor-level), 1386 (protein-level) (inference performed using proteotypic peptides only) [86:08] Quantification [86:09] Quantification information saved to \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-SILAC-B1_RC2_1_30641.d.quant

[86:09] File #92/97 [86:09] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-SILAC-B2_RH2_1_30646.d [86:35] 22897 library precursors are potentially detectable [86:35] Processing... [86:41] RT window set to 0.411818 [86:41] Recommended MS1 mass accuracy setting: 10.4672 ppm [86:48] Removing low confidence identifications [86:48] Removing interfering precursors [86:48] Training neural networks: 9110 targets, 4876 decoys [86:48] Number of IDs at 0.01 FDR: 5539 [86:48] Calculating protein q-values [86:48] Number of protein isoforms identified at 1% FDR: 1398 (precursor-level), 1351 (protein-level) (inference performed using proteotypic peptides only) [86:48] Quantification [86:49] Quantification information saved to \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-SILAC-B2_RH2_1_30646.d.quant

[86:49] File #93/97 [86:49] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-SILAC-B3_RC9_1_30719.d [87:17] 22897 library precursors are potentially detectable [87:17] Processing... [87:21] RT window set to 0.499132 [87:21] Recommended MS1 mass accuracy setting: 10.0954 ppm [87:28] Removing low confidence identifications [87:28] Removing interfering precursors [87:28] Training neural networks: 10186 targets, 5516 decoys [87:29] Number of IDs at 0.01 FDR: 6344 [87:29] Calculating protein q-values [87:29] Number of protein isoforms identified at 1% FDR: 1518 (precursor-level), 1436 (protein-level) (inference performed using proteotypic peptides only) [87:29] Quantification [87:30] Quantification information saved to \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-SILAC-B3_RC9_1_30719.d.quant

[87:30] File #94/97 [87:30] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-SILAC-B4_RH9_1_30724.d [88:00] 22897 library precursors are potentially detectable [88:00] Processing... [88:05] RT window set to 0.468665 [88:05] Recommended MS1 mass accuracy setting: 10.6091 ppm [88:12] Removing low confidence identifications [88:12] Removing interfering precursors [88:12] Training neural networks: 8972 targets, 4812 decoys [88:13] Number of IDs at 0.01 FDR: 5533 [88:13] Calculating protein q-values [88:13] Number of protein isoforms identified at 1% FDR: 1385 (precursor-level), 1301 (protein-level) (inference performed using proteotypic peptides only) [88:13] Quantification [88:14] Quantification information saved to \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-SILAC-B4_RH9_1_30724.d.quant

[88:14] File #95/97 [88:14] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-SILAC-C1_RC3_1_30651.d [88:38] 22897 library precursors are potentially detectable [88:38] Processing... [88:44] RT window set to 0.447125 [88:44] Recommended MS1 mass accuracy setting: 10.1075 ppm [88:50] Removing low confidence identifications [88:50] Removing interfering precursors [88:50] Training neural networks: 8696 targets, 4675 decoys [88:51] Number of IDs at 0.01 FDR: 4709 [88:51] Calculating protein q-values [88:51] Number of protein isoforms identified at 1% FDR: 1194 (precursor-level), 1068 (protein-level) (inference performed using proteotypic peptides only) [88:51] Quantification [88:52] Quantification information saved to \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-SILAC-C1_RC3_1_30651.d.quant

[88:52] File #96/97 [88:52] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-SILAC-C2_RH3_1_30656.d [89:15] 22897 library precursors are potentially detectable [89:15] Processing... [89:21] RT window set to 0.438467 [89:21] Recommended MS1 mass accuracy setting: 11.086 ppm [89:29] Removing low confidence identifications [89:29] Removing interfering precursors [89:29] Training neural networks: 8384 targets, 4468 decoys [89:29] Number of IDs at 0.01 FDR: 4405 [89:29] Calculating protein q-values [89:29] Number of protein isoforms identified at 1% FDR: 1162 (precursor-level), 1068 (protein-level) (inference performed using proteotypic peptides only) [89:29] Quantification [89:30] Quantification information saved to \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-SILAC-C2_RH3_1_30656.d.quant

[89:30] File #97/97 [89:30] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-SILAC-C3_RC10_1_30729.d [89:53] 22897 library precursors are potentially detectable [89:53] Processing... [89:59] RT window set to 0.437943 [89:59] Recommended MS1 mass accuracy setting: 10.7983 ppm [90:05] Removing low confidence identifications [90:05] Removing interfering precursors [90:06] Training neural networks: 9100 targets, 4918 decoys [90:06] Number of IDs at 0.01 FDR: 5255 [90:06] Calculating protein q-values [90:06] Number of protein isoforms identified at 1% FDR: 1291 (precursor-level), 1164 (protein-level) (inference performed using proteotypic peptides only) [90:06] Quantification [90:07] Quantification information saved to \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-SILAC-C3_RC10_1_30729.d.quant

[90:07] Cross-run analysis [90:07] Reading quantification information: 97 files [90:10] Quantifying peptides [90:14] Assembling protein groups [90:14] Quantifying proteins [90:14] Calculating q-values for protein and gene groups [90:14] Calculating global q-values for protein and gene groups [90:14] Protein groups with global q-value <= 0.01: 1942 [90:15] Compressed report saved to D:\HK2_library\forskyline2\report-first-pass.parquet. Use R 'arrow' or Python 'PyArrow' package to process [90:15] Writing report [90:21] Report saved to D:\HK2_library\forskyline2\report-first-pass.tsv. [90:21] Saving precursor levels matrix [90:21] Precursor levels matrix (1% precursor and protein group FDR) saved to D:\HK2_library\forskyline2\report-first-pass.pr_matrix.tsv. [90:21] Stats report saved to D:\HK2_library\forskyline2\report-first-pass.stats.tsv [90:21] Generating spectral library: [90:21] Saving spectral library to D:\HK2_library\forskyline2\report.tsv [90:23] 9027 target and 89 decoy precursors saved

[90:23] Loading spectral library D:\HK2_library\forskyline2\report.tsv [90:25] Spectral library loaded: 2061 protein isoforms, 2061 protein groups and 9116 precursors in 8445 elution groups. [90:25] Initialising library [90:25] Saving the library to D:\HK2_library\forskyline2\report.tsv.skyline.speclib

Second pass: using the newly created spectral library to reanalyse the data

[90:25] File #1/97 [90:25] Loading run Y:\TimsTOF-SCP\Data\240711_HK2_LIBRARY\HK2_LIBRARY_GN1_1_30168.d ERROR: either the dia-PASEF file is damaged or a .dia file produced by an older DIA-NN version has been loaded: performance might be suboptimal, regenerate the .dia file using this DIA-NN version WARNING: incorrectly recorded isolation window margins [90:39] 0 library precursors are potentially detectable [90:39] Processing... [90:39] Removing low confidence identifications [90:39] Removing interfering precursors [90:39] Too few confident identifications, neural networks will not be used [90:39] Number of IDs at 0.01 FDR: 0 [90:39] Calculating protein q-values [90:39] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [90:39] Quantification

[90:39] File #2/97 [90:39] Loading run Y:\TimsTOF-SCP\Data\240711_HK2_LIBRARY\HK2_LIBRARY_RC2_1_30145.d ERROR: either the dia-PASEF file is damaged or a .dia file produced by an older DIA-NN version has been loaded: performance might be suboptimal, regenerate the .dia file using this DIA-NN version WARNING: incorrectly recorded isolation window margins [90:53] 0 library precursors are potentially detectable [90:53] Processing... [90:53] Removing low confidence identifications [90:53] Removing interfering precursors [90:53] Too few confident identifications, neural networks will not be used [90:53] Number of IDs at 0.01 FDR: 0 [90:53] Calculating protein q-values [90:53] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [90:53] Quantification

[90:53] File #3/97 [90:53] Loading run Y:\TimsTOF-SCP\Data\240711_HK2_LIBRARY\HK2_LIBRARY_RC3_1_30146.d ERROR: either the dia-PASEF file is damaged or a .dia file produced by an older DIA-NN version has been loaded: performance might be suboptimal, regenerate the .dia file using this DIA-NN version WARNING: incorrectly recorded isolation window margins [90:59] 0 library precursors are potentially detectable [90:59] Processing... [90:59] Removing low confidence identifications [90:59] Removing interfering precursors [90:59] Too few confident identifications, neural networks will not be used [90:59] Number of IDs at 0.01 FDR: 0 [90:59] Calculating protein q-values [90:59] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [90:59] Quantification

[90:59] File #4/97 [90:59] Loading run Y:\TimsTOF-SCP\Data\240711_HK2_LIBRARY\HK2_LIBRARY_RC4_1_30147.d ERROR: either the dia-PASEF file is damaged or a .dia file produced by an older DIA-NN version has been loaded: performance might be suboptimal, regenerate the .dia file using this DIA-NN version WARNING: incorrectly recorded isolation window margins [91:16] 0 library precursors are potentially detectable [91:16] Processing... [91:16] Removing low confidence identifications [91:16] Removing interfering precursors [91:16] Too few confident identifications, neural networks will not be used [91:16] Number of IDs at 0.01 FDR: 0 [91:16] Calculating protein q-values [91:16] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [91:16] Quantification

[91:16] File #5/97 [91:16] Loading run Y:\TimsTOF-SCP\Data\240711_HK2_LIBRARY\HK2_LIBRARY_RC5_1_30148.d ERROR: either the dia-PASEF file is damaged or a .dia file produced by an older DIA-NN version has been loaded: performance might be suboptimal, regenerate the .dia file using this DIA-NN version WARNING: incorrectly recorded isolation window margins [91:33] 0 library precursors are potentially detectable [91:33] Processing... [91:33] Removing low confidence identifications [91:33] Removing interfering precursors [91:33] Too few confident identifications, neural networks will not be used [91:33] Number of IDs at 0.01 FDR: 0 [91:33] Calculating protein q-values [91:33] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [91:33] Quantification

[91:33] File #6/97 [91:33] Loading run Y:\TimsTOF-SCP\Data\240711_HK2_LIBRARY\HK2_LIBRARY_RC6_1_30149.d ERROR: either the dia-PASEF file is damaged or a .dia file produced by an older DIA-NN version has been loaded: performance might be suboptimal, regenerate the .dia file using this DIA-NN version WARNING: incorrectly recorded isolation window margins [91:47] 0 library precursors are potentially detectable [91:47] Processing... [91:47] Removing low confidence identifications [91:47] Removing interfering precursors [91:47] Too few confident identifications, neural networks will not be used [91:47] Number of IDs at 0.01 FDR: 0 [91:47] Calculating protein q-values [91:47] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [91:47] Quantification

[91:47] File #7/97 [91:47] Loading run Y:\TimsTOF-SCP\Data\240711_HK2_LIBRARY\HK2_LIBRARY_RC7_1_30150.d ERROR: either the dia-PASEF file is damaged or a .dia file produced by an older DIA-NN version has been loaded: performance might be suboptimal, regenerate the .dia file using this DIA-NN version WARNING: incorrectly recorded isolation window margins [92:04] 0 library precursors are potentially detectable [92:04] Processing... [92:04] Removing low confidence identifications [92:04] Removing interfering precursors [92:04] Too few confident identifications, neural networks will not be used [92:04] Number of IDs at 0.01 FDR: 0 [92:04] Calculating protein q-values [92:04] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [92:04] Quantification

[92:04] File #8/97 [92:04] Loading run Y:\TimsTOF-SCP\Data\240711_HK2_LIBRARY\HK2_LIBRARY_RC8_1_30151.d ERROR: either the dia-PASEF file is damaged or a .dia file produced by an older DIA-NN version has been loaded: performance might be suboptimal, regenerate the .dia file using this DIA-NN version WARNING: incorrectly recorded isolation window margins [92:18] 0 library precursors are potentially detectable [92:18] Processing... [92:18] Removing low confidence identifications [92:18] Removing interfering precursors [92:18] Too few confident identifications, neural networks will not be used [92:18] Number of IDs at 0.01 FDR: 0 [92:18] Calculating protein q-values [92:18] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [92:18] Quantification

[92:18] File #9/97 [92:18] Loading run Y:\TimsTOF-SCP\Data\240711_HK2_LIBRARY\HK2_LIBRARY_RC9_1_30152.d ERROR: either the dia-PASEF file is damaged or a .dia file produced by an older DIA-NN version has been loaded: performance might be suboptimal, regenerate the .dia file using this DIA-NN version WARNING: incorrectly recorded isolation window margins [92:31] 0 library precursors are potentially detectable [92:31] Processing... [92:31] Removing low confidence identifications [92:31] Removing interfering precursors [92:31] Too few confident identifications, neural networks will not be used [92:31] Number of IDs at 0.01 FDR: 0 [92:31] Calculating protein q-values [92:31] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [92:31] Quantification

[92:31] File #10/97 [92:31] Loading run Y:\TimsTOF-SCP\Data\240711_HK2_LIBRARY\HK2_LIBRARY_RC10_1_30153.d ERROR: either the dia-PASEF file is damaged or a .dia file produced by an older DIA-NN version has been loaded: performance might be suboptimal, regenerate the .dia file using this DIA-NN version WARNING: incorrectly recorded isolation window margins [92:45] 0 library precursors are potentially detectable [92:45] Processing... [92:45] Removing low confidence identifications [92:45] Removing interfering precursors [92:45] Too few confident identifications, neural networks will not be used [92:45] Number of IDs at 0.01 FDR: 0 [92:45] Calculating protein q-values [92:45] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [92:45] Quantification

[92:45] File #11/97 [92:45] Loading run Y:\TimsTOF-SCP\Data\240711_HK2_LIBRARY\HK2_LIBRARY_RC11_1_30154.d ERROR: either the dia-PASEF file is damaged or a .dia file produced by an older DIA-NN version has been loaded: performance might be suboptimal, regenerate the .dia file using this DIA-NN version WARNING: incorrectly recorded isolation window margins [93:00] 0 library precursors are potentially detectable [93:00] Processing... [93:00] Removing low confidence identifications [93:00] Removing interfering precursors [93:00] Too few confident identifications, neural networks will not be used [93:00] Number of IDs at 0.01 FDR: 0 [93:00] Calculating protein q-values [93:00] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [93:00] Quantification

[93:00] File #12/97 [93:00] Loading run Y:\TimsTOF-SCP\Data\240711_HK2_LIBRARY\HK2_LIBRARY_RC12_1_30155.d ERROR: either the dia-PASEF file is damaged or a .dia file produced by an older DIA-NN version has been loaded: performance might be suboptimal, regenerate the .dia file using this DIA-NN version WARNING: incorrectly recorded isolation window margins [93:14] 0 library precursors are potentially detectable [93:14] Processing... [93:14] Removing low confidence identifications [93:14] Removing interfering precursors [93:14] Too few confident identifications, neural networks will not be used [93:14] Number of IDs at 0.01 FDR: 0 [93:14] Calculating protein q-values [93:14] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [93:14] Quantification

[93:14] File #13/97 [93:14] Loading run Y:\TimsTOF-SCP\Data\240711_HK2_LIBRARY\HK2_LIBRARY_RC13_1_30156.d ERROR: either the dia-PASEF file is damaged or a .dia file produced by an older DIA-NN version has been loaded: performance might be suboptimal, regenerate the .dia file using this DIA-NN version WARNING: incorrectly recorded isolation window margins [93:28] 0 library precursors are potentially detectable [93:28] Processing... [93:28] Removing low confidence identifications [93:28] Removing interfering precursors [93:28] Too few confident identifications, neural networks will not be used [93:28] Number of IDs at 0.01 FDR: 0 [93:28] Calculating protein q-values [93:28] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [93:28] Quantification

[93:28] File #14/97 [93:28] Loading run Y:\TimsTOF-SCP\Data\240711_HK2_LIBRARY\HK2_LIBRARY_RC14_1_30157.d ERROR: either the dia-PASEF file is damaged or a .dia file produced by an older DIA-NN version has been loaded: performance might be suboptimal, regenerate the .dia file using this DIA-NN version WARNING: incorrectly recorded isolation window margins [93:43] 0 library precursors are potentially detectable [93:43] Processing... [93:43] Removing low confidence identifications [93:43] Removing interfering precursors [93:43] Too few confident identifications, neural networks will not be used [93:43] Number of IDs at 0.01 FDR: 0 [93:43] Calculating protein q-values [93:43] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [93:43] Quantification

[93:43] File #15/97 [93:43] Loading run Y:\TimsTOF-SCP\Data\240711_HK2_LIBRARY\HK2_LIBRARY_RC15_1_30158.d ERROR: either the dia-PASEF file is damaged or a .dia file produced by an older DIA-NN version has been loaded: performance might be suboptimal, regenerate the .dia file using this DIA-NN version WARNING: incorrectly recorded isolation window margins [93:57] 0 library precursors are potentially detectable [93:57] Processing... [93:57] Removing low confidence identifications [93:57] Removing interfering precursors [93:57] Too few confident identifications, neural networks will not be used [93:57] Number of IDs at 0.01 FDR: 0 [93:57] Calculating protein q-values [93:57] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [93:57] Quantification

[93:57] File #16/97 [93:57] Loading run Y:\TimsTOF-SCP\Data\240711_HK2_LIBRARY\HK2_LIBRARY_RC16_1_30159.d ERROR: either the dia-PASEF file is damaged or a .dia file produced by an older DIA-NN version has been loaded: performance might be suboptimal, regenerate the .dia file using this DIA-NN version WARNING: incorrectly recorded isolation window margins [94:15] 0 library precursors are potentially detectable [94:15] Processing... [94:15] Removing low confidence identifications [94:15] Removing interfering precursors [94:15] Too few confident identifications, neural networks will not be used [94:15] Number of IDs at 0.01 FDR: 0 [94:15] Calculating protein q-values [94:15] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [94:15] Quantification

[94:15] File #17/97 [94:15] Loading run Y:\TimsTOF-SCP\Data\240711_HK2_LIBRARY\HK2_LIBRARY_RC17_1_30160.d ERROR: either the dia-PASEF file is damaged or a .dia file produced by an older DIA-NN version has been loaded: performance might be suboptimal, regenerate the .dia file using this DIA-NN version WARNING: incorrectly recorded isolation window margins [94:32] 0 library precursors are potentially detectable [94:32] Processing... [94:32] Removing low confidence identifications [94:32] Removing interfering precursors [94:32] Too few confident identifications, neural networks will not be used [94:32] Number of IDs at 0.01 FDR: 0 [94:32] Calculating protein q-values [94:32] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [94:32] Quantification

[94:32] File #18/97 [94:32] Loading run Y:\TimsTOF-SCP\Data\240711_HK2_LIBRARY\HK2_LIBRARY_RC18_1_30161.d ERROR: either the dia-PASEF file is damaged or a .dia file produced by an older DIA-NN version has been loaded: performance might be suboptimal, regenerate the .dia file using this DIA-NN version WARNING: incorrectly recorded isolation window margins [94:46] 0 library precursors are potentially detectable [94:46] Processing... [94:46] Removing low confidence identifications [94:46] Removing interfering precursors [94:46] Too few confident identifications, neural networks will not be used [94:46] Number of IDs at 0.01 FDR: 0 [94:46] Calculating protein q-values [94:46] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [94:46] Quantification

[94:46] File #19/97 [94:46] Loading run Y:\TimsTOF-SCP\Data\240711_HK2_LIBRARY\HK2_LIBRARY_RC19_1_30162.d ERROR: either the dia-PASEF file is damaged or a .dia file produced by an older DIA-NN version has been loaded: performance might be suboptimal, regenerate the .dia file using this DIA-NN version WARNING: incorrectly recorded isolation window margins [95:01] 0 library precursors are potentially detectable [95:01] Processing... [95:01] Removing low confidence identifications [95:01] Removing interfering precursors [95:01] Too few confident identifications, neural networks will not be used [95:01] Number of IDs at 0.01 FDR: 0 [95:01] Calculating protein q-values [95:01] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [95:01] Quantification

[95:01] File #20/97 [95:01] Loading run Y:\TimsTOF-SCP\Data\240711_HK2_LIBRARY\HK2_LIBRARY_RC20_1_30163.d ERROR: either the dia-PASEF file is damaged or a .dia file produced by an older DIA-NN version has been loaded: performance might be suboptimal, regenerate the .dia file using this DIA-NN version WARNING: incorrectly recorded isolation window margins [95:15] 0 library precursors are potentially detectable [95:15] Processing... [95:15] Removing low confidence identifications [95:15] Removing interfering precursors [95:15] Too few confident identifications, neural networks will not be used [95:15] Number of IDs at 0.01 FDR: 0 [95:15] Calculating protein q-values [95:15] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [95:15] Quantification

[95:15] File #21/97 [95:15] Loading run Y:\TimsTOF-SCP\Data\240711_HK2_LIBRARY\HK2_LIBRARY_RC21_1_30164.d ERROR: either the dia-PASEF file is damaged or a .dia file produced by an older DIA-NN version has been loaded: performance might be suboptimal, regenerate the .dia file using this DIA-NN version WARNING: incorrectly recorded isolation window margins [95:31] 0 library precursors are potentially detectable [95:31] Processing... [95:31] Removing low confidence identifications [95:31] Removing interfering precursors [95:31] Too few confident identifications, neural networks will not be used [95:31] Number of IDs at 0.01 FDR: 0 [95:31] Calculating protein q-values [95:31] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [95:31] Quantification

[95:31] File #22/97 [95:31] Loading run Y:\TimsTOF-SCP\Data\240711_HK2_LIBRARY\HK2_LIBRARY_RC22_1_30165.d ERROR: either the dia-PASEF file is damaged or a .dia file produced by an older DIA-NN version has been loaded: performance might be suboptimal, regenerate the .dia file using this DIA-NN version WARNING: incorrectly recorded isolation window margins [95:45] 0 library precursors are potentially detectable [95:45] Processing... [95:45] Removing low confidence identifications [95:45] Removing interfering precursors [95:45] Too few confident identifications, neural networks will not be used [95:45] Number of IDs at 0.01 FDR: 0 [95:45] Calculating protein q-values [95:45] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [95:45] Quantification

[95:45] File #23/97 [95:45] Loading run Y:\TimsTOF-SCP\Data\240711_HK2_LIBRARY\HK2_LIBRARY_RC23_1_30166.d ERROR: either the dia-PASEF file is damaged or a .dia file produced by an older DIA-NN version has been loaded: performance might be suboptimal, regenerate the .dia file using this DIA-NN version WARNING: incorrectly recorded isolation window margins [96:00] 0 library precursors are potentially detectable [96:00] Processing... [96:00] Removing low confidence identifications [96:00] Removing interfering precursors [96:00] Too few confident identifications, neural networks will not be used [96:00] Number of IDs at 0.01 FDR: 0 [96:00] Calculating protein q-values [96:00] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [96:00] Quantification

[96:00] File #24/97 [96:00] Loading run Y:\TimsTOF-SCP\Data\240711_HK2_LIBRARY\HK2_LIBRARY_RC24_1_30167.d ERROR: either the dia-PASEF file is damaged or a .dia file produced by an older DIA-NN version has been loaded: performance might be suboptimal, regenerate the .dia file using this DIA-NN version WARNING: incorrectly recorded isolation window margins [96:18] 0 library precursors are potentially detectable [96:18] Processing... [96:18] Removing low confidence identifications [96:18] Removing interfering precursors [96:18] Too few confident identifications, neural networks will not be used [96:18] Number of IDs at 0.01 FDR: 0 [96:18] Calculating protein q-values [96:18] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [96:18] Quantification

[96:18] File #25/97 [96:18] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-A2_RA2_1_30639.d [96:46] 9027 library precursors are potentially detectable [96:46] Processing... [96:52] Cannot perform mass calibration, too few confidently identified precursors [96:52] Cannot perform MS1 mass calibration, too few confidently identified precursors [96:58] RT window set to 6.51391 [96:58] Cannot perform mass calibration, too few confidently identified precursors [96:58] Cannot perform MS1 mass calibration, too few confidently identified precursors [97:20] Removing low confidence identifications [97:20] Removing interfering precursors [97:20] Too few confident identifications, neural networks will not be used [97:20] Number of IDs at 0.01 FDR: 0 [97:20] Calculating protein q-values [97:20] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [97:20] Quantification

[97:20] File #26/97 [97:20] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-A3_RF8_1_30708.d [97:56] 9027 library precursors are potentially detectable [97:56] Processing... [97:58] RT window set to 0.28713 [97:58] Recommended MS1 mass accuracy setting: 10.6013 ppm [98:00] Removing low confidence identifications [98:00] Removing interfering precursors [98:00] Training neural networks: 6923 targets, 3637 decoys [98:01] Number of IDs at 0.01 FDR: 5803 [98:01] Calculating protein q-values [98:01] Number of protein isoforms identified at 1% FDR: 1529 (precursor-level), 1481 (protein-level) (inference performed using proteotypic peptides only) [98:01] Quantification

[98:01] File #27/97 [98:01] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-A4_GF7_1_30713.d [98:30] 9027 library precursors are potentially detectable [98:30] Processing... [98:34] RT window set to 0.28864 [98:34] Recommended MS1 mass accuracy setting: 10.4729 ppm [98:36] Removing low confidence identifications [98:36] Removing interfering precursors [98:36] Training neural networks: 6971 targets, 3640 decoys [98:37] Number of IDs at 0.01 FDR: 5866 [98:37] Calculating protein q-values [98:37] Number of protein isoforms identified at 1% FDR: 1528 (precursor-level), 1458 (protein-level) (inference performed using proteotypic peptides only) [98:37] Quantification

[98:37] File #28/97 [98:37] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-B1_RF2_1_30644.d [99:04] 9027 library precursors are potentially detectable [99:04] Processing... [99:09] RT window set to 0.285809 [99:09] Recommended MS1 mass accuracy setting: 10.7349 ppm [99:12] Removing low confidence identifications [99:12] Removing interfering precursors [99:12] Training neural networks: 6528 targets, 3415 decoys [99:12] Number of IDs at 0.01 FDR: 4604 [99:13] Calculating protein q-values [99:13] Number of protein isoforms identified at 1% FDR: 1234 (precursor-level), 1161 (protein-level) (inference performed using proteotypic peptides only) [99:13] Quantification

[99:13] File #29/97 [99:13] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-B2_RA3_1_30649.d [99:41] 9027 library precursors are potentially detectable [99:41] Processing... [99:48] Cannot perform mass calibration, too few confidently identified precursors [99:48] Cannot perform MS1 mass calibration, too few confidently identified precursors [99:54] RT window set to 5.92004 [99:54] Cannot perform mass calibration, too few confidently identified precursors [99:54] Cannot perform MS1 mass calibration, too few confidently identified precursors [100:17] Removing low confidence identifications [100:17] Removing interfering precursors [100:17] Too few confident identifications, neural networks will not be used [100:17] Number of IDs at 0.01 FDR: 0 [100:17] Calculating protein q-values [100:17] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [100:17] Quantification

[100:18] File #30/97 [100:18] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-B3_RF9_1_30722.d [100:43] 9027 library precursors are potentially detectable [100:43] Processing... [100:48] RT window set to 0.287984 [100:48] Recommended MS1 mass accuracy setting: 10.5272 ppm [100:51] Removing low confidence identifications [100:51] Removing interfering precursors [100:51] Training neural networks: 6457 targets, 3390 decoys [100:52] Number of IDs at 0.01 FDR: 4562 [100:52] Calculating protein q-values [100:52] Number of protein isoforms identified at 1% FDR: 1228 (precursor-level), 1166 (protein-level) (inference performed using proteotypic peptides only) [100:52] Quantification

[100:52] File #31/97 [100:52] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-B4_RA10_1_30727.d [101:15] 9027 library precursors are potentially detectable [101:15] Processing... [101:20] RT window set to 0.287268 [101:20] Recommended MS1 mass accuracy setting: 10.6087 ppm [101:23] Removing low confidence identifications [101:23] Removing interfering precursors [101:24] Training neural networks: 6675 targets, 3502 decoys [101:24] Number of IDs at 0.01 FDR: 5117 [101:24] Calculating protein q-values [101:24] Number of protein isoforms identified at 1% FDR: 1331 (precursor-level), 1279 (protein-level) (inference performed using proteotypic peptides only) [101:24] Quantification

[101:24] File #32/97 [101:24] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-C1_RF3_1_30654.d [101:49] 9027 library precursors are potentially detectable [101:49] Processing... [101:55] RT window set to 0.283742 [101:55] Recommended MS1 mass accuracy setting: 10.874 ppm [101:59] Removing low confidence identifications [101:59] Removing interfering precursors [101:59] Training neural networks: 5877 targets, 3063 decoys [101:59] Number of IDs at 0.01 FDR: 3316 [101:59] Calculating protein q-values [101:59] Number of protein isoforms identified at 1% FDR: 924 (precursor-level), 872 (protein-level) (inference performed using proteotypic peptides only) [101:59] Quantification

[101:59] File #33/97 [101:59] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-C2_RA4_1_30659.d [102:23] 9027 library precursors are potentially detectable [102:23] Processing... [102:29] Cannot perform mass calibration, too few confidently identified precursors [102:29] Cannot perform MS1 mass calibration, too few confidently identified precursors [102:35] RT window set to 7.05185 [102:35] Cannot perform mass calibration, too few confidently identified precursors [102:35] Cannot perform MS1 mass calibration, too few confidently identified precursors [102:59] Removing low confidence identifications [102:59] Removing interfering precursors [102:59] Too few confident identifications, neural networks will not be used [102:59] Number of IDs at 0.01 FDR: 0 [102:59] Calculating protein q-values [102:59] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [102:59] Quantification

[103:00] File #34/97 [103:00] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-C3_RF10_1_30732.d [103:26] 9027 library precursors are potentially detectable [103:26] Processing... [103:33] RT window set to 0.285837 [103:33] Recommended MS1 mass accuracy setting: 11.247 ppm [103:36] Removing low confidence identifications [103:36] Removing interfering precursors [103:36] Training neural networks: 6032 targets, 3152 decoys [103:37] Number of IDs at 0.01 FDR: 3526 [103:37] Calculating protein q-values [103:37] Number of protein isoforms identified at 1% FDR: 982 (precursor-level), 950 (protein-level) (inference performed using proteotypic peptides only) [103:37] Quantification

[103:37] File #35/97 [103:37] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-C4_RA11_1_30737.d [104:05] 9027 library precursors are potentially detectable [104:05] Processing... [104:10] RT window set to 0.28725 [104:10] Recommended MS1 mass accuracy setting: 10.8339 ppm [104:12] Removing low confidence identifications [104:12] Removing interfering precursors [104:13] Training neural networks: 6126 targets, 3225 decoys [104:13] Number of IDs at 0.01 FDR: 3962 [104:13] Calculating protein q-values [104:13] Number of protein isoforms identified at 1% FDR: 1079 (precursor-level), 1026 (protein-level) (inference performed using proteotypic peptides only) [104:13] Quantification

[104:13] File #36/97 [104:13] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-D1_RF4_1_30664.d [104:19] 9027 library precursors are potentially detectable [104:19] Processing... [104:22] RT window set to 0.821569 [104:22] Recommended MS1 mass accuracy setting: 10.1985 ppm [104:26] Removing low confidence identifications [104:26] Removing interfering precursors [104:26] Training neural networks: 3524 targets, 3298 decoys [104:26] Number of IDs at 0.01 FDR: 128 [104:26] Calculating protein q-values [104:26] Number of protein isoforms identified at 1% FDR: 70 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [104:26] Quantification

[104:26] File #37/97 [104:26] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-D2_GF5_1_30669.d [104:50] 9027 library precursors are potentially detectable [104:50] Processing... [104:57] Cannot perform mass calibration, too few confidently identified precursors [104:57] Cannot perform MS1 mass calibration, too few confidently identified precursors [105:03] RT window set to 5.64736 [105:03] Cannot perform mass calibration, too few confidently identified precursors [105:03] Cannot perform MS1 mass calibration, too few confidently identified precursors [105:27] Removing low confidence identifications [105:27] Removing interfering precursors [105:27] Too few confident identifications, neural networks will not be used [105:27] Number of IDs at 0.01 FDR: 0 [105:27] Calculating protein q-values [105:27] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [105:27] Quantification

[105:27] File #38/97 [105:27] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-D3_RF11_1_30742.d [105:52] 9027 library precursors are potentially detectable [105:52] Processing... [106:00] RT window set to 0.285603 [106:00] Recommended MS1 mass accuracy setting: 10.421 ppm [106:04] Removing low confidence identifications [106:04] Removing interfering precursors [106:04] Training neural networks: 4939 targets, 2573 decoys [106:05] Number of IDs at 0.01 FDR: 2401 [106:05] Calculating protein q-values [106:05] Number of protein isoforms identified at 1% FDR: 712 (precursor-level), 676 (protein-level) (inference performed using proteotypic peptides only) [106:05] Quantification

[106:05] File #39/97 [106:05] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-D4_RA12_1_30747.d [106:30] 9027 library precursors are potentially detectable [106:30] Processing... [106:38] RT window set to 0.279854 [106:38] Recommended MS1 mass accuracy setting: 11.0353 ppm [106:42] Removing low confidence identifications [106:42] Removing interfering precursors [106:42] Training neural networks: 4757 targets, 2474 decoys [106:42] Number of IDs at 0.01 FDR: 2363 [106:42] Calculating protein q-values [106:42] Number of protein isoforms identified at 1% FDR: 683 (precursor-level), 652 (protein-level) (inference performed using proteotypic peptides only) [106:42] Quantification

[106:43] File #40/97 [106:43] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-E1_RF5_1_30678.d [107:05] 9027 library precursors are potentially detectable [107:05] Processing... [107:17] RT window set to 0.71272 [107:17] Recommended MS1 mass accuracy setting: 12.1629 ppm [107:23] Removing low confidence identifications [107:23] Removing interfering precursors [107:23] Training neural networks: 4820 targets, 3989 decoys [107:23] Number of IDs at 0.01 FDR: 359 [107:23] Calculating protein q-values [107:23] Number of protein isoforms identified at 1% FDR: 130 (precursor-level), 102 (protein-level) (inference performed using proteotypic peptides only) [107:23] Quantification

[107:24] File #41/97 [107:24] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-E2_RA6_1_30683.d [107:48] 9027 library precursors are potentially detectable [107:48] Processing... [107:55] Cannot perform mass calibration, too few confidently identified precursors [107:55] Cannot perform MS1 mass calibration, too few confidently identified precursors [108:01] RT window set to 4.90293 [108:01] Cannot perform mass calibration, too few confidently identified precursors [108:01] Cannot perform MS1 mass calibration, too few confidently identified precursors [108:23] Removing low confidence identifications [108:23] Removing interfering precursors [108:23] Too few confident identifications, neural networks will not be used [108:23] Number of IDs at 0.01 FDR: 0 [108:23] Calculating protein q-values [108:23] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [108:23] Quantification

[108:23] File #42/97 [108:23] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-E3_RA17_1_30752.d [108:45] 9027 library precursors are potentially detectable [108:45] Processing... [108:58] RT window set to 7.15069 [108:58] Recommended MS1 mass accuracy setting: 13.9066 ppm [109:20] Removing low confidence identifications [109:20] Removing interfering precursors [109:20] Training neural networks: 7955 targets, 8084 decoys [109:21] Number of IDs at 0.01 FDR: 0 [109:21] Too low number of IDs with NNs: reverting to the linear classifier [109:21] Number of IDs at 0.01 FDR: 0 [109:21] Calculating protein q-values [109:21] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [109:21] Quantification

[109:21] File #43/97 [109:21] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-E4_GF9_1_30757.d [109:40] 9027 library precursors are potentially detectable [109:40] Processing... [109:46] Cannot perform mass calibration, too few confidently identified precursors [109:46] Cannot perform MS1 mass calibration, too few confidently identified precursors [109:52] RT window set to 10.5861 [109:52] Cannot perform mass calibration, too few confidently identified precursors [109:52] Cannot perform MS1 mass calibration, too few confidently identified precursors [110:14] Removing low confidence identifications [110:14] Removing interfering precursors [110:14] Training neural networks: 8083 targets, 8140 decoys [110:15] Number of IDs at 0.01 FDR: 0 [110:15] Too low number of IDs with NNs: reverting to the linear classifier [110:15] Number of IDs at 0.01 FDR: 0 [110:15] Calculating protein q-values [110:15] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [110:15] Quantification

[110:15] File #44/97 [110:15] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-F1_RF6_1_30688.d [110:34] 9027 library precursors are potentially detectable [110:34] Processing... [110:40] Cannot perform mass calibration, too few confidently identified precursors [110:40] Cannot perform MS1 mass calibration, too few confidently identified precursors [110:46] RT window set to 7.1264 [110:46] Cannot perform mass calibration, too few confidently identified precursors [110:46] Cannot perform MS1 mass calibration, too few confidently identified precursors [111:07] Removing low confidence identifications [111:07] Removing interfering precursors [111:07] Too few confident identifications, neural networks will not be used [111:07] Number of IDs at 0.01 FDR: 3 [111:07] Calculating protein q-values [111:07] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [111:07] Quantification

[111:07] File #45/97 [111:07] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-F2_RA7_1_30693.d [111:28] 9027 library precursors are potentially detectable [111:28] Processing... [111:34] Cannot perform mass calibration, too few confidently identified precursors [111:34] Cannot perform MS1 mass calibration, too few confidently identified precursors [111:41] RT window set to 5.97072 [111:41] Cannot perform mass calibration, too few confidently identified precursors [111:41] Cannot perform MS1 mass calibration, too few confidently identified precursors [112:04] Removing low confidence identifications [112:04] Removing interfering precursors [112:04] Too few confident identifications, neural networks will not be used [112:04] Number of IDs at 0.01 FDR: 0 [112:04] Calculating protein q-values [112:04] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [112:04] Quantification

[112:04] File #46/97 [112:04] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-F3_RB7_1_30766.d [112:25] 9027 library precursors are potentially detectable [112:25] Processing... [112:31] Cannot perform mass calibration, too few confidently identified precursors [112:31] Cannot perform MS1 mass calibration, too few confidently identified precursors [112:37] RT window set to 10.8033 [112:37] Cannot perform mass calibration, too few confidently identified precursors [112:37] Cannot perform MS1 mass calibration, too few confidently identified precursors [112:59] Removing low confidence identifications [112:59] Removing interfering precursors [112:59] Too few confident identifications, neural networks will not be used [112:59] Number of IDs at 0.01 FDR: 3 [112:59] Calculating protein q-values [112:59] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [112:59] Quantification

[113:00] File #47/97 [113:00] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-F4_RB12_1_30771.d [113:20] 9027 library precursors are potentially detectable [113:20] Processing... [113:30] RT window set to 0.289929 [113:30] Recommended MS1 mass accuracy setting: 11.334 ppm [113:34] Removing low confidence identifications [113:34] Removing interfering precursors [113:34] Training neural networks: 2459 targets, 1264 decoys [113:34] Number of IDs at 0.01 FDR: 520 [113:34] Calculating protein q-values [113:34] Number of protein isoforms identified at 1% FDR: 172 (precursor-level), 124 (protein-level) (inference performed using proteotypic peptides only) [113:34] Quantification

[113:35] File #48/97 [113:35] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-G1_RF7_1_30698.d [113:56] 9027 library precursors are potentially detectable [113:56] Processing... [114:02] Cannot perform mass calibration, too few confidently identified precursors [114:02] Cannot perform MS1 mass calibration, too few confidently identified precursors [114:08] RT window set to 8.40808 [114:08] Cannot perform mass calibration, too few confidently identified precursors [114:08] Cannot perform MS1 mass calibration, too few confidently identified precursors [114:32] Removing low confidence identifications [114:32] Removing interfering precursors [114:32] Too few confident identifications, neural networks will not be used [114:32] Number of IDs at 0.01 FDR: 0 [114:32] Calculating protein q-values [114:32] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [114:32] Quantification

[114:32] File #49/97 [114:32] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-G2_RA8_1_30703.d [114:56] 9027 library precursors are potentially detectable [114:56] Processing... [115:02] Cannot perform mass calibration, too few confidently identified precursors [115:02] Cannot perform MS1 mass calibration, too few confidently identified precursors [115:09] RT window set to 5.72954 [115:09] Cannot perform mass calibration, too few confidently identified precursors [115:09] Cannot perform MS1 mass calibration, too few confidently identified precursors [115:32] Removing low confidence identifications [115:32] Removing interfering precursors [115:32] Too few confident identifications, neural networks will not be used [115:32] Number of IDs at 0.01 FDR: 0 [115:32] Calculating protein q-values [115:32] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [115:32] Quantification

[115:32] File #50/97 [115:32] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-G3_RF10_1_30776.d [115:52] 9027 library precursors are potentially detectable [115:52] Processing... [116:04] RT window set to 0.404296 [116:04] Recommended MS1 mass accuracy setting: 12.3545 ppm [116:08] Removing low confidence identifications [116:08] Removing interfering precursors [116:08] Training neural networks: 4362 targets, 3511 decoys [116:09] Number of IDs at 0.01 FDR: 410 [116:09] Calculating protein q-values [116:09] Number of protein isoforms identified at 1% FDR: 132 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [116:09] Quantification

[116:09] File #51/97 [116:09] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-G4_RJ11_1_30781.d [116:28] 9027 library precursors are potentially detectable [116:28] Processing... [116:38] RT window set to 0.278223 [116:38] Recommended MS1 mass accuracy setting: 11.2376 ppm [116:42] Removing low confidence identifications [116:42] Removing interfering precursors [116:42] Training neural networks: 2373 targets, 1237 decoys [116:43] Number of IDs at 0.01 FDR: 608 [116:43] Calculating protein q-values [116:43] Number of protein isoforms identified at 1% FDR: 205 (precursor-level), 201 (protein-level) (inference performed using proteotypic peptides only) [116:43] Quantification

[116:43] File #52/97 [116:43] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-H1_RJ16_1_30786.d [117:03] 9027 library precursors are potentially detectable [117:03] Processing... [117:09] Cannot perform mass calibration, too few confidently identified precursors [117:09] Cannot perform MS1 mass calibration, too few confidently identified precursors [117:16] RT window set to 6.08834 [117:16] Cannot perform mass calibration, too few confidently identified precursors [117:16] Cannot perform MS1 mass calibration, too few confidently identified precursors [117:40] Removing low confidence identifications [117:40] Removing interfering precursors [117:40] Too few confident identifications, neural networks will not be used [117:40] Number of IDs at 0.01 FDR: 0 [117:40] Calculating protein q-values [117:40] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [117:40] Quantification

[117:40] File #53/97 [117:40] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-H2_RJ21_1_30791.d [117:59] 9027 library precursors are potentially detectable [117:59] Processing... [118:05] Cannot perform mass calibration, too few confidently identified precursors [118:05] Cannot perform MS1 mass calibration, too few confidently identified precursors [118:11] RT window set to 11.013 [118:11] Cannot perform mass calibration, too few confidently identified precursors [118:11] Cannot perform MS1 mass calibration, too few confidently identified precursors [118:34] Removing low confidence identifications [118:34] Removing interfering precursors [118:34] Training neural networks: 7754 targets, 7797 decoys [118:35] Number of IDs at 0.01 FDR: 0 [118:35] Too low number of IDs with NNs: reverting to the linear classifier [118:35] Number of IDs at 0.01 FDR: 0 [118:35] Calculating protein q-values [118:35] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [118:35] Quantification

[118:35] File #54/97 [118:35] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-H3_RK2_1_30796.d [118:55] 9027 library precursors are potentially detectable [118:55] Processing... [119:01] Cannot perform mass calibration, too few confidently identified precursors [119:01] Cannot perform MS1 mass calibration, too few confidently identified precursors [119:07] RT window set to 12.2608 [119:07] Cannot perform mass calibration, too few confidently identified precursors [119:07] Cannot perform MS1 mass calibration, too few confidently identified precursors [119:31] Removing low confidence identifications [119:31] Removing interfering precursors [119:31] Too few confident identifications, neural networks will not be used [119:31] Number of IDs at 0.01 FDR: 1 [119:31] Calculating protein q-values [119:31] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [119:31] Quantification

[119:31] File #55/97 [119:31] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2-H4_GF11_1_30801.d [119:52] 9027 library precursors are potentially detectable [119:52] Processing... [119:58] Cannot perform mass calibration, too few confidently identified precursors [119:58] Cannot perform MS1 mass calibration, too few confidently identified precursors [120:03] RT window set to 10.7448 [120:03] Cannot perform mass calibration, too few confidently identified precursors [120:03] Cannot perform MS1 mass calibration, too few confidently identified precursors [120:26] Removing low confidence identifications [120:26] Removing interfering precursors [120:26] Too few confident identifications, neural networks will not be used [120:26] Number of IDs at 0.01 FDR: 0 [120:26] Calculating protein q-values [120:26] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [120:26] Quantification

[120:26] File #56/97 [120:26] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-NUC-A2_RJ1_1_30638.d [120:47] 9027 library precursors are potentially detectable [120:47] Processing... [120:55] RT window set to 0.286539 [120:55] Recommended MS1 mass accuracy setting: 12.355 ppm [120:59] Removing low confidence identifications [120:59] Removing interfering precursors [120:59] Training neural networks: 3886 targets, 2013 decoys [120:59] Number of IDs at 0.01 FDR: 1341 [120:59] Calculating protein q-values [120:59] Number of protein isoforms identified at 1% FDR: 389 (precursor-level), 365 (protein-level) (inference performed using proteotypic peptides only) [120:59] Quantification

[121:00] File #57/97 [121:00] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-NUC-A3_RE8_1_30707.d [121:21] 9027 library precursors are potentially detectable [121:21] Processing... [121:29] RT window set to 0.28841 [121:29] Recommended MS1 mass accuracy setting: 11.0861 ppm [121:33] Removing low confidence identifications [121:33] Removing interfering precursors [121:33] Training neural networks: 4279 targets, 2227 decoys [121:34] Number of IDs at 0.01 FDR: 1853 [121:34] Calculating protein q-values [121:34] Number of protein isoforms identified at 1% FDR: 536 (precursor-level), 520 (protein-level) (inference performed using proteotypic peptides only) [121:34] Quantification

[121:34] File #58/97 [121:34] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-NUC-A4_RJ8_1_30712.d [121:54] 9027 library precursors are potentially detectable [121:54] Processing... [122:03] RT window set to 0.286914 [122:03] Recommended MS1 mass accuracy setting: 11.8098 ppm [122:07] Removing low confidence identifications [122:07] Removing interfering precursors [122:07] Training neural networks: 3884 targets, 2012 decoys [122:08] Number of IDs at 0.01 FDR: 1337 [122:08] Calculating protein q-values [122:08] Number of protein isoforms identified at 1% FDR: 395 (precursor-level), 254 (protein-level) (inference performed using proteotypic peptides only) [122:08] Quantification

[122:08] File #59/97 [122:08] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-NUC-B1_RE2_1_30643.d [122:29] 9027 library precursors are potentially detectable [122:29] Processing... [122:41] RT window set to 0.287399 [122:41] Recommended MS1 mass accuracy setting: 12.2915 ppm [122:45] Removing low confidence identifications [122:45] Removing interfering precursors [122:45] Training neural networks: 2397 targets, 1241 decoys [122:45] Number of IDs at 0.01 FDR: 709 [122:45] Calculating protein q-values [122:45] Number of protein isoforms identified at 1% FDR: 248 (precursor-level), 195 (protein-level) (inference performed using proteotypic peptides only) [122:45] Quantification

[122:46] File #60/97 [122:46] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-NUC-B2_RJ2_1_30648.d [123:08] 9027 library precursors are potentially detectable [123:08] Processing... [123:20] RT window set to 0.288687 [123:20] Recommended MS1 mass accuracy setting: 12.3002 ppm [123:24] Removing low confidence identifications [123:24] Removing interfering precursors [123:24] Training neural networks: 2464 targets, 1279 decoys [123:24] Number of IDs at 0.01 FDR: 501 [123:24] Calculating protein q-values [123:24] Number of protein isoforms identified at 1% FDR: 171 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [123:24] Quantification

[123:24] File #61/97 [123:24] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-NUC-B3_RE9_1_30721.d [123:47] 9027 library precursors are potentially detectable [123:47] Processing... [123:58] RT window set to 0.289925 [123:58] Recommended MS1 mass accuracy setting: 11.8314 ppm [124:02] Removing low confidence identifications [124:02] Removing interfering precursors [124:02] Training neural networks: 2703 targets, 1397 decoys [124:02] Number of IDs at 0.01 FDR: 759 [124:02] Calculating protein q-values [124:02] Number of protein isoforms identified at 1% FDR: 249 (precursor-level), 250 (protein-level) (inference performed using proteotypic peptides only) [124:02] Quantification

[124:03] File #62/97 [124:03] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-NUC-B4_RJ9_1_30726.d [124:23] 9027 library precursors are potentially detectable [124:23] Processing... [124:33] RT window set to 0.286907 [124:33] Recommended MS1 mass accuracy setting: 10.1441 ppm [124:37] Removing low confidence identifications [124:37] Removing interfering precursors [124:37] Training neural networks: 2689 targets, 1374 decoys [124:38] Number of IDs at 0.01 FDR: 746 [124:38] Calculating protein q-values [124:38] Number of protein isoforms identified at 1% FDR: 236 (precursor-level), 207 (protein-level) (inference performed using proteotypic peptides only) [124:38] Quantification

[124:38] File #63/97 [124:38] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-NUC-C1_RE3_1_30653.d [125:00] 9027 library precursors are potentially detectable [125:00] Processing... [125:12] RT window set to 3.38131 [125:12] Recommended MS1 mass accuracy setting: 11.5244 ppm [125:28] Removing low confidence identifications [125:28] Removing interfering precursors [125:28] Training neural networks: 4652 targets, 4212 decoys [125:28] Number of IDs at 0.01 FDR: 208 [125:28] Calculating protein q-values [125:28] Number of protein isoforms identified at 1% FDR: 75 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [125:28] Quantification

[125:29] File #64/97 [125:29] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-NUC-C2_RJ3_1_30658.d [125:52] 9027 library precursors are potentially detectable [125:52] Processing... [126:03] RT window set to 4.0127 [126:03] Recommended MS1 mass accuracy setting: 13.0331 ppm [126:20] Removing low confidence identifications [126:20] Removing interfering precursors [126:20] Training neural networks: 8099 targets, 8186 decoys [126:21] Number of IDs at 0.01 FDR: 141 [126:21] Calculating protein q-values [126:21] Number of protein isoforms identified at 1% FDR: 58 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [126:21] Quantification

[126:21] File #65/97 [126:21] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-NUC-C3_RE10_1_30731.d [126:46] 9027 library precursors are potentially detectable [126:46] Processing... [126:58] RT window set to 1.0515 [126:58] Recommended MS1 mass accuracy setting: 12.1599 ppm [127:06] Removing low confidence identifications [127:06] Removing interfering precursors [127:06] Training neural networks: 5035 targets, 4474 decoys [127:07] Number of IDs at 0.01 FDR: 321 [127:07] Calculating protein q-values [127:07] Number of protein isoforms identified at 1% FDR: 115 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [127:07] Quantification

[127:07] File #66/97 [127:07] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-NUC-C4_RJ10_1_30736.d [127:26] 9027 library precursors are potentially detectable [127:26] Processing... [127:38] RT window set to 0.775921 [127:38] Recommended MS1 mass accuracy setting: 10.4201 ppm [127:44] Removing low confidence identifications [127:44] Removing interfering precursors [127:44] Training neural networks: 4070 targets, 3484 decoys [127:45] Number of IDs at 0.01 FDR: 314 [127:45] Calculating protein q-values [127:45] Number of protein isoforms identified at 1% FDR: 113 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [127:45] Quantification

[127:45] File #67/97 [127:45] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-NUC-D1_RE4_1_30663.d [128:08] 9027 library precursors are potentially detectable [128:08] Processing... [128:19] RT window set to 6.1323 [128:19] Cannot perform mass calibration, too few confidently identified precursors [128:19] Cannot perform MS1 mass calibration, too few confidently identified precursors [128:40] Removing low confidence identifications [128:40] Removing interfering precursors [128:40] Training neural networks: 8032 targets, 8145 decoys [128:41] Number of IDs at 0.01 FDR: 0 [128:41] Too low number of IDs with NNs: reverting to the linear classifier [128:41] Number of IDs at 0.01 FDR: 0 [128:41] Calculating protein q-values [128:41] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [128:41] Quantification

[128:41] File #68/97 [128:41] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-NUC-D2_RJ4_1_30668.d [129:02] 9027 library precursors are potentially detectable [129:02] Processing... [129:08] Cannot perform mass calibration, too few confidently identified precursors [129:08] Cannot perform MS1 mass calibration, too few confidently identified precursors [129:13] RT window set to 5.94506 [129:13] Cannot perform mass calibration, too few confidently identified precursors [129:13] Cannot perform MS1 mass calibration, too few confidently identified precursors [129:33] Removing low confidence identifications [129:33] Removing interfering precursors [129:33] Training neural networks: 8006 targets, 8161 decoys [129:34] Number of IDs at 0.01 FDR: 0 [129:34] Too low number of IDs with NNs: reverting to the linear classifier [129:34] Number of IDs at 0.01 FDR: 0 [129:34] Calculating protein q-values [129:34] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [129:34] Quantification

[129:34] File #69/97 [129:34] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-NUC-D3_RE11_1_30741.d [129:59] 9027 library precursors are potentially detectable [129:59] Processing... [130:11] RT window set to 5.69924 [130:11] Recommended MS1 mass accuracy setting: 17.1977 ppm [130:32] Removing low confidence identifications [130:32] Removing interfering precursors [130:32] Training neural networks: 7717 targets, 8024 decoys [130:33] Number of IDs at 0.01 FDR: 0 [130:33] Calculating protein q-values [130:33] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [130:33] Quantification

[130:33] File #70/97 [130:33] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-NUC-D4_RJ11_1_30746.d [130:58] 9027 library precursors are potentially detectable [130:58] Processing... [131:08] RT window set to 0.281223 [131:08] Recommended MS1 mass accuracy setting: 10.9166 ppm [131:12] Removing low confidence identifications [131:12] Removing interfering precursors [131:12] Training neural networks: 2687 targets, 1414 decoys [131:13] Number of IDs at 0.01 FDR: 1143 [131:13] Calculating protein q-values [131:13] Number of protein isoforms identified at 1% FDR: 359 (precursor-level), 315 (protein-level) (inference performed using proteotypic peptides only) [131:13] Quantification

[131:13] File #71/97 [131:13] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-NUC-E1_RE5_1_30677.d [131:42] 9027 library precursors are potentially detectable [131:42] Processing... [131:48] Cannot perform mass calibration, too few confidently identified precursors [131:48] Cannot perform MS1 mass calibration, too few confidently identified precursors [131:54] RT window set to 8.51335 [131:54] Cannot perform mass calibration, too few confidently identified precursors [131:54] Cannot perform MS1 mass calibration, too few confidently identified precursors [132:18] Removing low confidence identifications [132:18] Removing interfering precursors [132:18] Too few confident identifications, neural networks will not be used [132:18] Number of IDs at 0.01 FDR: 2 [132:18] Calculating protein q-values [132:18] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [132:18] Quantification

[132:18] File #72/97 [132:18] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-NUC-E2_RJ5_1_30682.d [132:39] 9027 library precursors are potentially detectable [132:39] Processing... [132:45] Cannot perform mass calibration, too few confidently identified precursors [132:45] Cannot perform MS1 mass calibration, too few confidently identified precursors [132:51] RT window set to 8.07109 [132:51] Cannot perform mass calibration, too few confidently identified precursors [132:51] Cannot perform MS1 mass calibration, too few confidently identified precursors [133:14] Removing low confidence identifications [133:14] Removing interfering precursors [133:14] Too few confident identifications, neural networks will not be used [133:14] Number of IDs at 0.01 FDR: 4 [133:14] Calculating protein q-values [133:14] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [133:14] Quantification

[133:14] File #73/97 [133:14] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-NUC-E3_RA16_1_30751.d [133:36] 9027 library precursors are potentially detectable [133:36] Processing... [133:42] Cannot perform mass calibration, too few confidently identified precursors [133:42] Cannot perform MS1 mass calibration, too few confidently identified precursors [133:48] RT window set to 8.43594 [133:48] Cannot perform mass calibration, too few confidently identified precursors [133:48] Cannot perform MS1 mass calibration, too few confidently identified precursors [134:11] Removing low confidence identifications [134:11] Removing interfering precursors [134:11] Training neural networks: 8038 targets, 8153 decoys [134:12] Number of IDs at 0.01 FDR: 0 [134:12] Too low number of IDs with NNs: reverting to the linear classifier [134:12] Number of IDs at 0.01 FDR: 0 [134:12] Calculating protein q-values [134:12] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [134:12] Quantification

[134:12] File #74/97 [134:12] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-NUC-E4_RA21_1_30756.d [134:31] 9027 library precursors are potentially detectable [134:31] Processing... [134:37] Cannot perform mass calibration, too few confidently identified precursors [134:37] Cannot perform MS1 mass calibration, too few confidently identified precursors [134:43] RT window set to 10.1885 [134:43] Cannot perform mass calibration, too few confidently identified precursors [134:43] Cannot perform MS1 mass calibration, too few confidently identified precursors [135:04] Removing low confidence identifications [135:04] Removing interfering precursors [135:04] Too few confident identifications, neural networks will not be used [135:04] Number of IDs at 0.01 FDR: 0 [135:04] Calculating protein q-values [135:04] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [135:04] Quantification

[135:05] File #75/97 [135:05] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-NUC-F1_RE6_1_30687.d [135:24] 9027 library precursors are potentially detectable [135:24] Processing... [135:30] Cannot perform mass calibration, too few confidently identified precursors [135:30] Cannot perform MS1 mass calibration, too few confidently identified precursors [135:36] RT window set to 8.25749 [135:36] Cannot perform mass calibration, too few confidently identified precursors [135:36] Cannot perform MS1 mass calibration, too few confidently identified precursors [135:59] Removing low confidence identifications [135:59] Removing interfering precursors [135:59] Too few confident identifications, neural networks will not be used [135:59] Number of IDs at 0.01 FDR: 4 [135:59] Calculating protein q-values [135:59] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [135:59] Quantification

[135:59] File #76/97 [135:59] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-NUC-F2_RJ6_1_30692.d [136:22] 9027 library precursors are potentially detectable [136:22] Processing... [136:27] Cannot perform mass calibration, too few confidently identified precursors [136:27] Cannot perform MS1 mass calibration, too few confidently identified precursors [136:33] RT window set to 10.4683 [136:33] Cannot perform mass calibration, too few confidently identified precursors [136:33] Cannot perform MS1 mass calibration, too few confidently identified precursors [136:57] Removing low confidence identifications [136:57] Removing interfering precursors [136:57] Too few confident identifications, neural networks will not be used [136:57] Number of IDs at 0.01 FDR: 3 [136:57] Calculating protein q-values [136:57] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [136:57] Quantification

[136:57] File #77/97 [136:57] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-NUC-F3_RB6_1_30765.d [137:16] 9027 library precursors are potentially detectable [137:16] Processing... [137:22] Cannot perform mass calibration, too few confidently identified precursors [137:22] Cannot perform MS1 mass calibration, too few confidently identified precursors [137:28] RT window set to 8.76231 [137:28] Cannot perform mass calibration, too few confidently identified precursors [137:28] Cannot perform MS1 mass calibration, too few confidently identified precursors [137:50] Removing low confidence identifications [137:50] Removing interfering precursors [137:50] Training neural networks: 8189 targets, 8264 decoys [137:51] Number of IDs at 0.01 FDR: 0 [137:51] Too low number of IDs with NNs: reverting to the linear classifier [137:51] Number of IDs at 0.01 FDR: 0 [137:51] Calculating protein q-values [137:51] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [137:51] Quantification

[137:51] File #78/97 [137:51] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-NUC-F4_RB11_1_30770.d [138:11] 9027 library precursors are potentially detectable [138:11] Processing... [138:20] RT window set to 0.287985 [138:20] Recommended MS1 mass accuracy setting: 10.9042 ppm [138:24] Removing low confidence identifications [138:24] Removing interfering precursors [138:24] Training neural networks: 2933 targets, 1519 decoys [138:25] Number of IDs at 0.01 FDR: 884 [138:25] Calculating protein q-values [138:25] Number of protein isoforms identified at 1% FDR: 287 (precursor-level), 251 (protein-level) (inference performed using proteotypic peptides only) [138:25] Quantification

[138:25] File #79/97 [138:25] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-NUC-G1_RE7_1_30697.d [138:45] 9027 library precursors are potentially detectable [138:45] Processing... [138:51] Cannot perform mass calibration, too few confidently identified precursors [138:51] Cannot perform MS1 mass calibration, too few confidently identified precursors [138:57] RT window set to 9.54516 [138:57] Cannot perform mass calibration, too few confidently identified precursors [138:57] Cannot perform MS1 mass calibration, too few confidently identified precursors [139:22] Removing low confidence identifications [139:22] Removing interfering precursors [139:22] Too few confident identifications, neural networks will not be used [139:22] Number of IDs at 0.01 FDR: 3 [139:22] Calculating protein q-values [139:22] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [139:22] Quantification

[139:22] File #80/97 [139:22] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-NUC-G2_RJ7_1_30702.d [139:43] 9027 library precursors are potentially detectable [139:43] Processing... [139:49] Cannot perform mass calibration, too few confidently identified precursors [139:49] Cannot perform MS1 mass calibration, too few confidently identified precursors [139:55] RT window set to 6.8774 [139:55] Cannot perform mass calibration, too few confidently identified precursors [139:55] Cannot perform MS1 mass calibration, too few confidently identified precursors [140:17] Removing low confidence identifications [140:17] Removing interfering precursors [140:17] Too few confident identifications, neural networks will not be used [140:17] Number of IDs at 0.01 FDR: 0 [140:17] Calculating protein q-values [140:17] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [140:17] Quantification

[140:17] File #81/97 [140:17] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-NUC-G3_RE10_1_30775.d [140:40] 9027 library precursors are potentially detectable [140:40] Processing... [140:46] Cannot perform mass calibration, too few confidently identified precursors [140:46] Cannot perform MS1 mass calibration, too few confidently identified precursors [140:52] RT window set to 5.77784 [140:52] Cannot perform mass calibration, too few confidently identified precursors [140:52] Cannot perform MS1 mass calibration, too few confidently identified precursors [141:16] Removing low confidence identifications [141:16] Removing interfering precursors [141:16] Too few confident identifications, neural networks will not be used [141:16] Number of IDs at 0.01 FDR: 0 [141:16] Calculating protein q-values [141:16] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [141:16] Quantification

[141:16] File #82/97 [141:16] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-NUC-G4_RJ10_1_30780.d [141:40] 9027 library precursors are potentially detectable [141:40] Processing... [141:46] Cannot perform mass calibration, too few confidently identified precursors [141:46] Cannot perform MS1 mass calibration, too few confidently identified precursors [141:52] RT window set to 10.7224 [141:52] Cannot perform mass calibration, too few confidently identified precursors [141:52] Cannot perform MS1 mass calibration, too few confidently identified precursors [142:14] Removing low confidence identifications [142:14] Removing interfering precursors [142:14] Too few confident identifications, neural networks will not be used [142:14] Number of IDs at 0.01 FDR: 3 [142:14] Calculating protein q-values [142:14] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [142:14] Quantification

[142:15] File #83/97 [142:15] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-NUC-H1_RJ15_1_30785.d [142:39] 9027 library precursors are potentially detectable [142:39] Processing... [142:45] Cannot perform mass calibration, too few confidently identified precursors [142:45] Cannot perform MS1 mass calibration, too few confidently identified precursors [142:52] RT window set to 6.64423 [142:52] Cannot perform mass calibration, too few confidently identified precursors [142:52] Cannot perform MS1 mass calibration, too few confidently identified precursors [143:13] Removing low confidence identifications [143:13] Removing interfering precursors [143:13] Training neural networks: 7721 targets, 7950 decoys [143:14] Number of IDs at 0.01 FDR: 0 [143:14] Too low number of IDs with NNs: reverting to the linear classifier [143:14] Number of IDs at 0.01 FDR: 0 [143:14] Number of IDs at 0.01 FDR: 0 [143:14] Calculating protein q-values [143:14] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [143:14] Quantification

[143:14] File #84/97 [143:14] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-NUC-H2_RJ20_1_30790.d [143:38] 9027 library precursors are potentially detectable [143:38] Processing... [143:44] Cannot perform mass calibration, too few confidently identified precursors [143:44] Cannot perform MS1 mass calibration, too few confidently identified precursors [143:50] RT window set to 11.0711 [143:50] Cannot perform mass calibration, too few confidently identified precursors [143:50] Cannot perform MS1 mass calibration, too few confidently identified precursors [144:14] Removing low confidence identifications [144:14] Removing interfering precursors [144:14] Too few confident identifications, neural networks will not be used [144:14] Number of IDs at 0.01 FDR: 0 [144:14] Calculating protein q-values [144:14] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [144:14] Quantification

[144:14] File #85/97 [144:14] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-NUC-H3_RK1_1_30795.d [144:35] 9027 library precursors are potentially detectable [144:35] Processing... [144:41] Cannot perform mass calibration, too few confidently identified precursors [144:41] Cannot perform MS1 mass calibration, too few confidently identified precursors [144:46] RT window set to 10.9997 [144:46] Cannot perform mass calibration, too few confidently identified precursors [144:46] Cannot perform MS1 mass calibration, too few confidently identified precursors [145:10] Removing low confidence identifications [145:10] Removing interfering precursors [145:10] Training neural networks: 8185 targets, 8199 decoys [145:10] Number of IDs at 0.01 FDR: 0 [145:10] Too low number of IDs with NNs: reverting to the linear classifier [145:10] Number of IDs at 0.01 FDR: 0 [145:10] Calculating protein q-values [145:10] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [145:10] Quantification

[145:10] File #86/97 [145:10] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-NUC-H4_RK6_1_30800.d [145:34] 9027 library precursors are potentially detectable [145:34] Processing... [145:40] Cannot perform mass calibration, too few confidently identified precursors [145:40] Cannot perform MS1 mass calibration, too few confidently identified precursors [145:46] RT window set to 11.3647 [145:46] Cannot perform mass calibration, too few confidently identified precursors [145:46] Cannot perform MS1 mass calibration, too few confidently identified precursors [146:08] Removing low confidence identifications [146:08] Removing interfering precursors [146:08] Too few confident identifications, neural networks will not be used [146:08] Number of IDs at 0.01 FDR: 0 [146:08] Calculating protein q-values [146:08] Number of protein isoforms identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [146:08] Quantification

[146:09] File #87/97 [146:09] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-SILAC-A1_RC1_1_30631.d [146:41] 9027 library precursors are potentially detectable [146:41] Processing... [146:43] RT window set to 0.291923 [146:43] Recommended MS1 mass accuracy setting: 9.90974 ppm [146:46] Removing low confidence identifications [146:46] Removing interfering precursors [146:46] Training neural networks: 7940 targets, 4173 decoys [146:46] Number of IDs at 0.01 FDR: 7695 [146:46] Calculating protein q-values [146:46] Number of protein isoforms identified at 1% FDR: 1755 (precursor-level), 1730 (protein-level) (inference performed using proteotypic peptides only) [146:46] Quantification

[146:47] File #88/97 [146:47] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-SILAC-A2_RH1_1_30636.d [147:20] 9027 library precursors are potentially detectable [147:20] Processing... [147:22] RT window set to 0.288421 [147:22] Recommended MS1 mass accuracy setting: 10.2976 ppm [147:25] Removing low confidence identifications [147:25] Removing interfering precursors [147:25] Training neural networks: 7865 targets, 4103 decoys [147:25] Number of IDs at 0.01 FDR: 7368 [147:25] Calculating protein q-values [147:25] Number of protein isoforms identified at 1% FDR: 1726 (precursor-level), 1725 (protein-level) (inference performed using proteotypic peptides only) [147:25] Quantification

[147:26] File #89/97 [147:26] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-SILAC-A3_RC8_1_30705.d [148:03] 9027 library precursors are potentially detectable [148:03] Processing... [148:05] RT window set to 0.288785 [148:05] Recommended MS1 mass accuracy setting: 10.4432 ppm [148:07] Removing low confidence identifications [148:07] Removing interfering precursors [148:07] Training neural networks: 7758 targets, 4081 decoys [148:08] Number of IDs at 0.01 FDR: 7365 [148:08] Calculating protein q-values [148:08] Number of protein isoforms identified at 1% FDR: 1747 (precursor-level), 1734 (protein-level) (inference performed using proteotypic peptides only) [148:08] Quantification

[148:08] File #90/97 [148:08] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-SILAC-A4_RH8_1_30710.d [148:37] 9027 library precursors are potentially detectable [148:37] Processing... [148:39] RT window set to 0.288132 [148:39] Recommended MS1 mass accuracy setting: 10.3771 ppm [148:41] Removing low confidence identifications [148:41] Removing interfering precursors [148:41] Training neural networks: 7663 targets, 4018 decoys [148:42] Number of IDs at 0.01 FDR: 7123 [148:42] Calculating protein q-values [148:42] Number of protein isoforms identified at 1% FDR: 1719 (precursor-level), 1710 (protein-level) (inference performed using proteotypic peptides only) [148:42] Quantification

[148:42] File #91/97 [148:42] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-SILAC-B1_RC2_1_30641.d [149:13] 9027 library precursors are potentially detectable [149:13] Processing... [149:15] RT window set to 0.290061 [149:15] Recommended MS1 mass accuracy setting: 10.5665 ppm [149:17] Removing low confidence identifications [149:17] Removing interfering precursors [149:18] Training neural networks: 7468 targets, 3910 decoys [149:18] Number of IDs at 0.01 FDR: 6374 [149:18] Calculating protein q-values [149:18] Number of protein isoforms identified at 1% FDR: 1550 (precursor-level), 1498 (protein-level) (inference performed using proteotypic peptides only) [149:18] Quantification

[149:18] File #92/97 [149:18] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-SILAC-B2_RH2_1_30646.d [149:48] 9027 library precursors are potentially detectable [149:48] Processing... [149:51] RT window set to 0.288192 [149:51] Recommended MS1 mass accuracy setting: 11.2292 ppm [149:53] Removing low confidence identifications [149:53] Removing interfering precursors [149:54] Training neural networks: 7354 targets, 3841 decoys [149:54] Number of IDs at 0.01 FDR: 6072 [149:54] Calculating protein q-values [149:54] Number of protein isoforms identified at 1% FDR: 1491 (precursor-level), 1374 (protein-level) (inference performed using proteotypic peptides only) [149:54] Quantification

[149:54] File #93/97 [149:54] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-SILAC-B3_RC9_1_30719.d [150:37] 9027 library precursors are potentially detectable [150:37] Processing... [150:38] RT window set to 0.289702 [150:38] Recommended MS1 mass accuracy setting: 10.3869 ppm [150:41] Removing low confidence identifications [150:41] Removing interfering precursors [150:41] Training neural networks: 7495 targets, 3931 decoys [150:41] Number of IDs at 0.01 FDR: 6541 [150:41] Calculating protein q-values [150:41] Number of protein isoforms identified at 1% FDR: 1575 (precursor-level), 1526 (protein-level) (inference performed using proteotypic peptides only) [150:41] Quantification

[150:42] File #94/97 [150:42] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-SILAC-B4_RH9_1_30724.d [151:14] 9027 library precursors are potentially detectable [151:14] Processing... [151:20] RT window set to 0.287625 [151:20] Recommended MS1 mass accuracy setting: 11.3575 ppm [151:23] Removing low confidence identifications [151:23] Removing interfering precursors [151:23] Training neural networks: 7305 targets, 3798 decoys [151:23] Number of IDs at 0.01 FDR: 5915 [151:23] Calculating protein q-values [151:23] Number of protein isoforms identified at 1% FDR: 1462 (precursor-level), 1382 (protein-level) (inference performed using proteotypic peptides only) [151:23] Quantification

[151:24] File #95/97 [151:24] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-SILAC-C1_RC3_1_30651.d [151:50] 9027 library precursors are potentially detectable [151:50] Processing... [151:55] RT window set to 0.2869 [151:55] Recommended MS1 mass accuracy setting: 10.8873 ppm [151:58] Removing low confidence identifications [151:58] Removing interfering precursors [151:58] Training neural networks: 7100 targets, 3713 decoys [151:58] Number of IDs at 0.01 FDR: 5208 [151:58] Calculating protein q-values [151:58] Number of protein isoforms identified at 1% FDR: 1300 (precursor-level), 1227 (protein-level) (inference performed using proteotypic peptides only) [151:58] Quantification

[151:59] File #96/97 [151:59] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-SILAC-C2_RH3_1_30656.d [152:29] 9027 library precursors are potentially detectable [152:29] Processing... [152:33] RT window set to 0.286832 [152:33] Recommended MS1 mass accuracy setting: 10.7121 ppm [152:36] Removing low confidence identifications [152:36] Removing interfering precursors [152:37] Training neural networks: 6971 targets, 3640 decoys [152:37] Number of IDs at 0.01 FDR: 4743 [152:37] Calculating protein q-values [152:37] Number of protein isoforms identified at 1% FDR: 1225 (precursor-level), 1138 (protein-level) (inference performed using proteotypic peptides only) [152:37] Quantification

[152:37] File #97/97 [152:37] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-SILAC-C3_RC10_1_30729.d [153:05] 9027 library precursors are potentially detectable [153:05] Processing... [153:10] RT window set to 0.286691 [153:10] Recommended MS1 mass accuracy setting: 10.3319 ppm [153:13] Removing low confidence identifications [153:13] Removing interfering precursors [153:13] Training neural networks: 7168 targets, 3754 decoys [153:13] Number of IDs at 0.01 FDR: 5436 [153:14] Calculating protein q-values [153:14] Number of protein isoforms identified at 1% FDR: 1348 (precursor-level), 1322 (protein-level) (inference performed using proteotypic peptides only) [153:14] Quantification

[153:14] Cross-run analysis [153:14] Reading quantification information: 97 files [153:14] Quantifying peptides [153:40] Quantification parameters: 0.39801, 0.00293843, 0.00907134, 0.01447, 0.0138335, 0.0134056, 0.14321, 0.149364, 0.147074, 0.148347, 0.0155913, 0.0576069, 0.338962, 0.0284197, 0.0492956, 0.0687846 [153:42] Quantifying proteins [153:43] Calculating q-values for protein and gene groups [153:43] Calculating global q-values for protein and gene groups [153:43] Protein groups with global q-value <= 0.01: 1855 [153:43] Compressed report saved to D:\HK2_library\forskyline2\report.parquet. Use R 'arrow' or Python 'PyArrow' package to process [153:43] Writing report [153:50] Report saved to D:\HK2_library\forskyline2\report.tsv. [153:50] Saving precursor levels matrix [153:50] Precursor levels matrix (1% precursor and protein group FDR) saved to D:\HK2_library\forskyline2\report.pr_matrix.tsv. [153:50] Saving protein group levels matrix [153:50] Protein group levels matrix (1% precursor FDR and protein group FDR) saved to D:\HK2_library\forskyline2\report.pg_matrix.tsv. [153:50] Saving gene group levels matrix [153:50] Gene groups levels matrix (1% precursor FDR and protein group FDR) saved to D:\HK2_library\forskyline2\report.gg_matrix.tsv. [153:50] Saving unique genes levels matrix [153:50] Unique genes levels matrix (1% precursor FDR and protein group FDR) saved to D:\HK2_library\forskyline2\report.unique_genes_matrix.tsv. [153:50] Stats report saved to D:\HK2_library\forskyline2\report.stats.tsv

[vdemichev]

[0:01] Loading run Y:\TimsTOF-SCP\Data\240711_HK2_LIBRARY\HK2_LIBRARY_GN1_1_30168.d For most Slice/DIA-PASEF datasets it is better to manually fix both the MS1 and MS2 mass accuracies to values in the range 10-15 ppm. ERROR: either the dia-PASEF file is damaged or a .dia file produced by an older DIA-NN version has been loaded: performance might be suboptimal, regenerate the .dia file using this DIA-NN version WARNING: incorrectly recorded isolation window margins

Could it be that this is DDA (i.e. PASEF, not dia-PASEF) data?

--channels command is absent from the log, so this is the reason why it did not find any heavy peptides.|

Btw,

f \smb.researchcampus.csmc.edu\vaneykjlab-mshub\TimsTOF-SCP\Data\240726_Bora_NUC_SILAC_DIA\L-HK2--A1_RF1_1_30634.d

Files with double dash '--' in the name will not be processed, i.e. DIA-NN does not correctly parse those names. I would suggest to rename the two files with '--'.

[drstiltz]

I actually use this channels command --channels SILAC,L,KR,0:0; SILAC,H,KR,6.020129:10.008269 here is the new log after I searched my files using a regular library

my files that start with H- are supposed to be heavy, but I don't get any peptide hits on them report.log2.txt

[vdemichev]

If exact same settings are fine on an Orbitrap but not on timsTOF, the problem is most likely with the data, not the settings. Apart from warnings/errors printed by DIA-NN (they would not cause lack of IDs here), the log looks correct. What is report1.predicted.speclib and does it work with the Orbitrap data?

[drstiltz]

Hi again, Rather than running the samples on a TIMS-TOF, this time I ran bulk mixtures of normal proteome and heavy proteome from human cell lysates. This is the log I'm getting, but interestingly I don't get the peptide quantification results yet. The speclib file is a predicted speclib file of bulk proteome of the same cell from another experiment.

DIA-NN 1.9 (Data-Independent Acquisition by Neural Networks) Compiled on Jun 8 2024 20:00:31 Current date and time: Wed Sep 18 13:01:58 2024 CPU: GenuineIntel Intel(R) Xeon(R) CPU E5-2690 v4 @ 2.60GHz SIMD instructions: AVX AVX2 FMA SSE4.1 SSE4.2 Logical CPU cores: 16 diann.exe --f \smb.researchcampus.csmc.edu\vaneykjlab-mshub\Ascend\MeyerLab_Ascend_2024\Bora\SILAC_mix_2\Bora_mix1_20240917151044.mzML --f \smb.researchcampus.csmc.edu\vaneykjlab-mshub\Ascend\MeyerLab_Ascend_2024\Bora\SILAC_mix_2\Bora_mix2_20240917155448.mzML --f \smb.researchcampus.csmc.edu\vaneykjlab-mshub\Ascend\MeyerLab_Ascend_2024\Bora\SILAC_mix_2\Bora_mix3_20240917163839.mzML --f \smb.researchcampus.csmc.edu\vaneykjlab-mshub\Ascend\MeyerLab_Ascend_2024\Bora\SILAC_mix_2\Bora_mix4_20240917172228.mzML --f \smb.researchcampus.csmc.edu\vaneykjlab-mshub\Ascend\MeyerLab_Ascend_2024\Bora\SILAC_mix_2\Bora_mix5_20240917180622.mzML --f \smb.researchcampus.csmc.edu\vaneykjlab-mshub\Ascend\MeyerLab_Ascend_2024\Bora\SILAC_mix_2\Bora_mix6_20240917185027.mzML --f \smb.researchcampus.csmc.edu\vaneykjlab-mshub\Ascend\MeyerLab_Ascend_2024\Bora\SILAC_mix_2\Bora_mix7_20240917193430.mzML --f \smb.researchcampus.csmc.edu\vaneykjlab-mshub\Ascend\MeyerLab_Ascend_2024\Bora\SILAC_mix_2\Bora_mix8_20240917201734.mzML --f \smb.researchcampus.csmc.edu\vaneykjlab-mshub\Ascend\MeyerLab_Ascend_2024\Bora\SILAC_mix_2\Bora_mix9_20240917210046.mzML --f \smb.researchcampus.csmc.edu\vaneykjlab-mshub\Ascend\MeyerLab_Ascend_2024\Bora\SILAC_mix_2\Bora_mix10_20240917214403.mzML --f \smb.researchcampus.csmc.edu\vaneykjlab-mshub\Ascend\MeyerLab_Ascend_2024\Bora\SILAC_mix_2\Bora_mix11_20240917222644.mzML --f \smb.researchcampus.csmc.edu\vaneykjlab-mshub\Ascend\MeyerLab_Ascend_2024\Bora\SILAC_mix_2\Bora_mix12_20240917230946.mzML --f \smb.researchcampus.csmc.edu\vaneykjlab-mshub\Ascend\MeyerLab_Ascend_2024\Bora\SILAC_mix_2\Bora_mix13_20240917235229.mzML --f \smb.researchcampus.csmc.edu\vaneykjlab-mshub\Ascend\MeyerLab_Ascend_2024\Bora\SILAC_mix_2\Bora_mix14_20240917103944.mzML --f \smb.researchcampus.csmc.edu\vaneykjlab-mshub\Ascend\MeyerLab_Ascend_2024\Bora\SILAC_mix_2\Bora_mix15_20240917095530.mzML --f \smb.researchcampus.csmc.edu\vaneykjlab-mshub\Ascend\MeyerLab_Ascend_2024\Bora\SILAC_mix_2\Bora_mix16_20240917091113.mzML --f \smb.researchcampus.csmc.edu\vaneykjlab-mshub\Ascend\MeyerLab_Ascend_2024\Bora\SILAC_mix_2\Bora_mix17.mzML --f \smb.researchcampus.csmc.edu\vaneykjlab-mshub\Ascend\MeyerLab_Ascend_2024\Bora\SILAC_mix_2\Bora_mix18.mzML --lib D:\Ally\09052024\report1.predicted.speclib --threads 16 --verbose 1 --out D:\Ascend_SILAC_mix\report.tsv --qvalue 0.01 --matrices --out-lib D:\Ascend_SILAC_mix\report1.tsv --gen-spec-lib --predictor --unimod4 --mass-acc 10 --mass-acc-ms1 10 --reanalyse --relaxed-prot-inf --rt-profiling --fixed-mod SILAC,0.0,KR,label --channels SILAC,L,KR,0:0; SILAC,H,KR,6.020129:10.008269 --original-mods --strip-unknown-mods --peak-translation

Thread number set to 16 Output will be filtered at 0.01 FDR Precursor/protein x samples expression level matrices will be saved along with the main report A spectral library will be generated Deep learning will be used to generate a new in silico spectral library from peptides provided Cysteine carbamidomethylation enabled as a fixed modification A spectral library will be created from the DIA runs and used to reanalyse them; .quant files will only be saved to disk during the first step Heuristic protein grouping will be used, to reduce the number of protein groups obtained; this mode is recommended for benchmarking protein ID numbers, GO/pathway and system-scale analyses The spectral library (if generated) will retain the original spectra but will include empirically-aligned RTs Modification SILAC with mass delta 0 at KR will be considered as fixed label DIA-NN will not attempt to convert library modifications to the UniMod format WARNING: unrecognised option [--strip-unknown-mods] Translation of retention times between peptides within the same elution group enabled Mass accuracy will be fixed to 1e-05 (MS2) and 1e-05 (MS1) WARNING: protein inference is enabled but no FASTA provided - is this intended? ERROR: channel normalisation strategy must be specified. Use either --channel-run-norm (good e.g. for protein turnover studies) or --channel-spec-norm (good e.g. for multiplexing of independent samples using chemical labels) - see details in the documentation WARNING: setting channel normalisation to --channel-run-norm, make sure this is what is intended or reanalyse with the correct setting Registered SILAC channel L with following masses: K[0] R[0] Registered SILAC channel H with following masses: K[6.02013] R[10.0083] Registered SILAC channel decoy with following masses: K[12.0403] R[20.0165]

18 files will be processed [0:00] Loading spectral library D:\Ally\09052024\report1.predicted.speclib [0:00] Library annotated with sequence database(s): C:\Users\Admin-OnatB\Downloads\UP000005640_9606.fasta\UP000005640_9606.fasta [0:00] Gene names missing for some isoforms [0:00] Library contains 5932 proteins, and 5928 genes [0:00] Spectral library loaded: 5932 protein isoforms, 5817 protein groups and 30517 precursors in 28314 elution groups. [0:00] [0:00] [0:05] [0:06] [0:06] [0:06] Saving the library to D:\Ascend_SILAC_mix\report1.predicted.speclib [0:06] Initialising library [0:06] Splitting library entries across channels [0:06] 30517 unlabelled precursors detected [0:06] Assembling elution groups

First pass: generating a spectral library from DIA data

[0:06] File #1/18 [0:06] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\Ascend\MeyerLab_Ascend_2024\Bora\SILAC_mix_2\Bora_mix1_20240917151044.mzML [0:07] 22876 library precursors are potentially detectable [0:07] Processing... [0:12] RT window set to 9.93291 [0:12] Peak width: 4.38462 [0:12] Scan window radius set to 9 [0:12] Recommended MS1 mass accuracy setting: 3.42829 ppm [0:19] Removing low confidence identifications [0:19] Removing interfering precursors [0:19] Training neural networks: 2511 targets, 2173 decoys [0:19] Number of IDs at 0.01 FDR: 164 [0:19] Translating peaks within elution groups [0:19] Number of IDs at 0.01 FDR: 164 [0:19] Precursors with channel labels at 1% channel FDR: 0 out of 0 considered [0:19] Calculating protein q-values [0:19] Number of genes identified at 1% FDR: 100 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [0:19] Quantification [0:19] Quantification information saved to \smb.researchcampus.csmc.edu\vaneykjlab-mshub\Ascend\MeyerLab_Ascend_2024\Bora\SILAC_mix_2\Bora_mix1_20240917151044.mzML.quant

[0:19] File #2/18 [0:19] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\Ascend\MeyerLab_Ascend_2024\Bora\SILAC_mix_2\Bora_mix2_20240917155448.mzML [0:20] 22876 library precursors are potentially detectable [0:20] Processing... [0:25] RT window set to 9.09502 [0:25] Recommended MS1 mass accuracy setting: 4.26124 ppm [0:30] Removing low confidence identifications [0:30] Removing interfering precursors [0:30] Training neural networks: 12819 targets, 13956 decoys [0:31] Number of IDs at 0.01 FDR: 0 [0:31] Too low number of IDs with NNs: reverting to the linear classifier [0:31] Number of IDs at 0.01 FDR: 0 [0:31] Translating peaks within elution groups [0:31] Number of IDs at 0.01 FDR: 0 [0:31] Precursors with channel labels at 1% channel FDR: 0 out of 0 considered [0:31] Calculating protein q-values [0:31] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [0:31] Quantification [0:31] Quantification information saved to \smb.researchcampus.csmc.edu\vaneykjlab-mshub\Ascend\MeyerLab_Ascend_2024\Bora\SILAC_mix_2\Bora_mix2_20240917155448.mzML.quant

[0:31] File #3/18 [0:31] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\Ascend\MeyerLab_Ascend_2024\Bora\SILAC_mix_2\Bora_mix3_20240917163839.mzML [0:32] 22876 library precursors are potentially detectable [0:32] Processing... [0:35] RT window set to 9.20028 [0:35] Recommended MS1 mass accuracy setting: 3.87439 ppm [0:40] Removing low confidence identifications [0:40] Removing interfering precursors [0:40] Training neural networks: 13394 targets, 14996 decoys [0:41] Number of IDs at 0.01 FDR: 0 [0:41] Too low number of IDs with NNs: reverting to the linear classifier [0:41] Number of IDs at 0.01 FDR: 6 [0:41] Translating peaks within elution groups [0:41] Number of IDs at 0.01 FDR: 7 [0:41] Precursors with channel labels at 1% channel FDR: 0 out of 0 considered [0:41] Calculating protein q-values [0:41] Number of genes identified at 1% FDR: 6 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [0:41] Quantification [0:41] Quantification information saved to \smb.researchcampus.csmc.edu\vaneykjlab-mshub\Ascend\MeyerLab_Ascend_2024\Bora\SILAC_mix_2\Bora_mix3_20240917163839.mzML.quant

[0:41] File #4/18 [0:41] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\Ascend\MeyerLab_Ascend_2024\Bora\SILAC_mix_2\Bora_mix4_20240917172228.mzML [0:42] 22876 library precursors are potentially detectable [0:42] Processing... [0:44] RT window set to 1.54667 [0:44] Recommended MS1 mass accuracy setting: 4.29871 ppm [0:45] Removing low confidence identifications [0:45] Removing interfering precursors [0:45] Training neural networks: 3346 targets, 2841 decoys [0:46] Number of IDs at 0.01 FDR: 668 [0:46] Translating peaks within elution groups [0:46] Number of IDs at 0.01 FDR: 674 [0:46] Precursors with channel labels at 1% channel FDR: 0 out of 0 considered [0:46] Calculating protein q-values [0:46] Number of genes identified at 1% FDR: 390 (precursor-level), 189 (protein-level) (inference performed using proteotypic peptides only) [0:46] Quantification [0:46] Quantification information saved to \smb.researchcampus.csmc.edu\vaneykjlab-mshub\Ascend\MeyerLab_Ascend_2024\Bora\SILAC_mix_2\Bora_mix4_20240917172228.mzML.quant

[0:46] File #5/18 [0:46] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\Ascend\MeyerLab_Ascend_2024\Bora\SILAC_mix_2\Bora_mix5_20240917180622.mzML [0:46] 22876 library precursors are potentially detectable [0:46] Processing... [0:48] Cannot perform mass calibration, too few confidently identified precursors [0:48] Cannot perform MS1 mass calibration, too few confidently identified precursors [0:50] RT window set to 13.6205 [0:50] Cannot perform mass calibration, too few confidently identified precursors [0:50] Cannot perform MS1 mass calibration, too few confidently identified precursors [0:54] Removing low confidence identifications [0:54] Removing interfering precursors [0:54] Training neural networks: 10131 targets, 11344 decoys [0:55] Number of IDs at 0.01 FDR: 0 [0:55] Too low number of IDs with NNs: reverting to the linear classifier [0:55] Number of IDs at 0.01 FDR: 2 [0:55] Translating peaks within elution groups [0:55] Number of IDs at 0.01 FDR: 3 [0:55] Precursors with channel labels at 1% channel FDR: 0 out of 0 considered [0:55] Calculating protein q-values [0:55] Number of genes identified at 1% FDR: 2 (precursor-level), 4 (protein-level) (inference performed using proteotypic peptides only) [0:55] Quantification [0:55] Quantification information saved to \smb.researchcampus.csmc.edu\vaneykjlab-mshub\Ascend\MeyerLab_Ascend_2024\Bora\SILAC_mix_2\Bora_mix5_20240917180622.mzML.quant

[0:55] File #6/18 [0:55] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\Ascend\MeyerLab_Ascend_2024\Bora\SILAC_mix_2\Bora_mix6_20240917185027.mzML [0:55] 22876 library precursors are potentially detectable [0:55] Processing... [0:57] Cannot perform mass calibration, too few confidently identified precursors [0:57] Cannot perform MS1 mass calibration, too few confidently identified precursors [0:59] RT window set to 12.7666 [0:59] Cannot perform mass calibration, too few confidently identified precursors [0:59] Cannot perform MS1 mass calibration, too few confidently identified precursors [1:03] Removing low confidence identifications [1:03] Removing interfering precursors [1:03] Training neural networks: 8547 targets, 9645 decoys [1:04] Number of IDs at 0.01 FDR: 0 [1:04] Too low number of IDs with NNs: reverting to the linear classifier [1:04] Number of IDs at 0.01 FDR: 0 [1:04] Translating peaks within elution groups [1:04] Number of IDs at 0.01 FDR: 0 [1:04] Precursors with channel labels at 1% channel FDR: 0 out of 0 considered [1:04] Calculating protein q-values [1:04] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [1:04] Quantification [1:04] Quantification information saved to \smb.researchcampus.csmc.edu\vaneykjlab-mshub\Ascend\MeyerLab_Ascend_2024\Bora\SILAC_mix_2\Bora_mix6_20240917185027.mzML.quant

[1:04] File #7/18 [1:04] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\Ascend\MeyerLab_Ascend_2024\Bora\SILAC_mix_2\Bora_mix7_20240917193430.mzML [1:04] 22876 library precursors are potentially detectable [1:04] Processing... [1:06] Cannot perform mass calibration, too few confidently identified precursors [1:06] Cannot perform MS1 mass calibration, too few confidently identified precursors [1:08] RT window set to 13.5963 [1:08] Cannot perform mass calibration, too few confidently identified precursors [1:08] Cannot perform MS1 mass calibration, too few confidently identified precursors [1:11] Removing low confidence identifications [1:11] Removing interfering precursors [1:11] Training neural networks: 7912 targets, 8972 decoys [1:12] Number of IDs at 0.01 FDR: 0 [1:12] Too low number of IDs with NNs: reverting to the linear classifier [1:12] Number of IDs at 0.01 FDR: 7 [1:12] Translating peaks within elution groups [1:12] Number of IDs at 0.01 FDR: 8 [1:12] Precursors with channel labels at 1% channel FDR: 0 out of 0 considered [1:12] Calculating protein q-values [1:12] Number of genes identified at 1% FDR: 7 (precursor-level), 9 (protein-level) (inference performed using proteotypic peptides only) [1:12] Quantification [1:12] Quantification information saved to \smb.researchcampus.csmc.edu\vaneykjlab-mshub\Ascend\MeyerLab_Ascend_2024\Bora\SILAC_mix_2\Bora_mix7_20240917193430.mzML.quant

[1:12] File #8/18 [1:12] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\Ascend\MeyerLab_Ascend_2024\Bora\SILAC_mix_2\Bora_mix8_20240917201734.mzML [1:12] 22876 library precursors are potentially detectable [1:12] Processing... [1:14] RT window set to 1.39485 [1:14] Recommended MS1 mass accuracy setting: 3.30586 ppm [1:15] Removing low confidence identifications [1:15] Removing interfering precursors [1:15] Training neural networks: 1660 targets, 1361 decoys [1:15] Number of IDs at 0.01 FDR: 241 [1:15] Translating peaks within elution groups [1:15] Number of IDs at 0.01 FDR: 243 [1:16] Precursors with channel labels at 1% channel FDR: 0 out of 0 considered [1:16] Calculating protein q-values [1:16] Number of genes identified at 1% FDR: 161 (precursor-level), 123 (protein-level) (inference performed using proteotypic peptides only) [1:16] Quantification [1:16] Quantification information saved to \smb.researchcampus.csmc.edu\vaneykjlab-mshub\Ascend\MeyerLab_Ascend_2024\Bora\SILAC_mix_2\Bora_mix8_20240917201734.mzML.quant

[1:16] File #9/18 [1:16] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\Ascend\MeyerLab_Ascend_2024\Bora\SILAC_mix_2\Bora_mix9_20240917210046.mzML [1:16] 22876 library precursors are potentially detectable [1:16] Processing... [1:17] RT window set to 1.13157 [1:17] Recommended MS1 mass accuracy setting: 3.0617 ppm [1:18] Removing low confidence identifications [1:18] Removing interfering precursors [1:18] Training neural networks: 2603 targets, 2155 decoys [1:19] Number of IDs at 0.01 FDR: 656 [1:19] Translating peaks within elution groups [1:19] Number of IDs at 0.01 FDR: 660 [1:19] Precursors with channel labels at 1% channel FDR: 0 out of 0 considered [1:19] Calculating protein q-values [1:19] Number of genes identified at 1% FDR: 386 (precursor-level), 328 (protein-level) (inference performed using proteotypic peptides only) [1:19] Quantification [1:19] Quantification information saved to \smb.researchcampus.csmc.edu\vaneykjlab-mshub\Ascend\MeyerLab_Ascend_2024\Bora\SILAC_mix_2\Bora_mix9_20240917210046.mzML.quant

[1:19] File #10/18 [1:19] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\Ascend\MeyerLab_Ascend_2024\Bora\SILAC_mix_2\Bora_mix10_20240917214403.mzML [1:20] 22876 library precursors are potentially detectable [1:20] Processing... [1:22] RT window set to 1.18587 [1:22] Recommended MS1 mass accuracy setting: 4.3777 ppm [1:23] Removing low confidence identifications [1:23] Removing interfering precursors [1:23] Training neural networks: 3538 targets, 1993 decoys [1:24] Number of IDs at 0.01 FDR: 1823 [1:24] Translating peaks within elution groups [1:24] Number of IDs at 0.01 FDR: 1835 [1:24] Precursors with channel labels at 1% channel FDR: 0 out of 0 considered [1:24] Calculating protein q-values [1:24] Number of genes identified at 1% FDR: 899 (precursor-level), 879 (protein-level) (inference performed using proteotypic peptides only) [1:24] Quantification [1:24] Quantification information saved to \smb.researchcampus.csmc.edu\vaneykjlab-mshub\Ascend\MeyerLab_Ascend_2024\Bora\SILAC_mix_2\Bora_mix10_20240917214403.mzML.quant

[1:24] File #11/18 [1:24] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\Ascend\MeyerLab_Ascend_2024\Bora\SILAC_mix_2\Bora_mix11_20240917222644.mzML [1:25] 22876 library precursors are potentially detectable [1:25] Processing... [1:27] RT window set to 1.16868 [1:27] Recommended MS1 mass accuracy setting: 4.12233 ppm [1:28] Removing low confidence identifications [1:29] Removing interfering precursors [1:29] Training neural networks: 4378 targets, 2413 decoys [1:29] Number of IDs at 0.01 FDR: 2135 [1:29] Translating peaks within elution groups [1:29] Number of IDs at 0.01 FDR: 2157 [1:29] Precursors with channel labels at 1% channel FDR: 0 out of 0 considered [1:29] Calculating protein q-values [1:29] Number of genes identified at 1% FDR: 980 (precursor-level), 949 (protein-level) (inference performed using proteotypic peptides only) [1:29] Quantification [1:29] Quantification information saved to \smb.researchcampus.csmc.edu\vaneykjlab-mshub\Ascend\MeyerLab_Ascend_2024\Bora\SILAC_mix_2\Bora_mix11_20240917222644.mzML.quant

[1:29] File #12/18 [1:29] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\Ascend\MeyerLab_Ascend_2024\Bora\SILAC_mix_2\Bora_mix12_20240917230946.mzML [1:30] 22876 library precursors are potentially detectable [1:30] Processing... [1:33] RT window set to 1.58802 [1:33] Recommended MS1 mass accuracy setting: 3.61887 ppm [1:34] Removing low confidence identifications [1:34] Removing interfering precursors [1:34] Training neural networks: 1254 targets, 1022 decoys [1:34] Number of IDs at 0.01 FDR: 239 [1:34] Translating peaks within elution groups [1:34] Number of IDs at 0.01 FDR: 242 [1:34] Precursors with channel labels at 1% channel FDR: 0 out of 0 considered [1:34] Calculating protein q-values [1:34] Number of genes identified at 1% FDR: 132 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [1:34] Quantification [1:34] Quantification information saved to \smb.researchcampus.csmc.edu\vaneykjlab-mshub\Ascend\MeyerLab_Ascend_2024\Bora\SILAC_mix_2\Bora_mix12_20240917230946.mzML.quant

[1:34] File #13/18 [1:34] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\Ascend\MeyerLab_Ascend_2024\Bora\SILAC_mix_2\Bora_mix13_20240917235229.mzML [1:35] 22876 library precursors are potentially detectable [1:35] Processing... [1:36] RT window set to 1.36891 [1:36] Recommended MS1 mass accuracy setting: 2.7943 ppm [1:37] Removing low confidence identifications [1:37] Removing interfering precursors [1:37] Training neural networks: 2648 targets, 2270 decoys [1:38] Number of IDs at 0.01 FDR: 583 [1:38] Translating peaks within elution groups [1:38] Number of IDs at 0.01 FDR: 586 [1:38] Precursors with channel labels at 1% channel FDR: 0 out of 0 considered [1:38] Calculating protein q-values [1:38] Number of genes identified at 1% FDR: 327 (precursor-level), 283 (protein-level) (inference performed using proteotypic peptides only) [1:38] Quantification [1:38] Quantification information saved to \smb.researchcampus.csmc.edu\vaneykjlab-mshub\Ascend\MeyerLab_Ascend_2024\Bora\SILAC_mix_2\Bora_mix13_20240917235229.mzML.quant

[1:38] File #14/18 [1:38] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\Ascend\MeyerLab_Ascend_2024\Bora\SILAC_mix_2\Bora_mix14_20240917103944.mzML [1:39] 22876 library precursors are potentially detectable [1:39] Processing... [1:40] RT window set to 1.19742 [1:40] Recommended MS1 mass accuracy setting: 5.64845 ppm [1:41] Removing low confidence identifications [1:41] Removing interfering precursors [1:41] Training neural networks: 2069 targets, 1785 decoys [1:42] Number of IDs at 0.01 FDR: 380 [1:42] Translating peaks within elution groups [1:42] Number of IDs at 0.01 FDR: 384 [1:42] Precursors with channel labels at 1% channel FDR: 0 out of 0 considered [1:42] Calculating protein q-values [1:42] Number of genes identified at 1% FDR: 220 (precursor-level), 108 (protein-level) (inference performed using proteotypic peptides only) [1:42] Quantification [1:42] Quantification information saved to \smb.researchcampus.csmc.edu\vaneykjlab-mshub\Ascend\MeyerLab_Ascend_2024\Bora\SILAC_mix_2\Bora_mix14_20240917103944.mzML.quant

[1:42] File #15/18 [1:42] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\Ascend\MeyerLab_Ascend_2024\Bora\SILAC_mix_2\Bora_mix15_20240917095530.mzML [1:42] 22876 library precursors are potentially detectable [1:43] Processing... [1:44] RT window set to 1.10295 [1:44] Recommended MS1 mass accuracy setting: 3.82922 ppm [1:45] Removing low confidence identifications [1:45] Removing interfering precursors [1:45] Training neural networks: 2182 targets, 1210 decoys [1:46] Number of IDs at 0.01 FDR: 981 [1:46] Translating peaks within elution groups [1:46] Number of IDs at 0.01 FDR: 987 [1:46] Precursors with channel labels at 1% channel FDR: 0 out of 0 considered [1:46] Calculating protein q-values [1:46] Number of genes identified at 1% FDR: 525 (precursor-level), 296 (protein-level) (inference performed using proteotypic peptides only) [1:46] Quantification [1:46] Quantification information saved to \smb.researchcampus.csmc.edu\vaneykjlab-mshub\Ascend\MeyerLab_Ascend_2024\Bora\SILAC_mix_2\Bora_mix15_20240917095530.mzML.quant

[1:46] File #16/18 [1:46] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\Ascend\MeyerLab_Ascend_2024\Bora\SILAC_mix_2\Bora_mix16_20240917091113.mzML [1:47] 22876 library precursors are potentially detectable [1:47] Processing... [1:49] RT window set to 1.34365 [1:49] Recommended MS1 mass accuracy setting: 4.26752 ppm [1:51] Removing low confidence identifications [1:51] Removing interfering precursors [1:51] Training neural networks: 4543 targets, 2502 decoys [1:51] Number of IDs at 0.01 FDR: 2088 [1:51] Translating peaks within elution groups [1:51] Number of IDs at 0.01 FDR: 2109 [1:51] Precursors with channel labels at 1% channel FDR: 0 out of 0 considered [1:51] Calculating protein q-values [1:51] Number of genes identified at 1% FDR: 950 (precursor-level), 804 (protein-level) (inference performed using proteotypic peptides only) [1:51] Quantification [1:52] Quantification information saved to \smb.researchcampus.csmc.edu\vaneykjlab-mshub\Ascend\MeyerLab_Ascend_2024\Bora\SILAC_mix_2\Bora_mix16_20240917091113.mzML.quant

[1:52] File #17/18 [1:52] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\Ascend\MeyerLab_Ascend_2024\Bora\SILAC_mix_2\Bora_mix17.mzML [1:53] 22876 library precursors are potentially detectable [1:53] Processing... [1:55] RT window set to 1.21925 [1:55] Recommended MS1 mass accuracy setting: 3.79351 ppm [1:57] Removing low confidence identifications [1:57] Removing interfering precursors [1:58] Training neural networks: 4536 targets, 2445 decoys [1:58] Number of IDs at 0.01 FDR: 2031 [1:58] Translating peaks within elution groups [1:58] Number of IDs at 0.01 FDR: 2052 [1:58] Precursors with channel labels at 1% channel FDR: 0 out of 0 considered [1:58] Calculating protein q-values [1:58] Number of genes identified at 1% FDR: 962 (precursor-level), 858 (protein-level) (inference performed using proteotypic peptides only) [1:58] Quantification [1:58] Quantification information saved to \smb.researchcampus.csmc.edu\vaneykjlab-mshub\Ascend\MeyerLab_Ascend_2024\Bora\SILAC_mix_2\Bora_mix17.mzML.quant

[1:58] File #18/18 [1:58] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\Ascend\MeyerLab_Ascend_2024\Bora\SILAC_mix_2\Bora_mix18.mzML [1:59] 22876 library precursors are potentially detectable [1:59] Processing... [2:01] RT window set to 1.35122 [2:01] Recommended MS1 mass accuracy setting: 3.94177 ppm [2:04] Removing low confidence identifications [2:04] Removing interfering precursors [2:04] Training neural networks: 4567 targets, 2516 decoys [2:04] Number of IDs at 0.01 FDR: 2084 [2:04] Translating peaks within elution groups [2:05] Number of IDs at 0.01 FDR: 2102 [2:05] Precursors with channel labels at 1% channel FDR: 0 out of 0 considered [2:05] Calculating protein q-values [2:05] Number of genes identified at 1% FDR: 972 (precursor-level), 941 (protein-level) (inference performed using proteotypic peptides only) [2:05] Quantification [2:05] Quantification information saved to \smb.researchcampus.csmc.edu\vaneykjlab-mshub\Ascend\MeyerLab_Ascend_2024\Bora\SILAC_mix_2\Bora_mix18.mzML.quant

[2:05] Cross-run analysis [2:05] Reading quantification information: 18 files [2:05] Quantifying peptides [2:06] Assembling protein groups [2:06] Quantifying proteins [2:06] Calculating q-values for protein and gene groups [2:06] Calculating global q-values for protein and gene groups [2:06] Protein groups with global q-value <= 0.01: 1067 [2:06] Compressed report saved to D:\Ascend_SILAC_mix\report-first-pass.parquet. Use R 'arrow' or Python 'PyArrow' package to process [2:06] Writing report [2:07] Report saved to D:\Ascend_SILAC_mix\report-first-pass.tsv. [2:07] Saving precursor levels matrix [2:07] Precursor levels matrix (1% precursor and protein group FDR) saved to D:\Ascend_SILAC_mix\report-first-pass.pr_matrix_channels.tsv. [2:07] Saving precursor levels matrix [2:07] Precursor levels matrix (1% precursor and protein group FDR) saved to D:\Ascend_SILAC_mix\report-first-pass.pr_matrix_channels_ms1.tsv. [2:07] Saving precursor levels matrix [2:07] Precursor levels matrix (1% precursor and protein group FDR) saved to D:\Ascend_SILAC_mix\report-first-pass.pr_matrix_channels_ms1_extracted.tsv. [2:07] Stats report saved to D:\Ascend_SILAC_mix\report-first-pass.stats.tsv [2:07] Generating spectral library: [2:07] Saving spectral library to D:\Ascend_SILAC_mix\report1.tsv [2:08] 2800 target and 28 decoy precursors saved

[2:08] Loading spectral library D:\Ascend_SILAC_mix\report1.tsv [2:08] Spectral library loaded: 1257 protein isoforms, 1232 protein groups and 2828 precursors in 2784 elution groups. [2:08] [2:08] [2:09] [2:09] [2:09] [2:09] Saving the library to D:\Ascend_SILAC_mix\report1.predicted.speclib [2:09] Initialising library [2:09] Splitting library entries across channels [2:09] 2828 unlabelled precursors detected [2:09] Assembling elution groups

Second pass: using the newly created spectral library to reanalyse the data

[2:09] File #1/18 [2:09] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\Ascend\MeyerLab_Ascend_2024\Bora\SILAC_mix_2\Bora_mix1_20240917151044.mzML [2:10] 2800 library precursors are potentially detectable [2:10] Processing... [2:11] RT window set to 1.52835 [2:11] Recommended MS1 mass accuracy setting: 4.03214 ppm [2:11] Removing low confidence identifications [2:11] Removing interfering precursors [2:11] Training neural networks: 1266 targets, 994 decoys [2:12] Number of IDs at 0.01 FDR: 236 [2:12] Translating peaks within elution groups [2:12] Number of IDs at 0.01 FDR: 237 [2:12] Precursors with channel labels at 1% channel FDR: 0 out of 0 considered [2:12] No protein annotation, skipping protein q-value calculation [2:12] Quantification

[2:12] File #2/18 [2:12] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\Ascend\MeyerLab_Ascend_2024\Bora\SILAC_mix_2\Bora_mix2_20240917155448.mzML [2:13] 2800 library precursors are potentially detectable [2:13] Processing... [2:13] RT window set to 9.50301 [2:13] Recommended MS1 mass accuracy setting: 4.5456 ppm [2:14] Removing low confidence identifications [2:14] Removing interfering precursors [2:14] Training neural networks: 917 targets, 755 decoys [2:14] Number of IDs at 0.01 FDR: 125 [2:14] Translating peaks within elution groups [2:14] Number of IDs at 0.01 FDR: 124 [2:14] Precursors with channel labels at 1% channel FDR: 0 out of 0 considered [2:14] No protein annotation, skipping protein q-value calculation [2:14] Quantification

[2:14] File #3/18 [2:14] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\Ascend\MeyerLab_Ascend_2024\Bora\SILAC_mix_2\Bora_mix3_20240917163839.mzML [2:15] 2800 library precursors are potentially detectable [2:15] Processing... [2:15] RT window set to 9.64651 [2:15] Recommended MS1 mass accuracy setting: 3.80991 ppm [2:16] Removing low confidence identifications [2:16] Removing interfering precursors [2:16] Training neural networks: 1004 targets, 805 decoys [2:17] Number of IDs at 0.01 FDR: 125 [2:17] Translating peaks within elution groups [2:17] Number of IDs at 0.01 FDR: 126 [2:17] Precursors with channel labels at 1% channel FDR: 0 out of 0 considered [2:17] No protein annotation, skipping protein q-value calculation [2:17] Quantification

[2:17] File #4/18 [2:17] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\Ascend\MeyerLab_Ascend_2024\Bora\SILAC_mix_2\Bora_mix4_20240917172228.mzML [2:17] 2800 library precursors are potentially detectable [2:17] Processing... [2:18] RT window set to 1.10513 [2:18] Recommended MS1 mass accuracy setting: 4.26262 ppm [2:18] Removing low confidence identifications [2:18] Removing interfering precursors [2:18] Training neural networks: 1210 targets, 603 decoys [2:18] Number of IDs at 0.01 FDR: 703 [2:18] Translating peaks within elution groups [2:18] Number of IDs at 0.01 FDR: 707 [2:18] Precursors with channel labels at 1% channel FDR: 0 out of 0 considered [2:18] No protein annotation, skipping protein q-value calculation [2:18] Quantification

[2:18] File #5/18 [2:18] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\Ascend\MeyerLab_Ascend_2024\Bora\SILAC_mix_2\Bora_mix5_20240917180622.mzML [2:19] 2800 library precursors are potentially detectable [2:19] Processing... [2:19] Cannot perform mass calibration, too few confidently identified precursors [2:19] Cannot perform MS1 mass calibration, too few confidently identified precursors [2:20] RT window set to 14.6723 [2:20] Cannot perform mass calibration, too few confidently identified precursors [2:20] Cannot perform MS1 mass calibration, too few confidently identified precursors [2:20] Removing low confidence identifications [2:20] Removing interfering precursors [2:20] Training neural networks: 1651 targets, 1634 decoys [2:21] Number of IDs at 0.01 FDR: 5 [2:21] Too low number of IDs with NNs: reverting to the linear classifier [2:21] Number of IDs at 0.01 FDR: 3 [2:21] Translating peaks within elution groups [2:21] Number of IDs at 0.01 FDR: 3 [2:21] Precursors with channel labels at 1% channel FDR: 0 out of 0 considered [2:21] No protein annotation, skipping protein q-value calculation [2:21] Quantification

[2:21] File #6/18 [2:21] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\Ascend\MeyerLab_Ascend_2024\Bora\SILAC_mix_2\Bora_mix6_20240917185027.mzML [2:21] 2800 library precursors are potentially detectable [2:21] Processing... [2:21] Cannot perform MS1 mass calibration, too few confidently identified precursors [2:21] RT window set to 12.2709 [2:21] Recommended MS1 mass accuracy setting: 4.77772 ppm [2:22] Removing low confidence identifications [2:22] Removing interfering precursors [2:22] Training neural networks: 1438 targets, 1436 decoys [2:22] Number of IDs at 0.01 FDR: 2 [2:22] Too low number of IDs with NNs: reverting to the linear classifier [2:22] Number of IDs at 0.01 FDR: 0 [2:22] Translating peaks within elution groups [2:22] Number of IDs at 0.01 FDR: 0 [2:22] Precursors with channel labels at 1% channel FDR: 0 out of 0 considered [2:22] No protein annotation, skipping protein q-value calculation [2:22] Quantification

[2:22] File #7/18 [2:22] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\Ascend\MeyerLab_Ascend_2024\Bora\SILAC_mix_2\Bora_mix7_20240917193430.mzML [2:23] 2800 library precursors are potentially detectable [2:23] Processing... [2:23] Cannot perform mass calibration, too few confidently identified precursors [2:23] Cannot perform MS1 mass calibration, too few confidently identified precursors [2:23] RT window set to 12.9881 [2:23] Cannot perform mass calibration, too few confidently identified precursors [2:23] Cannot perform MS1 mass calibration, too few confidently identified precursors [2:24] Removing low confidence identifications [2:24] Removing interfering precursors [2:24] Training neural networks: 1276 targets, 1256 decoys [2:24] Number of IDs at 0.01 FDR: 0 [2:24] Too low number of IDs with NNs: reverting to the linear classifier [2:24] Number of IDs at 0.01 FDR: 0 [2:24] Translating peaks within elution groups [2:24] Number of IDs at 0.01 FDR: 0 [2:24] Precursors with channel labels at 1% channel FDR: 0 out of 0 considered [2:24] No protein annotation, skipping protein q-value calculation [2:24] Quantification

[2:24] File #8/18 [2:24] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\Ascend\MeyerLab_Ascend_2024\Bora\SILAC_mix_2\Bora_mix8_20240917201734.mzML [2:25] 2800 library precursors are potentially detectable [2:25] Processing... [2:25] RT window set to 1.54824 [2:25] Recommended MS1 mass accuracy setting: 4.02808 ppm [2:25] Removing low confidence identifications [2:25] Removing interfering precursors [2:25] Training neural networks: 593 targets, 306 decoys [2:25] Number of IDs at 0.01 FDR: 297 [2:25] Translating peaks within elution groups [2:25] Number of IDs at 0.01 FDR: 299 [2:25] Precursors with channel labels at 1% channel FDR: 0 out of 0 considered [2:25] No protein annotation, skipping protein q-value calculation [2:25] Quantification

[2:25] File #9/18 [2:25] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\Ascend\MeyerLab_Ascend_2024\Bora\SILAC_mix_2\Bora_mix9_20240917210046.mzML [2:26] 2800 library precursors are potentially detectable [2:26] Processing... [2:26] RT window set to 1.08382 [2:26] Recommended MS1 mass accuracy setting: 3.35065 ppm [2:26] Removing low confidence identifications [2:26] Removing interfering precursors [2:26] Training neural networks: 887 targets, 275 decoys [2:27] Number of IDs at 0.01 FDR: 637 [2:27] Translating peaks within elution groups [2:27] Number of IDs at 0.01 FDR: 638 [2:27] Precursors with channel labels at 1% channel FDR: 0 out of 0 considered [2:27] No protein annotation, skipping protein q-value calculation [2:27] Quantification

[2:27] File #10/18 [2:27] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\Ascend\MeyerLab_Ascend_2024\Bora\SILAC_mix_2\Bora_mix10_20240917214403.mzML [2:27] 2800 library precursors are potentially detectable [2:27] Processing... [2:28] RT window set to 1.10968 [2:28] Recommended MS1 mass accuracy setting: 4.14769 ppm [2:28] Removing low confidence identifications [2:28] Removing interfering precursors [2:28] Training neural networks: 2025 targets, 926 decoys [2:28] Number of IDs at 0.01 FDR: 1772 [2:28] Translating peaks within elution groups [2:28] Number of IDs at 0.01 FDR: 1773 [2:28] Precursors with channel labels at 1% channel FDR: 0 out of 0 considered [2:28] No protein annotation, skipping protein q-value calculation [2:28] Quantification

[2:28] File #11/18 [2:28] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\Ascend\MeyerLab_Ascend_2024\Bora\SILAC_mix_2\Bora_mix11_20240917222644.mzML [2:29] 2800 library precursors are potentially detectable [2:29] Processing... [2:30] RT window set to 1.07212 [2:30] Recommended MS1 mass accuracy setting: 4.0875 ppm [2:30] Removing low confidence identifications [2:30] Removing interfering precursors [2:30] Training neural networks: 2397 targets, 1228 decoys [2:31] Number of IDs at 0.01 FDR: 2030 [2:31] Translating peaks within elution groups [2:31] Number of IDs at 0.01 FDR: 2032 [2:31] Precursors with channel labels at 1% channel FDR: 0 out of 0 considered [2:31] No protein annotation, skipping protein q-value calculation [2:31] Quantification

[2:31] File #12/18 [2:31] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\Ascend\MeyerLab_Ascend_2024\Bora\SILAC_mix_2\Bora_mix12_20240917230946.mzML [2:31] 2800 library precursors are potentially detectable [2:31] Processing... [2:32] RT window set to 1.61355 [2:32] Recommended MS1 mass accuracy setting: 3.84253 ppm [2:32] Removing low confidence identifications [2:32] Removing interfering precursors [2:32] Training neural networks: 636 targets, 406 decoys [2:32] Number of IDs at 0.01 FDR: 253 [2:32] Translating peaks within elution groups [2:32] Number of IDs at 0.01 FDR: 253 [2:32] Precursors with channel labels at 1% channel FDR: 0 out of 0 considered [2:32] No protein annotation, skipping protein q-value calculation [2:32] Quantification

[2:32] File #13/18 [2:32] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\Ascend\MeyerLab_Ascend_2024\Bora\SILAC_mix_2\Bora_mix13_20240917235229.mzML [2:33] 2800 library precursors are potentially detectable [2:33] Processing... [2:33] RT window set to 1.07434 [2:33] Recommended MS1 mass accuracy setting: 2.78966 ppm [2:33] Removing low confidence identifications [2:33] Removing interfering precursors [2:33] Training neural networks: 857 targets, 291 decoys [2:33] Number of IDs at 0.01 FDR: 625 [2:33] Translating peaks within elution groups [2:33] Number of IDs at 0.01 FDR: 628 [2:33] Precursors with channel labels at 1% channel FDR: 0 out of 0 considered [2:33] No protein annotation, skipping protein q-value calculation [2:33] Quantification

[2:33] File #14/18 [2:33] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\Ascend\MeyerLab_Ascend_2024\Bora\SILAC_mix_2\Bora_mix14_20240917103944.mzML [2:34] 2800 library precursors are potentially detectable [2:34] Processing... [2:34] RT window set to 1.3497 [2:34] Recommended MS1 mass accuracy setting: 5.65315 ppm [2:34] Removing low confidence identifications [2:34] Removing interfering precursors [2:34] Training neural networks: 793 targets, 392 decoys [2:35] Number of IDs at 0.01 FDR: 408 [2:35] Translating peaks within elution groups [2:35] Number of IDs at 0.01 FDR: 410 [2:35] Precursors with channel labels at 1% channel FDR: 0 out of 0 considered [2:35] No protein annotation, skipping protein q-value calculation [2:35] Quantification

[2:35] File #15/18 [2:35] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\Ascend\MeyerLab_Ascend_2024\Bora\SILAC_mix_2\Bora_mix15_20240917095530.mzML [2:35] 2800 library precursors are potentially detectable [2:35] Processing... [2:36] RT window set to 1.10054 [2:36] Recommended MS1 mass accuracy setting: 4.04298 ppm [2:36] Removing low confidence identifications [2:36] Removing interfering precursors [2:36] Training neural networks: 1575 targets, 727 decoys [2:37] Number of IDs at 0.01 FDR: 1052 [2:37] Translating peaks within elution groups [2:37] Number of IDs at 0.01 FDR: 1056 [2:37] Precursors with channel labels at 1% channel FDR: 0 out of 0 considered [2:37] No protein annotation, skipping protein q-value calculation [2:37] Quantification

[2:37] File #16/18 [2:37] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\Ascend\MeyerLab_Ascend_2024\Bora\SILAC_mix_2\Bora_mix16_20240917091113.mzML [2:38] 2800 library precursors are potentially detectable [2:38] Processing... [2:38] RT window set to 1.14823 [2:38] Recommended MS1 mass accuracy setting: 3.94519 ppm [2:39] Removing low confidence identifications [2:39] Removing interfering precursors [2:39] Training neural networks: 2433 targets, 1234 decoys [2:39] Number of IDs at 0.01 FDR: 2085 [2:39] Translating peaks within elution groups [2:39] Number of IDs at 0.01 FDR: 2087 [2:39] Precursors with channel labels at 1% channel FDR: 0 out of 0 considered [2:39] No protein annotation, skipping protein q-value calculation [2:39] Quantification

[2:39] File #17/18 [2:39] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\Ascend\MeyerLab_Ascend_2024\Bora\SILAC_mix_2\Bora_mix17.mzML [2:40] 2800 library precursors are potentially detectable [2:40] Processing... [2:41] RT window set to 1.16358 [2:41] Recommended MS1 mass accuracy setting: 3.98611 ppm [2:41] Removing low confidence identifications [2:41] Removing interfering precursors [2:42] Training neural networks: 2478 targets, 1252 decoys [2:42] Number of IDs at 0.01 FDR: 1985 [2:42] Translating peaks within elution groups [2:42] Number of IDs at 0.01 FDR: 1993 [2:42] Precursors with channel labels at 1% channel FDR: 0 out of 0 considered [2:42] No protein annotation, skipping protein q-value calculation [2:42] Quantification

[2:42] File #18/18 [2:42] Loading run \smb.researchcampus.csmc.edu\vaneykjlab-mshub\Ascend\MeyerLab_Ascend_2024\Bora\SILAC_mix_2\Bora_mix18.mzML [2:43] 2800 library precursors are potentially detectable [2:43] Processing... [2:44] RT window set to 1.17655 [2:44] Recommended MS1 mass accuracy setting: 3.9555 ppm [2:44] Removing low confidence identifications [2:44] Removing interfering precursors [2:44] Training neural networks: 2483 targets, 1276 decoys [2:45] Number of IDs at 0.01 FDR: 2120 [2:45] Translating peaks within elution groups [2:45] Number of IDs at 0.01 FDR: 2125 [2:45] Precursors with channel labels at 1% channel FDR: 0 out of 0 considered [2:45] No protein annotation, skipping protein q-value calculation [2:45] Quantification

[2:45] Cross-run analysis [2:45] Reading quantification information: 18 files [2:45] Quantifying peptides [2:47] Quantification parameters: 0.367565, 0.00856456, 0.0035864, 0.824431, 0.0121747, 0.0108425, 0.0802778, 0.337287, 0.323148, 0.0122885, 0.0138992, 0.0138582, 0.778322, 0.0507414, 0.069243, 0.0107151 [2:48] Quantifying proteins [2:48] Calculating q-values for protein and gene groups [2:48] Calculating global q-values for protein and gene groups [2:48] Protein groups with global q-value <= 0.01: 1163 [2:48] Compressed report saved to D:\Ascend_SILAC_mix\report.parquet. Use R 'arrow' or Python 'PyArrow' package to process [2:48] Writing report [2:49] Report saved to D:\Ascend_SILAC_mix\report.tsv. [2:49] Saving precursor levels matrix [2:49] Precursor levels matrix (1% precursor and protein group FDR) saved to D:\Ascend_SILAC_mix\report.pr_matrix_channels.tsv. [2:49] Saving precursor levels matrix [2:49] Precursor levels matrix (1% precursor and protein group FDR) saved to D:\Ascend_SILAC_mix\report.pr_matrix_channels_ms1.tsv. [2:49] Saving precursor levels matrix [2:49] Precursor levels matrix (1% precursor and protein group FDR) saved to D:\Ascend_SILAC_mix\report.pr_matrix_channels_ms1_extracted.tsv. [2:49] Stats report saved to D:\Ascend_SILAC_mix\report.stats.tsv