Closed tobiasko closed 3 years ago
tobiasko
commented
3 years ago I just realised that the right MSFileReader version is not installed on the system. I guess this explains the error. A more informative error message would be helpful: "Could not find MSFileReader. Please ... "
vdemichev
commented
3 years ago Yep, that's how it reacts to the missing DLL. DIA-NN uses a third-party library (mstoolkit) to read Thermo files. In the future we might switch to the new Thermo reader, and then the messages will be more informative.
Vadim
cattlemer
commented
1 year ago Hi, how do you resolve this? I got a bunch of DIA data from Exploris 480 (core facility) as well and have similar error message. I downloaded and installed the most recent MSFileReader on my computer for DIA-NN to run but still getting the same error message. When you say the wrong version MSFileReader version installed on the system, do you mean by the acquisition computer (the one connected to the orbitrap) or the processing computer?
Wenting
cattlemer
commented
1 year ago DIA-NN 1.8.1 (Data-Independent Acquisition by Neural Networks) Compiled on Apr 14 2022 15:31:19 Current date and time: Fri Dec 2 16:43:23 2022 CPU: GenuineIntel Intel(R) Core(TM) i7-10750H CPU @ 2.60GHz SIMD instructions: AVX AVX2 FMA SSE4.1 SSE4.2 Logical CPU cores: 12 diann.exe --f C:\Users\niuji\Box\2022_postdoc\Proteomics_Data\20221129_proteomics_core\Ex191122_Wenting5uL_60m_1.raw --f C:\Users\niuji\Box\2022_postdoc\Proteomics_Data\20221129_proteomics_core\Ex191122_Wenting5uL_60m_2.raw --f C:\Users\niuji\Box\2022_postdoc\Proteomics_Data\20221129_proteomics_core\Ex191122_Wenting5uL_60m_3.raw --f C:\Users\niuji\Box\2022_postdoc\Proteomics_Data\20221129_proteomics_core\Ex191122_Wenting5uL_60m_4.raw --f C:\Users\niuji\Box\2022_postdoc\Proteomics_Data\20221129_proteomics_core\Ex191122_Wenting5uL_60m_5.raw --f C:\Users\niuji\Box\2022_postdoc\Proteomics_Data\20221129_proteomics_core\Ex191122_Wenting5uL_60m_6.raw --f C:\Users\niuji\Box\2022_postdoc\Proteomics_Data\20221129_proteomics_core\Ex191122_Wenting5uL_60m_7.raw --f C:\Users\niuji\Box\2022_postdoc\Proteomics_Data\20221129_proteomics_core\Ex191122_Wenting5uL_60m_8.raw --lib C:\Users\niuji\Box\2022_postdoc\Proteomics_Data\244122_proteomics_core\report-lib_n.predicted.speclib --threads 6 --verbose 1 --out C:\DIA-NN\1.8.1\report_llnl.tsv --qvalue 0.01 --matrices --out-lib C:\DIA-NN\1.8.1\repor_llnlt-lib.tsv --gen-spec-lib --fasta C:\Users\niuji\Box\2022_postdoc\fasta\2022-11-23-contam-spike_N_bsa.fasta --met-excision --cut K,R --var-mods 1 --var-mod UniMod:35,15.994915,M --reanalyse --relaxed-prot-inf --smart-profiling --peak-center --no-ifs-removal
Thread number set to 6 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 N-terminal methionine excision enabled In silico digest will involve cuts at K,R Maximum number of variable modifications set to 1 Modification UniMod:35 with mass delta 15.9949 at M will be considered as variable 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 Highly heuristic protein grouping will be used, to reduce the number of protein groups obtained; this mode is recommended for benchmarking protein ID numbers; use with caution for anything else When generating a spectral library, in silico predicted spectra will be retained if deemed more reliable than experimental ones Fixed-width center of each elution peak will be used for quantification Interference removal from fragment elution curves disabled DIA-NN will optimise the mass accuracy automatically using the first run in the experiment. This is useful primarily for quick initial analyses, when it is not yet known which mass accuracy setting works best for a particular acquisition scheme.
8 files will be processed [0:00] Loading spectral library C:\Users\niuji\Box\2022_postdoc\Proteomics_Data\244122_proteomics_core\report-lib_n.predicted.speclib [0:00] Library annotated with sequence database(s): C:\Users\niuji\Box\2022_postdoc\fasta\2022-11-23-contam-spike_N_bsa.fasta [0:00] Spectral library loaded: 142 protein isoforms, 262 protein groups and 39734 precursors in 9488 elution groups. [0:00] Loading protein annotations from FASTA C:\Users\niuji\Box\2022_postdoc\fasta\2022-11-23-contam-spike_N_bsa.fasta [0:00] Annotating library proteins with information from the FASTA database [0:00] Protein names missing for some isoforms [0:00] Gene names missing for some isoforms [0:00] Library contains 103 proteins, and 103 genes [0:00] Initialising library
[0:00] First pass: generating a spectral library from DIA data [0:00] File #1/8 [0:00] Loading run C:\Users\niuji\Box\2022_postdoc\Proteomics_Data\20221129_proteomics_core\Ex191122_Wenting5uL_60m_1.raw No MS2 spectra: aborting ERROR: cannot load the file, skipping [0:00] 0 library precursors are potentially detectable [0:00] Processing... [0:00] Using MS1 mass accuracy: 20 ppm [0:00] Using mass accuracy: 20 ppm [0:00] Removing low confidence identifications [0:00] Removing interfering precursors [0:00] Too few confident identifications, neural networks will not be used [0:00] Number of IDs at 0.01 FDR: 0 [0:00] Calculating protein q-values [0:00] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [0:00] Quantification [0:00] Quantification information saved to C:\Users\niuji\Box\2022_postdoc\Proteomics_Data\20221129_proteomics_core\Ex191122_Wenting5uL_60m_1.raw.quant.
[0:00] File #2/8 [0:00] Loading run C:\Users\niuji\Box\2022_postdoc\Proteomics_Data\20221129_proteomics_core\Ex191122_Wenting5uL_60m_2.raw No MS2 spectra: aborting ERROR: cannot load the file, skipping [0:00] 0 library precursors are potentially detectable [0:00] Processing... [0:00] Using MS1 mass accuracy: 20 ppm [0:00] Using mass accuracy: 20 ppm [0:00] Removing low confidence identifications [0:00] Removing interfering precursors [0:00] Too few confident identifications, neural networks will not be used [0:00] Number of IDs at 0.01 FDR: 0 [0:00] Calculating protein q-values [0:00] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [0:00] Quantification [0:00] Quantification information saved to C:\Users\niuji\Box\2022_postdoc\Proteomics_Data\20221129_proteomics_core\Ex191122_Wenting5uL_60m_2.raw.quant.
[0:00] File #3/8 [0:00] Loading run C:\Users\niuji\Box\2022_postdoc\Proteomics_Data\20221129_proteomics_core\Ex191122_Wenting5uL_60m_3.raw No MS2 spectra: aborting ERROR: cannot load the file, skipping [0:00] 0 library precursors are potentially detectable [0:00] Processing... [0:00] Using MS1 mass accuracy: 20 ppm [0:00] Using mass accuracy: 20 ppm [0:00] Removing low confidence identifications [0:00] Removing interfering precursors [0:00] Too few confident identifications, neural networks will not be used [0:00] Number of IDs at 0.01 FDR: 0 [0:00] Calculating protein q-values [0:00] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [0:00] Quantification [0:00] Quantification information saved to C:\Users\niuji\Box\2022_postdoc\Proteomics_Data\20221129_proteomics_core\Ex191122_Wenting5uL_60m_3.raw.quant.
[0:00] File #4/8 [0:00] Loading run C:\Users\niuji\Box\2022_postdoc\Proteomics_Data\20221129_proteomics_core\Ex191122_Wenting5uL_60m_4.raw No MS2 spectra: aborting ERROR: cannot load the file, skipping [0:00] 0 library precursors are potentially detectable [0:00] Processing... [0:00] Using MS1 mass accuracy: 20 ppm [0:00] Using mass accuracy: 20 ppm [0:00] Removing low confidence identifications [0:00] Removing interfering precursors [0:00] Too few confident identifications, neural networks will not be used [0:00] Number of IDs at 0.01 FDR: 0 [0:00] Calculating protein q-values [0:00] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [0:00] Quantification [0:00] Quantification information saved to C:\Users\niuji\Box\2022_postdoc\Proteomics_Data\20221129_proteomics_core\Ex191122_Wenting5uL_60m_4.raw.quant.
[0:00] File #5/8 [0:00] Loading run C:\Users\niuji\Box\2022_postdoc\Proteomics_Data\20221129_proteomics_core\Ex191122_Wenting5uL_60m_5.raw No MS2 spectra: aborting ERROR: cannot load the file, skipping [0:00] 0 library precursors are potentially detectable [0:00] Processing... [0:00] Using MS1 mass accuracy: 20 ppm [0:00] Using mass accuracy: 20 ppm [0:00] Removing low confidence identifications [0:00] Removing interfering precursors [0:00] Too few confident identifications, neural networks will not be used [0:00] Number of IDs at 0.01 FDR: 0 [0:00] Calculating protein q-values [0:00] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [0:00] Quantification [0:00] Quantification information saved to C:\Users\niuji\Box\2022_postdoc\Proteomics_Data\20221129_proteomics_core\Ex191122_Wenting5uL_60m_5.raw.quant.
[0:00] File #6/8 [0:00] Loading run C:\Users\niuji\Box\2022_postdoc\Proteomics_Data\20221129_proteomics_core\Ex191122_Wenting5uL_60m_6.raw No MS2 spectra: aborting ERROR: cannot load the file, skipping [0:00] 0 library precursors are potentially detectable [0:00] Processing... [0:00] Using MS1 mass accuracy: 20 ppm [0:00] Using mass accuracy: 20 ppm [0:00] Removing low confidence identifications [0:00] Removing interfering precursors [0:00] Too few confident identifications, neural networks will not be used [0:00] Number of IDs at 0.01 FDR: 0 [0:00] Calculating protein q-values [0:00] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [0:00] Quantification [0:00] Quantification information saved to C:\Users\niuji\Box\2022_postdoc\Proteomics_Data\20221129_proteomics_core\Ex191122_Wenting5uL_60m_6.raw.quant.
[0:00] File #7/8 [0:00] Loading run C:\Users\niuji\Box\2022_postdoc\Proteomics_Data\20221129_proteomics_core\Ex191122_Wenting5uL_60m_7.raw No MS2 spectra: aborting ERROR: cannot load the file, skipping [0:00] 0 library precursors are potentially detectable [0:00] Processing... [0:00] Using MS1 mass accuracy: 20 ppm [0:00] Using mass accuracy: 20 ppm [0:00] Removing low confidence identifications [0:00] Removing interfering precursors [0:00] Too few confident identifications, neural networks will not be used [0:00] Number of IDs at 0.01 FDR: 0 [0:00] Calculating protein q-values [0:00] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [0:00] Quantification [0:00] Quantification information saved to C:\Users\niuji\Box\2022_postdoc\Proteomics_Data\20221129_proteomics_core\Ex191122_Wenting5uL_60m_7.raw.quant.
[0:00] File #8/8 [0:00] Loading run C:\Users\niuji\Box\2022_postdoc\Proteomics_Data\20221129_proteomics_core\Ex191122_Wenting5uL_60m_8.raw No MS2 spectra: aborting ERROR: cannot load the file, skipping [0:00] 0 library precursors are potentially detectable [0:00] Processing... [0:00] Using MS1 mass accuracy: 20 ppm [0:00] Using mass accuracy: 20 ppm [0:00] Removing low confidence identifications [0:00] Removing interfering precursors [0:00] Too few confident identifications, neural networks will not be used [0:00] Number of IDs at 0.01 FDR: 0 [0:00] Calculating protein q-values [0:00] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [0:00] Quantification [0:00] Quantification information saved to C:\Users\niuji\Box\2022_postdoc\Proteomics_Data\20221129_proteomics_core\Ex191122_Wenting5uL_60m_8.raw.quant.
ERROR: DIA-NN tried but failed to load the following files: C:\Users\niuji\Box\2022_postdoc\Proteomics_Data\20221129_proteomics_core\Ex191122_Wenting5uL_60m_1.raw, C:\Users\niuji\Box\2022_postdoc\Proteomics_Data\20221129_proteomics_core\Ex191122_Wenting5uL_60m_2.raw, C:\Users\niuji\Box\2022_postdoc\Proteomics_Data\20221129_proteomics_core\Ex191122_Wenting5uL_60m_3.raw, C:\Users\niuji\Box\2022_postdoc\Proteomics_Data\20221129_proteomics_core\Ex191122_Wenting5uL_60m_4.raw, C:\Users\niuji\Box\2022_postdoc\Proteomics_Data\20221129_proteomics_core\Ex191122_Wenting5uL_60m_5.raw, C:\Users\niuji\Box\2022_postdoc\Proteomics_Data\20221129_proteomics_core\Ex191122_Wenting5uL_60m_6.raw, C:\Users\niuji\Box\2022_postdoc\Proteomics_Data\20221129_proteomics_core\Ex191122_Wenting5uL_60m_7.raw, C:\Users\niuji\Box\2022_postdoc\Proteomics_Data\20221129_proteomics_core\Ex191122_Wenting5uL_60m_8.raw [0:00] Cross-run analysis [0:00] Reading quantification information: 8 files [0:00] Quantifying peptides WARNING: not enough peptides for normalisation [0:00] Assembling protein groups [0:00] Quantifying proteins [0:00] Calculating q-values for protein and gene groups [0:00] Calculating global q-values for protein and gene groups [0:00] Writing report [0:00] Report saved to C:\DIA-NN\1.8.1\report_llnl-first-pass.tsv. [0:00] Saving precursor levels matrix [0:00] Precursor levels matrix (1% precursor and protein group FDR) saved to C:\DIA-NN\1.8.1\report_llnl-first-pass.pr_matrix.tsv. [0:00] Saving protein group levels matrix [0:00] Saving gene group levels matrix [0:00] Saving unique genes levels matrix [0:00] Stats report saved to C:\DIA-NN\1.8.1\report_llnl-first-pass.stats.tsv [0:00] Generating spectral library: [0:00] 0 precursors passing the FDR threshold are to be extracted [0:00] Saving spectral library to C:\DIA-NN\1.8.1\repor_llnlt-lib.tsv [0:00] 0 precursors saved [0:00] Loading the generated library and saving it in the .speclib format [0:00] Loading spectral library C:\DIA-NN\1.8.1\repor_llnlt-lib.tsv [0:00] Spectral library loaded: 0 protein isoforms, 0 protein groups and 0 precursors in 1 elution groups. [0:00] Loading protein annotations from FASTA C:\Users\niuji\Box\2022_postdoc\fasta\2022-11-23-contam-spike_N_bsa.fasta [0:00] Library contains 0 proteins, and 0 genes [0:00] Saving the library to C:\DIA-NN\1.8.1\repor_llnlt-lib.tsv.speclib
[0:00] Second pass: using the newly created spectral library to reanalyse the data [0:00] File #1/8 [0:00] Loading run C:\Users\niuji\Box\2022_postdoc\Proteomics_Data\20221129_proteomics_core\Ex191122_Wenting5uL_60m_1.raw No MS2 spectra: aborting ERROR: cannot load the file, skipping [0:00] 0 library precursors are potentially detectable [0:00] Processing... [0:00] Using MS1 mass accuracy: 20 ppm [0:00] Using mass accuracy: 20 ppm [0:00] Removing low confidence identifications [0:00] Removing interfering precursors [0:00] Too few confident identifications, neural networks will not be used [0:00] Number of IDs at 0.01 FDR: 0 [0:00] Calculating protein q-values [0:00] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [0:00] Quantification
[0:00] File #2/8 [0:00] Loading run C:\Users\niuji\Box\2022_postdoc\Proteomics_Data\20221129_proteomics_core\Ex191122_Wenting5uL_60m_2.raw No MS2 spectra: aborting ERROR: cannot load the file, skipping [0:00] 0 library precursors are potentially detectable [0:00] Processing... [0:00] Using MS1 mass accuracy: 20 ppm [0:00] Using mass accuracy: 20 ppm [0:00] Removing low confidence identifications [0:00] Removing interfering precursors [0:00] Too few confident identifications, neural networks will not be used [0:00] Number of IDs at 0.01 FDR: 0 [0:00] Calculating protein q-values [0:00] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [0:00] Quantification
[0:00] File #3/8 [0:00] Loading run C:\Users\niuji\Box\2022_postdoc\Proteomics_Data\20221129_proteomics_core\Ex191122_Wenting5uL_60m_3.raw No MS2 spectra: aborting ERROR: cannot load the file, skipping [0:00] 0 library precursors are potentially detectable [0:00] Processing... [0:00] Using MS1 mass accuracy: 20 ppm [0:00] Using mass accuracy: 20 ppm [0:00] Removing low confidence identifications [0:00] Removing interfering precursors [0:00] Too few confident identifications, neural networks will not be used [0:00] Number of IDs at 0.01 FDR: 0 [0:00] Calculating protein q-values [0:00] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [0:00] Quantification
[0:00] File #4/8 [0:00] Loading run C:\Users\niuji\Box\2022_postdoc\Proteomics_Data\20221129_proteomics_core\Ex191122_Wenting5uL_60m_4.raw No MS2 spectra: aborting ERROR: cannot load the file, skipping [0:00] 0 library precursors are potentially detectable [0:00] Processing... [0:00] Using MS1 mass accuracy: 20 ppm [0:00] Using mass accuracy: 20 ppm [0:00] Removing low confidence identifications [0:00] Removing interfering precursors [0:00] Too few confident identifications, neural networks will not be used [0:00] Number of IDs at 0.01 FDR: 0 [0:00] Calculating protein q-values [0:00] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [0:00] Quantification
[0:00] File #5/8 [0:00] Loading run C:\Users\niuji\Box\2022_postdoc\Proteomics_Data\20221129_proteomics_core\Ex191122_Wenting5uL_60m_5.raw No MS2 spectra: aborting ERROR: cannot load the file, skipping [0:01] 0 library precursors are potentially detectable [0:01] Processing... [0:01] Using MS1 mass accuracy: 20 ppm [0:01] Using mass accuracy: 20 ppm [0:01] Removing low confidence identifications [0:01] Removing interfering precursors [0:01] Too few confident identifications, neural networks will not be used [0:01] Number of IDs at 0.01 FDR: 0 [0:01] Calculating protein q-values [0:01] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [0:01] Quantification
[0:01] File #6/8 [0:01] Loading run C:\Users\niuji\Box\2022_postdoc\Proteomics_Data\20221129_proteomics_core\Ex191122_Wenting5uL_60m_6.raw No MS2 spectra: aborting ERROR: cannot load the file, skipping [0:01] 0 library precursors are potentially detectable [0:01] Processing... [0:01] Using MS1 mass accuracy: 20 ppm [0:01] Using mass accuracy: 20 ppm [0:01] Removing low confidence identifications [0:01] Removing interfering precursors [0:01] Too few confident identifications, neural networks will not be used [0:01] Number of IDs at 0.01 FDR: 0 [0:01] Calculating protein q-values [0:01] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [0:01] Quantification
[0:01] File #7/8 [0:01] Loading run C:\Users\niuji\Box\2022_postdoc\Proteomics_Data\20221129_proteomics_core\Ex191122_Wenting5uL_60m_7.raw No MS2 spectra: aborting ERROR: cannot load the file, skipping [0:01] 0 library precursors are potentially detectable [0:01] Processing... [0:01] Using MS1 mass accuracy: 20 ppm [0:01] Using mass accuracy: 20 ppm [0:01] Removing low confidence identifications [0:01] Removing interfering precursors [0:01] Too few confident identifications, neural networks will not be used [0:01] Number of IDs at 0.01 FDR: 0 [0:01] Calculating protein q-values [0:01] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [0:01] Quantification
[0:01] File #8/8 [0:01] Loading run C:\Users\niuji\Box\2022_postdoc\Proteomics_Data\20221129_proteomics_core\Ex191122_Wenting5uL_60m_8.raw No MS2 spectra: aborting ERROR: cannot load the file, skipping [0:01] 0 library precursors are potentially detectable [0:01] Processing... [0:01] Using MS1 mass accuracy: 20 ppm [0:01] Using mass accuracy: 20 ppm [0:01] Removing low confidence identifications [0:01] Removing interfering precursors [0:01] Too few confident identifications, neural networks will not be used [0:01] Number of IDs at 0.01 FDR: 0 [0:01] Calculating protein q-values [0:01] Number of genes identified at 1% FDR: 0 (precursor-level), 0 (protein-level) (inference performed using proteotypic peptides only) [0:01] Quantification
ERROR: DIA-NN tried but failed to load the following files: C:\Users\niuji\Box\2022_postdoc\Proteomics_Data\20221129_proteomics_core\Ex191122_Wenting5uL_60m_1.raw, C:\Users\niuji\Box\2022_postdoc\Proteomics_Data\20221129_proteomics_core\Ex191122_Wenting5uL_60m_2.raw, C:\Users\niuji\Box\2022_postdoc\Proteomics_Data\20221129_proteomics_core\Ex191122_Wenting5uL_60m_3.raw, C:\Users\niuji\Box\2022_postdoc\Proteomics_Data\20221129_proteomics_core\Ex191122_Wenting5uL_60m_4.raw, C:\Users\niuji\Box\2022_postdoc\Proteomics_Data\20221129_proteomics_core\Ex191122_Wenting5uL_60m_5.raw, C:\Users\niuji\Box\2022_postdoc\Proteomics_Data\20221129_proteomics_core\Ex191122_Wenting5uL_60m_6.raw, C:\Users\niuji\Box\2022_postdoc\Proteomics_Data\20221129_proteomics_core\Ex191122_Wenting5uL_60m_7.raw, C:\Users\niuji\Box\2022_postdoc\Proteomics_Data\20221129_proteomics_core\Ex191122_Wenting5uL_60m_8.raw [0:01] Cross-run analysis [0:01] Reading quantification information: 8 files [0:01] Quantifying peptides WARNING: not enough peptides for normalisation [0:01] Quantifying proteins [0:01] Calculating q-values for protein and gene groups [0:01] Calculating global q-values for protein and gene groups [0:01] Writing report [0:01] Report saved to C:\DIA-NN\1.8.1\report_llnl.tsv. [0:01] Saving precursor levels matrix [0:01] Precursor levels matrix (1% precursor and protein group FDR) saved to C:\DIA-NN\1.8.1\report_llnl.pr_matrix.tsv. [0:01] Saving protein group levels matrix [0:01] Saving gene group levels matrix [0:01] Saving unique genes levels matrix [0:01] Stats report saved to C:\DIA-NN\1.8.1\report_llnl.stats.tsv
Finished
li-jiamiao
commented
3 months ago Hi, have you solved this problem? I have both skyline daily and MSFileReader Core 31. I still got the erro
Hi, how do you resolve this? I got a bunch of DIA data from Exploris 480 (core facility) as well and have similar error message. I downloaded and installed the most recent MSFileReader on my computer for DIA-NN to run but still getting the same error message. When you say the wrong version MSFileReader version installed on the system, do you mean by the acquisition computer (the one connected to the orbitrap) or the processing computer?
Wenting
Hi, have you solved this problem? I have both skyline daily and MSFileReader Core 31. I still got the same error message.
vdemichev
commented
3 months ago Hi,
You need to install MSFileReader using the link here https://github.com/vdemichev/DiaNN?tab=readme-ov-file#raw-data-formats. Version 31 will not work, need specifically the one by the link provided.
Best, Vadim
li-jiamiao
commented
3 months ago Owner
Thank you very much! With appreciation.
ekglover
commented
2 months ago I've had this error message too but only for the 19th file out of 20. I have the correct version of MSFileReader and get an appropriate output for all the other files so I assume this is not the issue. I'm checking with the MS department if there are any issues with the MS2 data in the file but just wanted to confirm if I could be doing something wrong in DIANN that would only affect one file in this way. Log attached. Many thanks for any light you can shed on this.
vdemichev
commented
2 months ago You can try again (specifically that file), see maybe if it's an accidental error with disk access?
I got the following when running Dia-NN on a set of six Thermo raw files:
Not clear why this happens. The data was recorded with the following method:
and contains many, many, many DIA scans. Could it be that the Dia-NN has a problem with scan headers written by the Exploris 480?