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MaxQuant and Perseus Bug Reporting
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Different MaxQuant versions identify vastly different number of Protein groups via MS/MS in the same sample #110

Open Johanhw-ms opened 3 months ago

Johanhw-ms commented 3 months ago

I am new to analyzing mass spectrometry data, so for my first experiment (an IP experiment with trypsin digestion), we let our mass spec core facility (the experts) run MaxQuant on the raw data for us. We used match between runs + LFQ. The core facility uses MaxQuant version 2.4.7.0, and this version identified about 3000+ protein groups in my sample, of which more than 1000 were identified via MS/MS in each sample. The enriched proteins identified in the Perseus volcano plot also "made sense" in the way that the antigen I was trying to precipitate was enriched.

I wanted to recreate this result myself, so I downloaded the newest version of MaxQuant, and ran the same raw data using the same MaxQuant parameters. This time, only about half of the protein groups were identified! When I filtered for protein groups identified via MS/MS, some of the samples had very few hits (under 100). Ihe antigen I was enriching had also disappeared from the list of identified proteins.

This led to a lot of troubleshooting:

  1. MaxQuant version 2.4.7.0 (which runs on .NET core 3.1 and .NET framework 4.7.2) gives us the results we expected (3000+ identified protein groups, 900+ protein groups identified via MS/MS per sample)
  2. MaxQuant version 2.5.0.0 (which runs on the newer .NET 7.0) gives us half as many identified protein groups, and one sample has as little as 23 protein groups identified via MS/MS!
  3. MaxQuant version 2.6.3.0 (the newest version running on .NET 8.0) looks like the one from v2.5.0.0
  4. We ran the same raw data on PEAKS, and their results look a lot more like the ones from MaxQuant v.2.4.7.0
  5. We took the mqpar file from v2.5.0.0 and ran it using v.2.4.7.0, just to be 100% sure it wasn't a change in default parameters or something. The results from this run look just like the last time we ran 2.4.7.0.

OS: Windows 10 (we also tried Linux - Ubuntu 22.04)

To us, it seems like MaxQuant version 2.5.0.0 and newer somehow analyses our data differently, and this leads to us losing ca. half of the identifiable protein groups. Does anyone have any idea what could cause this? Is it .NET? I would have assumed that if there was a problem with the dependencies then MaxQuant would just crash, not produce totally different results.. We are at our wits end I'm afraid.

Best regards, Johanna

WalterViegener commented 3 months ago

Dear Johanna, Could you please share your data with us at this link? It will be handled confidentially. If possible please also upload all mqpar files of the mentioned versions.

Also please let us know if it is DDA/DIA and what other settings might be important.

Best, Walter

Johanhw-ms commented 3 months ago

Hello Walter!

I got an error message while uploading the data, telling me there was "not enough free space". There are nine folders (one for each sample) totalling to about 44GB. Did you not want the mass spectrometry raw data?

The dataset is DDA. It is an immunoprecipitation experiment on human brain tissue. We used magnetic beads to isolate antibodies and other attached proteins from the tissue before digesting them using trypsin. As our peptide reference library, we used the human proteome (Reviewed proteins with isoforms, downloaded from UniProt) + "Human_IgG_library_MS.fasta", which contains all the peptide sequences of the antibodies we use for immunoprecipitation.

Best regards, Johanna

From: WalterViegener @.***> Sent: 21 August 2024 14:35:53 To: cox-labs/CoxLab_Bug_Reporting Cc: Johanna Henny Wagnerberger; Author Subject: Re: [cox-labs/CoxLab_Bug_Reporting] Different MaxQuant versions identify vastly different number of Protein groups via MS/MS in the same sample (Issue #110)

Dear Johanna, Could you please share your data with us at this linkhttps://datashare.biochem.mpg.de/s/2gSvjCZHOBZIcGU? It will be handled confidentially.

Also please let us know if it is DDA/DIA and what other settings might be important.

Best, Walter

— Reply to this email directly, view it on GitHubhttps://github.com/cox-labs/CoxLab_Bug_Reporting/issues/110#issuecomment-2301947685, or unsubscribehttps://github.com/notifications/unsubscribe-auth/BKSQETKED3PQGQPLKRYTVDDZSSCSTAVCNFSM6AAAAABMUIYZYOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGMBRHE2DONRYGU. You are receiving this because you authored the thread.Message ID: @.***>

WalterViegener commented 3 months ago

Dear Johanna, Thanks for providing your data. Please upload again at this folder. Also, based on you current upload I think each folder had the ending .d? If so, please create a .zip of each .d folder and upload that. Also I would appreciate the mqpar files and the mentioned fasta files you used for your tests.

Johanhw-ms commented 3 months ago

Dear Walter,

The data is now uploaded.

Please delete/disregard the free files starting with "analysis.", they were the beginning upload of an unzipped folder which I aborted so they are not needed.

I have also uploaded an mqpar (from MaxQuant version 2.5.0.0) that we used, and the reference fasta files (the human proteome is compressed).

Best regards,

Johanna Wagnerberger

From: WalterViegener @.***> Sent: 22 August 2024 14:27:47 To: cox-labs/CoxLab_Bug_Reporting Cc: Johanna Henny Wagnerberger; Author Subject: Re: [cox-labs/CoxLab_Bug_Reporting] Different MaxQuant versions identify vastly different number of Protein groups via MS/MS in the same sample (Issue #110)

Dear Johanna, Thanks for providing your data. Please upload again at this https://datashare.biochem.mpg.de/s/4ZHEDh8byQWqef5 folder. Also, based on you current upload I think each folder had the ending .d? If so, please create a .zip of each .d folder and upload that. Also I would appreciate the mqpar files and the mentioned fasta files you used for your tests.

— Reply to this email directly, view it on GitHubhttps://github.com/cox-labs/CoxLab_Bug_Reporting/issues/110#issuecomment-2304546209, or unsubscribehttps://github.com/notifications/unsubscribe-auth/BKSQETMC664D3K5OY5ZEQDTZSXKMHAVCNFSM6AAAAABMUIYZYOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGMBUGU2DMMRQHE. You are receiving this because you authored the thread.Message ID: @.***>

Johanhw-ms commented 2 months ago

hello Walter!

Have you had time to look into this issue? We are very interested to know what could be casing these discrepancies.

Best regards,

Johanna

From: Johanna Henny Wagnerberger Sent: 22 August 2024 16:10:12 To: cox-labs/CoxLab_Bug_Reporting; cox-labs/CoxLab_Bug_Reporting Cc: Author Subject: Re: [cox-labs/CoxLab_Bug_Reporting] Different MaxQuant versions identify vastly different number of Protein groups via MS/MS in the same sample (Issue #110)

Dear Walter,

The data is now uploaded.

Please delete/disregard the free files starting with "analysis.", they were the beginning upload of an unzipped folder which I aborted so they are not needed.

I have also uploaded an mqpar (from MaxQuant version 2.5.0.0) that we used, and the reference fasta files (the human proteome is compressed).

Best regards,

Johanna Wagnerberger

From: WalterViegener @.***> Sent: 22 August 2024 14:27:47 To: cox-labs/CoxLab_Bug_Reporting Cc: Johanna Henny Wagnerberger; Author Subject: Re: [cox-labs/CoxLab_Bug_Reporting] Different MaxQuant versions identify vastly different number of Protein groups via MS/MS in the same sample (Issue #110)

Dear Johanna, Thanks for providing your data. Please upload again at this https://datashare.biochem.mpg.de/s/4ZHEDh8byQWqef5 folder. Also, based on you current upload I think each folder had the ending .d? If so, please create a .zip of each .d folder and upload that. Also I would appreciate the mqpar files and the mentioned fasta files you used for your tests.

— Reply to this email directly, view it on GitHubhttps://github.com/cox-labs/CoxLab_Bug_Reporting/issues/110#issuecomment-2304546209, or unsubscribehttps://github.com/notifications/unsubscribe-auth/BKSQETMC664D3K5OY5ZEQDTZSXKMHAVCNFSM6AAAAABMUIYZYOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGMBUGU2DMMRQHE. You are receiving this because you authored the thread.Message ID: @.***>

JinqiuXiao commented 2 months ago

Hi Johanna,

This is Jinqiu, I'm Walter's colleague. He's still on holiday and I took over this issue. We didn't change much for DDA analysis for the past releases, so I tried some parameters and found out what's going on there. In MaxQuant there's a parameter called "Split protein groups by taxonomy ID" (as shown in the screenshot), you can find it in "Global parameters->Identification". In multi species dataset, if you take proteomes from uniprot, the taxonomy ID will be automatically assigned to each species, then during the identification, the protein from different species will not be combined into protein groups.

image

For 2.4.7 it was off by default, but we switch it on for the NET7 and NET8 version. Your dataset was kind of special, since you have two database from homo sampiens, and one of them is not from uniprot, so the taxonomy id was not recognized properly, it made some confusion during the identification and lead to fewer identifications. Your dataset only has sequence from homo sanpiens so you can switch it off. I tried to run latest MQ version with default settings, and like you mentioned, I only identified around 1500 protein groups, but by switch this parameter off I identified 3300 protein groups. You can try to switch it off and run it again, please let us know how it works :)

We'll look into this issue afterwards, thank you for letting us know about it!

Best, Jinqiu

Johanhw-ms commented 2 months ago

Hello Jinqiu,

I tried this on our PC now, but I still got about 1500 hits.

See attached mqpar and the resulting proteingroups file (I unchecked "split protein groups by taxonomy ID" and changed the identifier for my homemade fasta file to ">.") This time, I ran MQ v.2.6.4.0 with .NET 8.0.302.

But I also don't understand how trouble with identifying taxonomy IDs can lead to the loss of so many protein hits. My homemade fasta only contains 54 sequences, and they are all IgG, so they should only group with immunoglobulin sequences in the UniProt file.

Thank you for looking into this!

Best regards,

Johanna

From: JinqiuXiao @.***> Sent: 05 September 2024 10:46:54 To: cox-labs/CoxLab_Bug_Reporting Cc: Johanna Henny Wagnerberger; Author Subject: Re: [cox-labs/CoxLab_Bug_Reporting] Different MaxQuant versions identify vastly different number of Protein groups via MS/MS in the same sample (Issue #110)

Hi Johanna,

This is Jinqiu, I'm Walter's colleague. He's still on holiday and I took over this issue. We didn't change much for DDA analysis for the past releases, so I tried some parameters and found out what's going on there. In MaxQuant there's a parameter called "Split protein groups by taxonomy ID" (as shown in the screenshot), you can find it in "Global parameters->Identification". In multi species dataset, if you take proteomes from uniprot, the taxonomy ID will be automatically assigned to each species, then during the identification, the protein from different species will not be combined into protein groups.

image.png (view on web)https://github.com/user-attachments/assets/bf810966-986d-404e-b754-f49f2205a3bd

For 2.4.7 it was off by default, but we switch it on for the NET7 and NET8 version. Your dataset was kind of special, since you have two database from homo sampiens, and one of them is not from uniprot, so the taxonomy id was not recognized properly, it made some confusion during some identification. So for your dataset you can switch it off. I tried to run latest MQ version with default settings, and like you mentioned, I only identified around 1500 protein groups, but by switch this parameter off I identified 3300 protein groups. You can try to switch it off and run it again, please let us know how it works :)

We'll look into this issue afterwards, thank you for letting us know about it!

Best, Jinqiu

— Reply to this email directly, view it on GitHubhttps://github.com/cox-labs/CoxLab_Bug_Reporting/issues/110#issuecomment-2330956371, or unsubscribehttps://github.com/notifications/unsubscribe-auth/BKSQETK6KYPCILYIWA65ECLZVAK75AVCNFSM6AAAAABMUIYZYOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGMZQHE2TMMZXGE. You are receiving this because you authored the thread.Message ID: @.***>

Protein IDs Majority protein IDs Peptide counts (all) Peptide counts (razor+unique) Peptide counts (unique) Protein names Gene names Fasta headers Number of proteins Peptides Razor + unique peptides Unique peptides Peptides gCAM_B1_Slot1-34_1_3290 Peptides gCAM_B2_Slot1-35_1_3291 Peptides gCAM_B3_Slot1-36_1_3292 Peptides NA2_B1_Slot1-28_1_3282 Peptides NA2_B2_Slot1-29_1_3283 Peptides NA2_B3_Slot1-30_1_3284 Peptides NR1_B1_Slot1-31_1_3286 Peptides NR1_B2_Slot1-32_1_3287 Peptides NR1_B3_Slot1-33_1_3288 Razor + unique peptides gCAM_B1_Slot1-34_1_3290 Razor + unique peptides gCAM_B2_Slot1-35_1_3291 Razor + unique peptides gCAM_B3_Slot1-36_1_3292 Razor + unique peptides NA2_B1_Slot1-28_1_3282 Razor + unique peptides NA2_B2_Slot1-29_1_3283 Razor + unique peptides NA2_B3_Slot1-30_1_3284 Razor + unique peptides NR1_B1_Slot1-31_1_3286 Razor + unique peptides NR1_B2_Slot1-32_1_3287 Razor + unique peptides NR1_B3_Slot1-33_1_3288 Unique peptides gCAM_B1_Slot1-34_1_3290 Unique peptides gCAM_B2_Slot1-35_1_3291 Unique peptides gCAM_B3_Slot1-36_1_3292 Unique peptides NA2_B1_Slot1-28_1_3282 Unique peptides NA2_B2_Slot1-29_1_3283 Unique peptides NA2_B3_Slot1-30_1_3284 Unique peptides NR1_B1_Slot1-31_1_3286 Unique peptides NR1_B2_Slot1-32_1_3287 Unique peptides NR1_B3_Slot1-33_1_3288 Sequence coverage [%] Unique + razor sequence coverage [%] Unique sequence coverage [%] Mol. weight [kDa] Sequence length Sequence lengths Q-value Score Identification type gCAM_B1_Slot1-34_1_3290 Identification type gCAM_B2_Slot1-35_1_3291 Identification type gCAM_B3_Slot1-36_1_3292 Identification type NA2_B1_Slot1-28_1_3282 Identification type NA2_B2_Slot1-29_1_3283 Identification type NA2_B3_Slot1-30_1_3284 Identification type NR1_B1_Slot1-31_1_3286 Identification type NR1_B2_Slot1-32_1_3287 Identification type NR1_B3_Slot1-33_1_3288 Sequence coverage gCAM_B1_Slot1-34_1_3290 [%] Sequence coverage gCAM_B2_Slot1-35_1_3291 [%] Sequence coverage gCAM_B3_Slot1-36_1_3292 [%] Sequence coverage NA2_B1_Slot1-28_1_3282 [%] Sequence coverage NA2_B2_Slot1-29_1_3283 [%] Sequence coverage NA2_B3_Slot1-30_1_3284 [%] Sequence coverage NR1_B1_Slot1-31_1_3286 [%] Sequence coverage NR1_B2_Slot1-32_1_3287 [%] Sequence coverage NR1_B3_Slot1-33_1_3288 [%] Intensity Intensity gCAM_B1_Slot1-34_1_3290 Intensity gCAM_B2_Slot1-35_1_3291 Intensity gCAM_B3_Slot1-36_1_3292 Intensity NA2_B1_Slot1-28_1_3282 Intensity NA2_B2_Slot1-29_1_3283 Intensity NA2_B3_Slot1-30_1_3284 Intensity NR1_B1_Slot1-31_1_3286 Intensity NR1_B2_Slot1-32_1_3287 Intensity NR1_B3_Slot1-33_1_3288 LFQ intensity gCAM_B1_Slot1-34_1_3290 LFQ intensity gCAM_B2_Slot1-35_1_3291 LFQ intensity gCAM_B3_Slot1-36_1_3292 LFQ intensity NA2_B1_Slot1-28_1_3282 LFQ intensity NA2_B2_Slot1-29_1_3283 LFQ intensity NA2_B3_Slot1-30_1_3284 LFQ intensity NR1_B1_Slot1-31_1_3286 LFQ intensity NR1_B2_Slot1-32_1_3287 LFQ intensity NR1_B3_Slot1-33_1_3288 MS/MS count gCAM_B1_Slot1-34_1_3290 MS/MS count gCAM_B2_Slot1-35_1_3291 MS/MS count gCAM_B3_Slot1-36_1_3292 MS/MS count NA2_B1_Slot1-28_1_3282 MS/MS count NA2_B2_Slot1-29_1_3283 MS/MS count NA2_B3_Slot1-30_1_3284 MS/MS count NR1_B1_Slot1-31_1_3286 MS/MS count NR1_B2_Slot1-32_1_3287 MS/MS count NR1_B3_Slot1-33_1_3288 MS/MS count Peptide sequences Only identified by site Reverse Potential contaminant id Peptide IDs Peptide is razor Mod. peptide IDs Evidence IDs MS/MS IDs Best MS/MS Oxidation (M) site IDs Oxidation (M) site positions Taxonomy IDs Taxonomy names A0A0C4DH67;A0A0C4DH69;A0A075B6S5 A0A0C4DH67;A0A0C4DH69;A0A075B6S5 1;1;1 1;1;1 1;1;1 Immunoglobulin kappa variable 1-8;Immunoglobulin kappa variable 1-9;Immunoglobulin kappa variable 1-27 IGKV1-8;IGKV1-9;IGKV1-27 sp|A0A0C4DH67|KV108_HUMAN Immunoglobulin kappa variable 1-8 OS=Homo sapiens OX=9606 GN=IGKV1-8 PE=3 SV=1;sp|A0A0C4DH69|KV109_HUMAN Immunoglobulin kappa variable 1-9 OS=Homo sapiens OX=9606 GN=IGKV1-9 PE=3 SV=1;sp|A0A075B6S5|KV127_HUMAN Immunoglobulin kappa 3 1 1 1 0 0 1 0 0 1 0 0 0 0 0 1 0 0 1 0 0 0 0 0 1 0 0 1 0 0 0 13.9 13.9 13.9 12.537 115 115;117;117 0 30.264 None None By MS/MS None None By matching None None None 0 0 13.9 0 0 13.9 0 0 0 307650 0 0 48676 0 0 258970 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 LLIYAASTLQSGVPSR 0 1955 True 1975 11493;11494 3636 3636 -1;-1;-1 ;; P06310;A0A075B6S6 P06310;A0A075B6S6 1;1 1;1 1;1 Immunoglobulin kappa variable 2-30;Immunoglobulin kappa variable 2D-30 IGKV2-30;IGKV2D-30 sp|P06310|KV230_HUMAN Immunoglobulin kappa variable 2-30 OS=Homo sapiens OX=9606 GN=IGKV2-30 PE=3 SV=2;sp|A0A075B6S6|KVD30_HUMAN Immunoglobulin kappa variable 2D-30 OS=Homo sapiens OX=9606 GN=IGKV2D-30 PE=3 SV=1 2 1 1 1 1 1 1 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 21.7 21.7 21.7 13.185 120 120;120 0 323.31 By MS/MS By MS/MS By MS/MS None None None None None None 21.7 21.7 21.7 0 0 0 0 0 0 34427000 7015700 6747300 20663000 0 0 0 0 0 0 3540400 1926300 9082100 0 0 0 0 0 0 4 3 2 0 0 0 0 0 0 9 SSQSLVYSDGNTYLNWFQQRPGQSPR 1 2874 True 2911 16608;16609;16610;16611;16612;16613;16614;16615;16616;16617 5200;5201;5202;5203;5204;5205;5206;5207;5208 5201 -1;-1 ; P04433;A0A0A0MRZ8 P04433;A0A0A0MRZ8 1;1 1;1 1;1 Immunoglobulin kappa variable 3-11;Immunoglobulin kappa variable 3D-11 IGKV3-11;IGKV3D-11 sp|P04433|KV311_HUMAN Immunoglobulin kappa variable 3-11 OS=Homo sapiens OX=9606 GN=IGKV3-11 PE=1 SV=1;sp|A0A0A0MRZ8|KVD11_HUMAN Immunoglobulin kappa variable 3D-11 OS=Homo sapiens OX=9606 GN=IGKV3D-11 PE=3 SV=6 2 1 1 1 0 0 0 0 0 1 0 0 1 0 0 0 0 0 1 0 0 1 0 0 0 0 0 1 0 0 1 13 13 13 12.575 115 115;115 0 101.66 None None None None None By MS/MS None None By MS/MS 0 0 0 0 0 13 0 0 13 876310 0 0 0 0 0 441230 0 0 435080 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 2 ASQSVSSYLAWYQQK 2 255 True 259 1435;1436 478;479 478 -1;-1 ; P0DPI2;A0A0B4J2D5 P0DPI2;A0A0B4J2D5 1;1 1;1 1;1 Glutamine amidotransferase-like class 1 domain-containing protein 3, mitochondrial;Putative glutamine amidotransferase-like class 1 domain-containing protein 3B, mitochondrial GATD3;GATD3B sp|P0DPI2|GAL3A_HUMAN Glutamine amidotransferase-like class 1 domain-containing protein 3A, mitochondrial OS=Homo sapiens OX=9606 GN=GATD3A PE=1 SV=1;sp|A0A0B4J2D5|GAL3B_HUMAN Glutamine amidotransferase-like class 1 domain-containing protein 3B, mitochondr 2 1 1 1 0 0 1 1 1 1 1 1 1 0 0 1 1 1 1 1 1 1 0 0 1 1 1 1 1 1 1 5.6 5.6 5.6 28.17 268 268;268 0.0080754 5.6964 None None By matching By matching By matching By MS/MS By matching By matching By MS/MS 0 0 5.6 5.6 5.6 5.6 5.6 5.6 5.6 103640 0 0 18065 5767.5 15082 20736 9770.2 12325 21894 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 2 GVEVTVGHEQEEGGK 3 1247 True 1263 7428;7429;7430;7431;7432;7433;7434 2401;2402 2401 -1;-1 ; P01619;A0A0C4DH25 P01619;A0A0C4DH25 1;1 1;1 1;1 Immunoglobulin kappa variable 3-20;Immunoglobulin kappa variable 3D-20 IGKV3-20;IGKV3D-20 sp|P01619|KV320_HUMAN Immunoglobulin kappa variable 3-20 OS=Homo sapiens OX=9606 GN=IGKV3-20 PE=1 SV=2;sp|A0A0C4DH25|KVD20_HUMAN Immunoglobulin kappa variable 3D-20 OS=Homo sapiens OX=9606 GN=IGKV3D-20 PE=3 SV=1 2 1 1 1 0 0 0 0 0 1 0 0 1 0 0 0 0 0 1 0 0 1 0 0 0 0 0 1 0 0 1 13.8 13.8 13.8 12.557 116 116;116 0 323.31 None None None None None By matching None None By MS/MS 0 0 0 0 0 13.8 0 0 13.8 6149800 0 0 0 0 0 5125900 0 0 1023900 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 FSGSGSGTDFTLTISR 4 993 True 1006 5925;5926 1888 1888 -1;-1 ; A0AVT1 A0AVT1 4 4 4 Ubiquitin-like modifier-activating enzyme 6 UBA6 sp|A0AVT1|UBA6_HUMAN Ubiquitin-like modifier-activating enzyme 6 OS=Homo sapiens OX=9606 GN=UBA6 PE=1 SV=1 1 4 4 4 0 2 1 0 1 2 3 4 4 0 2 1 0 1 2 3 4 4 0 2 1 0 1 2 3 4 4 5.7 5.7 5.7 117.97 1052 1052 0 113.35 None By matching By matching None By matching By MS/MS By MS/MS By MS/MS By MS/MS 0 3.3 1.9 0 1.2 2.7 4.6 5.7 5.7 1335500 0 147290 92050 0 108990 286060 289540 235260 176320 0 0 0 0 0 76515 45957 24786 21002 0 0 0 0 0 1 2 2 2 7 ALQLLHCFPLDIR;FISADVHGIWSR;KPNVGCQQDSEELLK;NCFLNLAIPIVVFTETTEVR 5 166;941;1715;2321 True;True;True;True 170;954;1734;2351 978;979;980;981;982;983;984;5488;5489;10061;10062;10063;10064;10065;13614;13615;13616;13617;13618 326;327;328;1750;1751;3222;4299 327;1751;3222;4299 -1
A0FGR8 A0FGR8 1 1 1 Extended synaptotagmin-2 ESYT2 sp|A0FGR8|ESYT2_HUMAN Extended synaptotagmin-2 OS=Homo sapiens OX=9606 GN=ESYT2 PE=1 SV=1 1 1 1 1 0 1 0 0 1 0 0 0 0 0 1 0 0 1 0 0 0 0 0 1 0 0 1 0 0 0 0 1 1 1 102.36 921 921 0.005102 5.9739 None By MS/MS None None By matching None None None None 0 1 0 0 1 0 0 0 0 90210 0 83054 0 0 7155.6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 RQDLEVEVR 6 2679 True 2714 15675;15676 4910 4910 -1
A0M8Q6 A0M8Q6 3 1 1 Immunoglobulin lambda constant 7 IGLC7 sp|A0M8Q6|IGLC7_HUMAN Immunoglobulin lambda constant 7 OS=Homo sapiens OX=9606 GN=IGLC7 PE=1 SV=3 1 3 1 1 2 1 1 2 2 2 2 3 3 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 26.4 9.4 9.4 11.253 106 106 0 126.27 By matching By matching By matching By matching By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 23.6 9.4 9.4 23.6 23.6 23.6 23.6 26.4 26.4 7981600 412900 3661900 290970 263730 648410 606510 844370 712580 540300 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 1 2 2 9 VTHEGSTVEK;YAASSYLSLTPEQWK;YAASSYLSLTPEQWKSHR 7 3400;3674;3675 True;False;False 3441;3716;3717 19556;19557;19558;19559;19560;19561;19562;19563;19564;19565;19566;19567;19568;19569;19570;19571;19572;19573;19574;19575;19576;19577;19578;19579;21213;21214;21215;21216;21217;21218;21219;21220;21221 6157;6158;6159;6160;6161;6162;6163;6164;6165;6664;6665 6161;6664;6665 -1
A0MZ66 A0MZ66 1 1 1 Shootin-1 SHTN1 sp|A0MZ66|SHOT1_HUMAN Shootin-1 OS=Homo sapiens OX=9606 GN=SHTN1 PE=1 SV=4 1 1 1 1 0 1 0 0 1 1 0 0 1 0 1 0 0 1 1 0 0 1 0 1 0 0 1 1 0 0 1 2.4 2.4 2.4 71.639 631 631 0.0080808 5.6967 None By matching None None By MS/MS By matching None None By matching 0 2.4 0 0 2.4 2.4 0 0 2.4 120630 0 3030.2 0 0 63093 35824 0 0 18678 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 1 VKELEEQLENETLHK 8 3287 True 3326 18924;18925;18926;18927 5954 5954 -1
A1L0T0 A1L0T0 1 1 1 2-hydroxyacyl-CoA lyase 2 ILVBL sp|A1L0T0|HACL2_HUMAN 2-hydroxyacyl-CoA lyase 2 OS=Homo sapiens OX=9606 GN=ILVBL PE=1 SV=2 1 1 1 1 0 1 0 0 1 1 1 0 1 0 1 0 0 1 1 1 0 1 0 1 0 0 1 1 1 0 1 3.6 3.6 3.6 67.867 632 632 0 95.508 None By matching None None By matching By matching By matching None By MS/MS 0 3.6 0 0 3.6 3.6 3.6 0 3.6 1345700 0 446030 0 0 462440 272130 95683 0 69410 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 NAQMAQSPILLLGGAASTLLQNR 9 2313 True 2343 13578;13579;13580;13581;13582 4289 4289 -1
A1XBS5 A1XBS5 1 1 1 CBY1-interacting BAR domain-containing protein 1 CIBAR1 sp|A1XBS5|FA92A_HUMAN Protein FAM92A OS=Homo sapiens OX=9606 GN=FAM92A PE=1 SV=2 1 1 1 1 0 0 0 1 0 0 1 0 0 0 0 0 1 0 0 1 0 0 0 0 0 1 0 0 1 0 0 3.1 3.1 3.1 33.43 289 289 1 -2 None None None By MS/MS None None By MS/MS None None 0 0 0 3.1 0 0 3.1 0 0 36264000 0 0 0 21221000 0 0 15043000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 2 MMRRTLENR + 10 2251 True 2279 13238;13239 4188;4189 4188 0;1 1;2 -1
Q99755;A2A3N6 Q99755;A2A3N6 1;1 1;1 1;1 Phosphatidylinositol 4-phosphate 5-kinase type-1 alpha;Putative PIP5K1A and PSMD4-like protein PIP5K1A;PIPSL sp|Q99755|PI51A_HUMAN Phosphatidylinositol 4-phosphate 5-kinase type-1 alpha OS=Homo sapiens OX=9606 GN=PIP5K1A PE=1 SV=1;sp|A2A3N6|PIPSL_HUMAN Putative PIP5K1A and PSMD4-like protein OS=Homo sapiens OX=9606 GN=PIPSL PE=5 SV=1 2 1 1 1 0 1 1 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 2.7 2.7 2.7 62.633 562 562;862 0.0023077 6.3362 None By MS/MS By MS/MS None None None None None None 0 2.7 2.7 0 0 0 0 0 0 52393 0 34627 17766 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 2 LLLYIGIIDILQSYR 11 1959 True 1979 11513;11514 3642;3643 3642 -1;-1 ; A5YM72 A5YM72 1 1 1 Carnosine synthase 1 CARNS1 sp|A5YM72|CRNS1_HUMAN Carnosine synthase 1 OS=Homo sapiens OX=9606 GN=CARNS1 PE=1 SV=3 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1.9 1.9 1.9 88.483 827 827 0 6.6629 By matching By matching By matching By matching By matching By matching By MS/MS By MS/MS By matching 1.9 1.9 1.9 1.9 1.9 1.9 1.9 1.9 1.9 492220 36452 50935 7524.9 126800 59802 20805 151550 33774 4580.6 0 0 0 0 0 0 32367 6722.3 0 0 0 0 0 0 0 1 1 0 2 AELGAVVDTVLALLEK 12 51 True 53 321;322;323;324;325;326;327;328;329;330;331;332;333;334;335;336 118;119 118 -1
A6NDG6 A6NDG6 4 4 4 Glycerol-3-phosphate phosphatase PGP sp|A6NDG6|PGP_HUMAN Glycerol-3-phosphate phosphatase OS=Homo sapiens OX=9606 GN=PGP PE=1 SV=1 1 4 4 4 3 1 3 3 4 3 2 2 4 3 1 3 3 4 3 2 2 4 3 1 3 3 4 3 2 2 4 19.3 19.3 19.3 34.006 321 321 0 79.277 By matching By matching By matching By matching By MS/MS By matching By MS/MS By MS/MS By MS/MS 14.6 4.4 13.4 14.6 19.3 15 10.3 10.3 19.3 5421600 195390 49471 99646 833370 1243400 1196700 619730 553030 630940 95030 0 94016 153380 183610 142520 144070 134910 150230 0 0 0 0 2 0 1 1 3 7 AVVVGFDPHFSYMK;LDTDILLGATCGLK;MVPDFYVDSIADLLPALQG;TILTLTGVSTLGDVK 13 305;1806;2294;3016 True;True;True;True 310;1825;2323;3054 1767;1768;1769;1770;1771;1772;10592;10593;10594;10595;10596;10597;10598;10599;13460;13461;13462;13463;13464;13465;13466;17431;17432;17433;17434 592;3370;4253;4254;4255;5482;5483 592;3370;4254;5483 -1
A6NHL2 A6NHL2 1 1 1 Tubulin alpha chain-like 3 TUBAL3 sp|A6NHL2|TBAL3_HUMAN Tubulin alpha chain-like 3 OS=Homo sapiens OX=9606 GN=TUBAL3 PE=1 SV=2 1 1 1 1 0 1 0 1 1 1 1 1 1 0 1 0 1 1 1 1 1 1 0 1 0 1 1 1 1 1 1 3.8 3.8 3.8 49.908 446 446 0 95.127 None By matching None By matching By matching By matching By matching By matching By MS/MS 0 3.8 0 3.8 3.8 3.8 3.8 3.8 3.8 452870 0 58726 0 12797 39443 19407 84951 92794 144750 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 SFGGGTGSGFTSLLMER 14 2746 True 2782 16005;16006;16007;16008;16009;16010;16011 5005 5005 2 161 -1
P61224;A6NIZ1 P61224;A6NIZ1 1;1 1;1 1;1 Ras-related protein Rap-1b;Ras-related protein Rap-1b-like protein RAP1B;RAP1BL sp|P61224|RAP1B_HUMAN Ras-related protein Rap-1b OS=Homo sapiens OX=9606 GN=RAP1B PE=1 SV=1;sp|A6NIZ1|RP1BL_HUMAN Ras-related protein Rap-1b-like protein OS=Homo sapiens OX=9606 PE=2 SV=1 2 1 1 1 0 0 0 1 1 1 1 1 0 0 0 0 1 1 1 1 1 0 0 0 0 1 1 1 1 1 0 7.1 7.1 7.1 20.825 184 184;184 0.0037821 6.1956 None None None By MS/MS By MS/MS By matching By matching By MS/MS None 0 0 0 7.1 7.1 7.1 7.1 7.1 0 1134400 0 0 0 233370 220760 212720 172150 295440 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 1 0 3 QWNNCAFLESSAK 15 2641 True 2675 15462;15463;15464;15465;15466 4849;4850;4851 4849 -1;-1 ; P07355;A6NMY6 P07355;A6NMY6 3;3 3;3 3;3 Annexin A2;Putative annexin A2-like protein ANXA2;ANXA2P2 sp|P07355|ANXA2_HUMAN Annexin A2 OS=Homo sapiens OX=9606 GN=ANXA2 PE=1 SV=2;sp|A6NMY6|AXA2L_HUMAN Putative annexin A2-like protein OS=Homo sapiens OX=9606 GN=ANXA2P2 PE=5 SV=2 2 3 3 3 0 1 0 1 0 2 1 1 2 0 1 0 1 0 2 1 1 2 0 1 0 1 0 2 1 1 2 11.5 11.5 11.5 38.604 339 339;339 0 25.278 None By matching None By matching None By MS/MS By matching By matching By MS/MS 0 4.7 0 3.5 0 6.8 4.7 4.7 8 749400 0 85715 0 6941.3 0 256310 20660 35976 343790 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 2 4 SALSGHLETVILGLLK;SYSPYDMLESIR;TPAQYDASELK 16 2703;2924;3065 True;True;True 2738;2961;3104 15794;15795;15796;15797;16924;16925;17695;17696 4938;5306;5568;5569 4938;5306;5569 -1;-1 ; A8K8P3 A8K8P3 1 1 1 Protein SFI1 homolog SFI1 sp|A8K8P3|SFI1_HUMAN Protein SFI1 homolog OS=Homo sapiens OX=9606 GN=SFI1 PE=1 SV=2 1 1 1 1 0 0 0 1 1 1 1 1 1 0 0 0 1 1 1 1 1 1 0 0 0 1 1 1 1 1 1 0.6 0.6 0.6 147.66 1242 1242 1 -2 None None None By matching By matching By matching By matching By matching By MS/MS 0 0 0 0.6 0.6 0.6 0.6 0.6 0.6 3314200 0 0 0 365910 256290 591170 665960 439800 995030 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 QKMRQAWK + 17 2573 True 2607 15109;15110;15111;15112;15113;15114 4748 4748 3 187 -1
P02533;CONP02533;CONQ6IFX2;CONQ61782 P02533;CONP02533 7;7;2;1 6;6;2;1 3;3;0;1 Keratin, type I cytoskeletal 14 KRT14 sp|P02533|K1C14_HUMAN Keratin, type I cytoskeletal 14 OS=Homo sapiens OX=9606 GN=KRT14 PE=1 SV=4; 4 7 6 3 4 2 2 3 4 5 5 6 5 4 2 2 3 3 4 4 5 5 2 1 1 1 2 2 2 3 2 22.7 20.8 13.3 51.561 472 472;472;452;93 0 323.31 By matching By matching By matching By matching By MS/MS By matching By MS/MS By MS/MS By MS/MS 14.4 6.8 6.8 9.5 13.1 15.3 15.7 20.1 15.9 13697000 1290400 748950 221590 2763000 515580 1612300 867170 1839600 3838000 245760 225620 130570 337760 131130 205720 214200 211480 569120 0 0 0 0 1 0 1 1 4 7 ADLEMQIESLKEELAYLK;ALEEANADLEVK;EVATNSELVQSGK;LLEGEDAHLSSSQFSSGSQSSR;NHEEEMNALR;VTMQNLNDR;YCMQLAQIQEMIGSVEEQLAQLR + 18 20;146;828;1942;2357;3407;3518 True;True;True;True;True;False;True 20;149;837;1962;2389;3448;3559 127;128;129;130;131;878;879;4782;4783;4784;4785;4786;4787;4788;11415;11416;11417;11418;11419;11420;11421;11422;11423;13812;13813;13814;13815;13816;13817;13818;19628;19629;19630;19631;20356;20357 49;293;1489;3615;3616;4366;6182;6183;6392 49;293;1489;3615;4366;6182;6392 4 368 -1;-1;-1;-1 ;;; P02768;CONP02768-1 P02768;CONP02768-1 1;1 1;1 1;1 Albumin ALB sp|P02768|ALBU_HUMAN Albumin OS=Homo sapiens OX=9606 GN=ALB PE=1 SV=2; 2 1 1 1 0 0 1 0 1 0 1 1 1 0 0 1 0 1 0 1 1 1 0 0 1 0 1 0 1 1 1 2 2 2 69.366 609 609;609 0.0075549 5.7603 None None By matching None By matching None By matching By MS/MS By matching 0 0 2 0 2 0 2 2 2 493970 0 0 105340 0 62295 0 54880 114330 157130 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 YICENQDSISSK + 19 3571 True 3612 20638;20639;20640;20641;20642 6483 6483 -1;-1 ; CONP02769 CONP02769 2 2 2 1 2 2 2 0 0 2 1 2 2 2 2 0 0 0 2 1 2 2 2 2 0 0 0 2 1 2 2 2 2 0 4.1 4.1 4.1 69.293 607 607 0 323.31 None None By MS/MS By matching By MS/MS By MS/MS By MS/MS By MS/MS None 0 0 4.1 2 4.1 4.1 4.1 4.1 0 1776000 0 0 762550 41310 141000 147480 372600 311070 0 0 0 310610 0 40997 44861 109870 71466 0 0 0 4 0 1 2 1 1 0 9 DAFLGSFLYEYSR;YICDNQDTISSK + 20 360;3570 True;True 365;3611 2029;2030;2031;2032;2033;2034;2035;2036;20631;20632;20633;20634;20635;20636;20637 669;670;671;672;673;674;675;6481;6482 670;6481 -1
P08779;CONP08779;CONQ9Z2K1;CONQ3ZAW8 P08779;CONP08779 5;5;2;2 3;3;1;1 3;3;1;1 Keratin, type I cytoskeletal 16 KRT16 sp|P08779|K1C16_HUMAN Keratin, type I cytoskeletal 16 OS=Homo sapiens OX=9606 GN=KRT16 PE=1 SV=4; 4 5 3 3 1 1 0 1 1 3 4 3 3 1 1 0 1 0 2 2 2 2 1 1 0 1 0 2 2 2 2 14.2 9.7 9.7 51.267 473 473;473;469;474 0 272.28 By matching By MS/MS None By MS/MS By matching By MS/MS By matching By MS/MS By MS/MS 4.9 4.9 0 2.1 1.9 6.8 11.4 6.8 7.4 2248600 204790 76138 0 544760 0 601890 57354 342410 421280 0 0 0 0 0 162280 0 84503 115160 0 1 0 1 0 1 0 1 2 6 ALEEANADLEVK;EVASNSELVQSSR;NHEEEMLALR;VTMQNLNDR;YCMQLSQIQGLIGSVEEQLAQLR + 21 146;827;2356;3407;3519 False;True;True;False;True 149;836;2388;3448;3560 878;879;4779;4780;4781;13807;13808;13809;13810;13811;19628;19629;19630;19631;20358;20359;20360 293;1487;1488;4363;4364;4365;6182;6183;6393 293;1487;4364;6182;6393 5 370 -1;-1;-1;-1 ;;; P13645;CONP13645;CONP02535-1;Q7Z3Z0;Q7Z3Y8;Q7Z3Y7;CONQ7Z3Z0;CONQ7Z3Y8;CONQ148H6;CONQ7Z3Y7;Q7Z3Y9;CONA2A4G1;CONQ7Z3Y9 P13645;CONP13645 17;17;5;2;2;2;2;2;2;2;1;1;1 17;17;5;2;2;2;2;2;2;2;1;1;1 14;14;2;1;1;1;1;1;1;1;0;0;0 Keratin, type I cytoskeletal 10 KRT10 sp|P13645|K1C10_HUMAN Keratin, type I cytoskeletal 10 OS=Homo sapiens OX=9606 GN=KRT10 PE=1 SV=6; 13 17 17 14 11 13 9 9 14 12 13 16 15 11 13 9 9 14 12 13 16 15 9 11 8 8 11 9 11 13 13 35.3 35.3 31.8 58.826 584 584;593;570;450;459;464;450;459;464;486;468;456;468 0 323.31 By MS/MS By MS/MS By MS/MS By matching By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 21.6 24 20 20.2 28.9 22.8 25.7 33.7 32.2 322800000 29210000 43357000 13959000 88516000 12830000 23489000 18643000 31532000 61266000 12299000 8127800 5972500 5537700 1504200 3525400 2587400 3992600 5883000 1 4 2 0 10 1 8 13 20 59 ADLEMQIESLTEELAYLK;ADLEMQIESLTEELAYLKK;ALEESNYELEGK;DAEAWFNEK;ELTTEIDNNIEQISSYK;LENEIQTYR;NQILNLTTDNANILLQIDNAR;NVQALEIELQSQLALK;NVSTGDVNVEMNAAPGVDLTQLLNNMR;QSVEADINGLR;QSVEADINGLRR;RVLDELTLTK;SGGGGGGGGCGGGGGVSSLR;SLLEGEGSSGGGGR;SQYEQLAEQNR;SQYEQLAEQNRK;VTMQNLNDR + 22 21;22;147;358;749;1830;2428;2465;2468;2625;2626;2690;2758;2805;2850;2851;3407 True;True;True;True;True;True;True;True;True;True;True;True;True;True;True;True;True 21;22;23;150;363;758;1849;2461;2499;2502;2659;2660;2725;2795;2842;2887;2888;3448 132;133;134;135;136;137;138;139;140;141;142;143;144;145;146;147;148;149;150;151;152;153;154;155;156;157;158;159;160;161;162;163;164;165;166;167;168;169;170;171;172;173;174;175;176;177;178;179;180;181;880;881;882;883;884;885;886;887;2006;2007;2008;2009;2010;2011;2012;2013;4381;4382;4383;4384;4385;4386;10739;10740;10741;14267;14268;14269;14270;14271;14272;14273;14515;14516;14517;14518;14519;14520;14521;14522;14523;14524;14525;14526;14527;14528;14529;14530;14531;14532;14533;14534;14535;14536;14537;14538;14539;14540;14541;14542;14543;14544;14545;14546;14547;14548;14549;14550;14551;14552;14553;14554;14555;14556;14557;14558;14559;14576;14577;14578;15361;15362;15363;15364;15365;15366;15367;15368;15369;15370;15371;15372;15373;15374;15375;15376;15377;15378;15379;15725;15726;15727;15728;15729;15730;15731;16066;16067;16068;16069;16070;16071;16072;16300;16301;16302;16303;16304;16305;16306;16507;16508;16509;16510;16511;16512;16513;16514;16515;16516;16517;16518;16519;19628;19629;19630;19631 50;51;52;53;54;55;56;57;58;59;60;61;62;63;64;65;66;294;295;665;666;1373;3410;3411;4493;4494;4567;4568;4569;4570;4571;4572;4573;4574;4575;4576;4577;4578;4579;4586;4817;4818;4819;4820;4821;4822;4823;4824;4825;4923;5024;5099;5100;5101;5167;5168;5169;6182;6183 51;66;294;666;1373;3410;4493;4579;4586;4821;4822;4923;5024;5100;5167;5169;6182 6 271 -1;-1;-1;-1;-1;-1;-1;-1;-1;-1;-1;-1;-1 ;;;;;;;;;;;; P13647;CONP13647 P13647;CONP13647 7;7 5;5 1;1 Keratin, type II cytoskeletal 5 KRT5 sp|P13647|K2C5_HUMAN Keratin, type II cytoskeletal 5 OS=Homo sapiens OX=9606 GN=KRT5 PE=1 SV=3; 2 7 5 1 4 5 2 5 2 4 4 5 5 3 4 2 3 1 3 3 4 4 1 1 0 0 1 1 0 1 0 10.3 8.6 1.5 62.378 590 590;590 0 323.31 By matching By matching By matching By MS/MS By matching By MS/MS By matching By MS/MS By MS/MS 6.6 8.3 3.4 7.1 3.2 6.3 6.8 8 8.5 10379000 1074800 1597900 398680 1204100 119470 726360 522610 1779700 2955700 603920 411430 330310 430660 0 170540 113180 609160 534930 0 0 0 1 0 1 0 2 4 8 AQYEEIANR;NKYEDEINKR;RQLDSIVGER;VDALMDEINFMK;WTLLQEQGTK;YEDEINKR;YEELQQTAGR + 23 233;2380;2680;3184;3497;3530;3534 True;False;True;True;True;False;True 237;2412;2715;3223;3538;3571;3575 1297;1298;1299;1300;1301;13954;13955;13956;13957;13958;15677;15678;15679;15680;15681;15682;15683;18348;18349;20176;20177;20178;20179;20180;20181;20411;20412;20413;20414;20427;20428;20429;20430;20431;20432;20433;20434 434;4404;4405;4911;5773;5774;6346;6347;6409;6413;6414 434;4405;4911;5773;6347;6409;6414 7;8 297;303 -1;-1 ; P19013;CONP19013 P19013;CONP19013 2;2 1;1 1;1 Keratin, type II cytoskeletal 4 KRT4 sp|P19013|K2C4_HUMAN Keratin, type II cytoskeletal 4 OS=Homo sapiens OX=9606 GN=KRT4 PE=1 SV=5; 2 2 1 1 1 1 0 1 1 2 1 1 1 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 4 4 4 56.143 520 520;594 0 84.898 By matching By matching None By matching By matching By MS/MS By matching By matching By matching 1.7 1.7 0 1.7 1.7 4 1.7 1.7 1.7 55723 0 0 0 0 0 55723 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 AQYEEIAQR;NLDLDSIIAEVRAQYEEIAQR + 24 234;2383 False;True 238;2415 1302;1303;1304;1305;1306;1307;1308;1309;1310;13975 435;436;437;438;4410 438;4410 -1;-1 ; P20930;CONP20930 P20930;CONP20930 1;1 1;1 1;1 Filaggrin FLG sp|P20930|FILA_HUMAN Filaggrin OS=Homo sapiens OX=9606 GN=FLG PE=1 SV=3; 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0.4 0.4 0.4 435.16 4061 4061;4061 0 129.41 By matching By matching By matching By matching By matching By matching By matching By matching By MS/MS 0.4 0.4 0.4 0.4 0.4 0.4 0.4 0.4 0.4 805370 175160 261940 79726 47861 35908 39506 14480 34848 115950 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 STLLENIFAIINLFK + 25 2890 True 2927 16713;16714;16715;16716;16717;16718;16719;16720;16721 5237 5237 -1;-1 ; P35527;CONP35527 P35527;CONP35527 11;11 11;11 11;11 Keratin, type I cytoskeletal 9 KRT9 sp|P35527|K1C9_HUMAN Keratin, type I cytoskeletal 9 OS=Homo sapiens OX=9606 GN=KRT9 PE=1 SV=3; 2 11 11 11 2 3 1 7 6 8 7 8 10 2 3 1 7 6 8 7 8 10 2 3 1 7 6 8 7 8 10 23.4 23.4 23.4 62.064 623 623;623 0 323.31 By matching By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 4.3 6.6 2.6 12.7 12 14.1 12.8 17.2 21.5 39003000 1130000 885650 400880 13525000 813350 1637600 2289700 9024800 9295400 453180 169060 0 1518800 110530 279770 343890 2055200 1686000 0 1 1 1 2 2 3 6 8 24 DQIVDLTVGNNK;HGVQELEIELQSQLSK;HGVQELEIELQSQLSKK;IQDWYDKK;NHKEEMSQLTGQNSGDVNVEINVAPGK;NYSPYYNTIDDLK;QEYEQLIAK;QGVDADINGLR;SDLEMQYETLQEELMALKK;SGGGGGGGLGSGGSIR;VQALEEANNDLENK + 26 514;1329;1330;1584;2359;2478;2550;2558;2718;2759;3368 True;True;True;True;True;True;True;True;True;True;True 522;1346;1347;1602;2391;2512;2584;2592;2753;2796;3409 2907;2908;7875;7876;7877;7878;7879;7880;7881;7882;7883;7884;7885;7886;9363;9364;9365;9366;9367;13824;13825;14632;14633;14634;14635;14636;14995;14996;14997;14998;14999;15031;15032;15033;15034;15035;15869;16073;16074;16075;16076;16077;16078;16079;16080;16081;16082;19375;19376;19377;19378;19379;19380 933;2540;2541;2542;3018;4368;4369;4605;4606;4607;4608;4716;4728;4958;5025;5026;5027;5028;5029;5030;5031;6101;6102;6103 933;2541;2542;3018;4369;4607;4716;4728;4958;5025;6103 9;10 276;286 -1;-1 ; P35908;CONP35908v2;CONP35908;CONENSEMBL:ENSBTAP00000038253 P35908;CONP35908v2;CON__P35908 15;15;15;3 13;13;13;1 12;12;12;0 Keratin, type II cytoskeletal 2 epidermal KRT2 sp|P35908|K22E_HUMAN Keratin, type II cytoskeletal 2 epidermal OS=Homo sapiens OX=9606 GN=KRT2 PE=1 SV=2;; 4 15 13 12 9 8 6 14 10 13 12 12 13 8 7 5 12 9 11 11 11 11 7 6 5 11 8 10 10 10 10 29.4 26.3 24.9 65.432 639 639;639;645;606 0 323.31 By matching By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 19.7 18.2 11.1 28 19.4 27.2 21.1 22.5 25 73303000 2242400 3238000 1192400 17358000 4404300 10590000 5975700 12884000 15418000 1323300 849170 521940 1456500 451190 566770 555640 976020 1423700 0 4 1 1 2 2 4 7 9 30 AQYEEIAQR;EEAEALYHSK;FLEQQNQVLQTK;GGSSSGGGYGSGGGGSSSVK;HGGGGGGFGGGGFGSR;LNDLEEALQQAK;MSGDLSSNVTVSVTSSTISSNVASK;NKLNDLEEALQQAK;NVQDAIADAEQR;TSQNSELNNMQDLVEDYKK;TAAENDFVTLKK;WELLQQMNVGTR;YEDEINKR;YEELQVTVGR;YLDGLTAER + 27 234;621;947;1127;1322;1993;2278;2378;2466;3102;3151;3466;3530;3535;3586 True;True;False;True;True;True;True;True;True;True;True;True;False;True;True 238;629;960;1141;1339;2014;2306;2410;2500;3141;3190;3507;3571;3576;3627 1302;1303;1304;1305;1306;1307;1308;1309;1310;3666;3667;3668;3669;3670;3671;3672;3673;5519;5520;5521;5522;5523;5524;5525;5526;5527;5528;5529;5530;5531;5532;6671;6672;6673;6674;6675;6676;7837;7838;7839;7840;7841;7842;7843;7844;11683;11684;11685;11686;11687;11688;11689;13367;13368;13369;13370;13371;13372;13947;13948;13949;13950;14560;14561;14562;14563;14564;14565;14566;14567;17931;17932;17933;17934;17935;18174;18175;18176;18177;18178;18179;18180;20010;20011;20012;20013;20014;20411;20412;20413;20414;20435;20436;20437;20438;20439;20440;20441;20725;20726;20727;20728;20729;20730;20731;20732;20733;20734;20735 435;436;437;438;1151;1152;1153;1762;1763;1764;2143;2144;2529;2530;2531;2532;3695;3696;3697;4228;4402;4580;4581;4582;4583;4584;5641;5717;6302;6409;6415;6416;6510;6511 438;1152;1762;2144;2529;3696;4228;4402;4583;5641;5717;6302;6409;6416;6510 11 216 -1;-1;-1;-1 ;;; Q04695;CONQ9QWL7;CONQ04695 Q04695;CONQ9QWL7;CONQ04695 4;4;4 2;2;2 2;2;2 Keratin, type I cytoskeletal 17 KRT17 sp|Q04695|K1C17_HUMAN Keratin, type I cytoskeletal 17 OS=Homo sapiens OX=9606 GN=KRT17 PE=1 SV=2;; 3 4 2 2 4 2 2 3 1 3 3 3 4 2 1 1 1 0 1 2 1 2 2 1 1 1 0 1 2 1 2 13.7 8.3 8.3 48.105 432 432;433;432 0 21.716 By matching By matching By matching By matching By matching By matching By MS/MS By matching By MS/MS 13.7 5.3 5.3 8.3 3 8.3 11.3 8.3 13.7 1166300 517160 195760 18961 111400 0 57428 111670 31376 122580 0 0 0 0 0 0 26261 0 35354 0 0 0 0 0 0 1 0 1 2 EVATNSELVQSGK;LLEGEDAHLTQYK;NHEEEMNALR;YCVQLSQIQGLIGSVEEQLAQLR + 28 828;1943;2357;3520 False;True;False;True 837;1963;2389;3561 4782;4783;4784;4785;4786;4787;4788;11424;11425;11426;11427;11428;11429;11430;11431;13812;13813;13814;13815;13816;13817;13818;20361;20362;20363 1489;3617;4366;6394 1489;3617;4366;6394 -1;-1;-1 ;; Q3SY84;Q7RTS7;Q86Y46;Q14CN4;CONQ14CN4-1;CONQ6IME9;CONQ3SY84;CONQ7RTS7;CONQ32MB2 Q3SY84;Q7RTS7;Q86Y46;Q14CN4;CONQ14CN4-1;CONQ6IME9;CONQ3SY84;CONQ7RTS7;CONQ32MB2 1;1;1;1;1;1;1;1;1 1;1;1;1;1;1;1;1;1 1;1;1;1;1;1;1;1;1 Keratin, type II cytoskeletal 71;Keratin, type II cytoskeletal 74;Keratin, type II cytoskeletal 73;Keratin, type II cytoskeletal 72 KRT71;KRT74;KRT73;KRT72 sp|Q3SY84|K2C71_HUMAN Keratin, type II cytoskeletal 71 OS=Homo sapiens OX=9606 GN=KRT71 PE=1 SV=3;sp|Q7RTS7|K2C74_HUMAN Keratin, type II cytoskeletal 74 OS=Homo sapiens OX=9606 GN=KRT74 PE=1 SV=2;sp|Q86Y46|K2C73_HUMAN Keratin, type II cytoskeletal 73 OS=Ho 9 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2.3 2.3 2.3 57.291 523 523;529;540;511;511;520;523;529;540 0 77.996 By matching By MS/MS By matching By matching By matching By matching By matching By matching By MS/MS 2.3 2.3 2.3 2.3 2.3 2.3 2.3 2.3 2.3 6143200 651170 1018500 407480 796250 134590 588340 318870 758220 1469700 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 3 4 FLEQQNQVLETK + 29 946 True 959 5502;5503;5504;5505;5506;5507;5508;5509;5510;5511;5512;5513;5514;5515;5516;5517;5518 1758;1759;1760;1761 1759 -1;-1;-1;-1;-1;-1;-1;-1;-1 ;;;;;;;; P06396;CONQ3SX14 P06396;CONQ3SX14 3;3 3;3 3;3 Gelsolin GSN sp|P06396|GELS_HUMAN Gelsolin OS=Homo sapiens OX=9606 GN=GSN PE=1 SV=1; 2 3 3 3 2 3 3 2 3 3 2 2 1 2 3 3 2 3 3 2 2 1 2 3 3 2 3 3 2 2 1 4.6 4.6 4.6 85.696 782 782;781 0 66.226 By matching By MS/MS By matching By matching By MS/MS By matching By matching By matching By matching 3.1 4.6 4.6 2.7 4.6 4.6 2.7 3.5 1.9 9695700 154390 3985600 1850800 150070 2838100 373290 93188 176510 73714 113840 356730 280340 90438 945260 109420 69552 94997 0 0 1 0 0 3 0 0 0 0 4 DSQEEEKTEALTSAK;PALPAGTEDTAK;YIETDPANR + 30 533;2487;3572 True;True;True 541;2521;3613 3006;3007;3008;3009;3010;3011;3012;14677;14678;14679;14680;14681;14682;14683;20643;20644;20645;20646;20647;20648;20649 963;4625;6484;6485 963;4625;6485 -1;-1 ; Q5D862;CONQ5D862 Q5D862;CONQ5D862 3;3 3;3 3;3 Filaggrin-2 FLG2 sp|Q5D862|FILA2_HUMAN Filaggrin-2 OS=Homo sapiens OX=9606 GN=FLG2 PE=1 SV=1; 2 3 3 3 3 3 3 2 0 2 2 3 2 3 3 3 2 0 2 2 3 2 3 3 3 2 0 2 2 3 2 1.3 1.3 1.3 248.07 2391 2391;2391 0 158 By matching By matching By MS/MS By matching None By MS/MS By matching By MS/MS By MS/MS 1.3 1.3 1.3 1.3 0 0.5 1.3 1.3 1.3 1062900 142530 451430 83699 27301 0 73879 30357 161590 92155 90676 101810 50563 0 0 17586 0 33708 0 0 0 1 0 0 2 0 1 1 5 LDFTEFLLMIFK;NPDDPDTVDVIMHMLDR;RLDFTEFLLMIFK + 31 1789;2414;2663 True;True;True 1808;2447;2698 10498;10499;10500;10501;10502;14191;14192;14193;14194;14195;14196;14197;14198;15591;15592;15593;15594;15595;15596;15597;15598 3342;3343;4472;4473;4883 3342;4473;4883 12;13 60;77 -1;-1 ; Q6KB66;CONQ6KB66-1 Q6KB66;CON__Q6KB66-1 1;1 1;1 1;1 Keratin, type II cytoskeletal 80 KRT80 sp|Q6KB66|K2C80_HUMAN Keratin, type II cytoskeletal 80 OS=Homo sapiens OX=9606 GN=KRT80 PE=1 SV=2; 2 1 1 1 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 3.1 3.1 3.1 50.525 452 452;452 0 6.7017 None By MS/MS None None None None None None None 0 3.1 0 0 0 0 0 0 0 37347 0 37347 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 TAEEQGELAFQDAK + 32 2934 True 2971 16976 5322 5322 -1;-1 ; Q7Z794;CONQ7Z794 Q7Z794;CONQ7Z794 4;4 2;2 2;2 Keratin, type II cytoskeletal 1b KRT77 sp|Q7Z794|K2C1B_HUMAN Keratin, type II cytoskeletal 1b OS=Homo sapiens OX=9606 GN=KRT77 PE=1 SV=3; 2 4 2 2 2 2 3 3 1 2 2 1 4 1 1 2 1 0 0 1 0 2 1 1 2 1 0 0 1 0 2 8.1 4.7 4.7 61.901 578 578;578 0 31.124 By matching By matching By MS/MS By MS/MS By matching By matching By matching By matching By matching 4.7 4.7 6.7 5.5 2.1 3.5 4.2 1.4 8.1 965190 139540 359430 135430 142140 0 0 24268 0 164380 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 2 FLEQQNQVLQTK;LQDLEEALQQSK;QIEQMQSLISDAEER;YEDEINKR + 33 947;2028;2564;3530 False;True;True;False 960;2049;2598;3571 5519;5520;5521;5522;5523;5524;5525;5526;5527;5528;5529;5530;5531;5532;11912;11913;11914;11915;15063;15064;15065;15066;20411;20412;20413;20414 1762;1763;1764;3764;4734;6409 1762;3764;4734;6409 -1;-1 ; E9PAV3;Q13765;Q9BZK3 E9PAV3;Q13765;Q9BZK3 2;2;1 2;2;1 2;2;1 Nascent polypeptide-associated complex subunit alpha, muscle-specific form;Nascent polypeptide-associated complex subunit alpha;Putative nascent polypeptide-associated complex subunit alpha-like protein NACA;NACA4P sp|E9PAV3|NACAM_HUMAN Nascent polypeptide-associated complex subunit alpha, muscle-specific form OS=Homo sapiens OX=9606 GN=NACA PE=1 SV=1;sp|Q13765|NACA_HUMAN Nascent polypeptide-associated complex subunit alpha OS=Homo sapiens OX=9606 GN=NACA PE=1 SV=1;s 3 2 2 2 1 1 1 0 0 1 1 2 1 1 1 1 0 0 1 1 2 1 1 1 1 0 0 1 1 2 1 1.3 1.3 1.3 205.42 2078 2078;215;213 0 12.408 By matching By matching By matching None None By matching By MS/MS By MS/MS By matching 0.6 0.6 0.6 0 0 0.7 0.6 1.3 0.6 1362600 35245 42106 49933 0 0 80013 465850 401490 287970 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 2 NILFVITKPDVYK;SPASDTYIVFGEAK 34 2370;2832 True;True 2402;2869 13886;13887;13888;13889;13890;13891;16437;16438 4387;5142 4387;5142 -1;-1;-1 ;; P01857;G1m1|JHW;P0DOX5;P4MS7_322_5831650_H|JHW;P4MS16_73_5834961_H|JHW;MVN_H|JHW;P4MS6_274_5832372_H|JHW;P4MS2_25_5830775_H|JHW;P4MS9_39_5832501_H|JHW;P4MS21_162_5835047_H|JHW;P4MS12_146_5834563_H|JHW;P4MS27_14_5835783_H|JHW;P4MS26_85_5841729_H|JHW;P4MS9_178_5832590_H|JHW;P4MS19_266_5835761_H|JHW;P4MS21_165_5835131_H|JHW;P4MS1_300_5830763_H|JHW;P4MS2_80_5830805_H|JHW;P4MS16_50_5834917_H|JHW;P4MS23_311_5841750_H|JHW;P4MS26_38_5841653_H|JHW;P4MS16_58_5834929_H|JHW;P4MS7_307_5831688_H|JHW;P4MS7_372_5831683_H|JHW;P4MS12_88_5834473_H|JHW;P4MS2_30_5830787_H|JHW;P4MS28_115_5841778_H|JHW;P01861 P01857;G1m1|JHW;P0DOX5 11;11;11;2;2;2;2;2;2;2;2;2;2;2;2;2;2;2;2;2;2;2;2;2;2;2;2;1 11;11;11;2;2;2;2;2;2;2;2;2;2;2;2;2;2;2;2;2;2;2;2;2;2;2;2;1 1;1;1;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0 Immunoglobulin heavy constant gamma 1;Immunoglobulin gamma-1 heavy chain IGHG1 sp|P01857|IGHG1_HUMAN Immunoglobulin heavy constant gamma 1 OS=Homo sapiens OX=9606 GN=IGHG1 PE=1 SV=1;G1m1|JHW;sp|P0DOX5|IGG1_HUMAN Immunoglobulin gamma-1 heavy chain OS=Homo sapiens OX=9606 PE=1 SV=2 28 11 11 1 9 9 8 7 7 8 8 9 10 9 9 8 7 7 8 8 9 10 1 1 0 0 0 1 0 0 1 47.6 47.6 4.8 36.105 330 330;330;449;155;148;145;161;160;160;160;158;158;157;156;156;155;149;154;154;154;153;153;153;153;151;150;155;327 0 323.31 By matching By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 42.4 42.4 40.9 37.6 37.6 42.4 40.9 46.1 47.6 162500000 19381000 11591000 10049000 13967000 9741000 9477600 18965000 29808000 39524000 6520600 2028000 3850600 1711800 918890 851180 1919700 2034400 5358000 0 10 5 1 10 4 10 21 26 87 EPQVYTLPPSR;EPQVYTLPPSRDELTK;FNWYVDGVEVHNAK;GPSVFPLAPSSK;STSGGTAALGCLVK;THTCPPCPAPELLGGPSVFLFPPK;THTCPPCPAPELLGGPSVFLFPPKPK;TPEVTCVVVDVSHEDPEVK;TTPPVLDSDGSFFLYSK;VVSVLTVLHQDWLNGK;WQQGNVFSCSVMHEALHNHYTQK 35 778;779;969;1201;2892;3008;3009;3070;3117;3435;3492 True;True;True;True;True;True;True;True;True;True;True 787;788;982;1217;2929;3046;3047;3109;3156;3476;3533 4526;4527;4528;4529;4530;4531;4532;4533;4534;4535;5631;5632;5633;5634;5635;5636;5637;5638;5639;5640;5641;5642;5643;5644;5645;5646;5647;5648;5649;5650;5651;5652;5653;5654;5655;5656;5657;5658;5659;5660;5661;5662;5663;5664;5665;5666;5667;5668;5669;5670;5671;5672;5673;5674;5675;5676;5677;5678;5679;5680;5681;5682;5683;5684;5685;5686;5687;5688;5689;5690;5691;5692;5693;5694;5695;5696;5697;5698;5699;5700;5701;5702;5703;5704;5705;5706;5707;5708;5709;5710;5711;5712;5713;5714;5715;5716;5717;5718;5719;5720;5721;5722;5723;5724;5725;5726;5727;5728;5729;5730;5731;5732;5733;5734;5735;5736;5737;5738;5739;5740;5741;5742;5743;5744;5745;5746;5747;5748;5749;5750;5751;5752;5753;5754;5755;5756;5757;5758;5759;5760;5761;5762;5763;5764;5765;5766;5767;5768;5769;5770;5771;5772;5773;5774;5775;5776;5777;5778;5779;5780;5781;5782;5783;5784;5785;5786;5787;7178;7179;7180;7181;7182;7183;7184;7185;7186;7187;16725;16726;16727;16728;16729;16730;16731;16732;16733;16734;16735;16736;16737;16738;16739;16740;16741;16742;16743;16744;16745;17379;17380;17381;17382;17383;17384;17385;17386;17387;17388;17389;17390;17391;17392;17393;17394;17395;17396;17397;17398;17399;17400;17401;17402;17403;17404;17405;17717;17718;17719;17720;17721;17722;17723;17724;17725;17726;17727;17728;17729;17730;17731;17732;17733;17734;17735;17736;17737;17738;17739;17740;17741;17742;17743;17744;17745;17746;17747;17748;17749;17750;17751;17752;17753;17754;17755;17756;17757;18006;18007;18008;19791;19792;19793;19794;19795;19796;19797;19798;19799;19800;19801;19802;19803;19804;19805;19806;19807;19808;19809;19810;19811;19812;19813;19814;19815;19816;19817;19818;19819;19820;19821;19822;19823;19824;19825;19826;19827;19828;19829;19830;19831;19832;19833;19834;19835;19836;19837;20135;20136;20137;20138;20139;20140;20141;20142;20143;20144;20145;20146;20147;20148;20149 1414;1415;1416;1801;1802;1803;1804;1805;1806;1807;1808;1809;1810;1811;1812;1813;1814;1815;1816;1817;1818;1819;1820;1821;1822;1823;1824;1825;1826;1827;1828;1829;1830;1831;1832;1833;1834;1835;1836;1837;1838;1839;1840;1841;1842;1843;1844;2318;2319;5240;5241;5242;5243;5244;5465;5466;5467;5468;5469;5470;5577;5578;5579;5580;5581;5582;5583;5584;5585;5586;5587;5665;5666;6234;6235;6236;6237;6238;6239;6240;6241;6242;6243;6244;6245;6338;6339 1414;1415;1806;2319;5243;5465;5469;5584;5666;6244;6338 14 311 -1;-1;-1;-1;-1;-1;-1;-1;-1;-1;-1;-1;-1;-1;-1;-1;-1;-1;-1;-1;-1;-1;-1;-1;-1;-1;-1;-1 ;;;;;;;;;;;;;;;;;;;;;;;;;;; P63165;G2XKQ0 P63165;G2XKQ0 1;1 1;1 1;1 Small ubiquitin-related modifier 1;Small ubiquitin-related modifier 5 SUMO1;SUMO1P1 sp|P63165|SUMO1_HUMAN Small ubiquitin-related modifier 1 OS=Homo sapiens OX=9606 GN=SUMO1 PE=1 SV=1;sp|G2XKQ0|SUMO5_HUMAN Small ubiquitin-related modifier 5 OS=Homo sapiens OX=9606 GN=SUMO1P1 PE=1 SV=2 2 1 1 1 0 0 0 0 1 1 0 0 1 0 0 0 0 1 1 0 0 1 0 0 0 0 1 1 0 0 1 11.9 11.9 11.9 11.557 101 101;101 0.0080321 5.6836 None None None None By MS/MS By matching None None By matching 0 0 0 0 11.9 11.9 0 0 11.9 111830 0 0 0 0 69328 35775 0 0 6727.7 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 1 VIGQDSSEIHFK 36 3273 True 3312 18841;18842;18843 5928 5928 -1;-1 ; gCAM_H|JHW gCAM_H|JHW 1 1 1 gCAM_H|JHW 1 1 1 1 1 1 1 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 16.4 16.4 16.4 12.803 116 116 0 7.0576 By matching By MS/MS By MS/MS None None None None None None 16.4 16.4 16.4 0 0 0 0 0 0 268750 82217 47097 139440 0 0 0 0 0 0 42408 0 44357 0 0 0 0 0 0 0 1 2 0 0 0 0 0 0 3 LSCVSSGFTFSNYWMSWVR 37 2063 True 2084 12099;12100;12101;12102;12103 3814;3815;3816 3814 -1
gCAM_K|JHW;P4MS2_30_5831081_K|JHW;P4MS16_73_5835241_K|JHW;P4MS6_274_5833045_K|JHW;P4MS19_266_5835649_K|JHW;P4MS7_372_5831914_K|JHW;P4MS7_322_5831879_K|JHW;P4MS21_165_5835423_K|JHW;P4MS9_39_5833164_K|JHW;P4MS2_80_5831104_K|JHW;P4MS16_50_5835198_K|JHW;P4MS9_78_5833058_K|JHW;P4MS16_58_5835209_K|JHW;P4MS23_311_5841860_K|JHW;P4MS26_85_5841907_K|JHW;P4MS28_115_5841914_K|JHW;P4MS7_307_5831921_K|JHW;P4MS12_146_5834659_K|JHW;P4MS1_300_5831056_K|JHW;P4MS2_25_5831067_K|JHW;MVN_K|JHW gCAM_K|JHW 4;1;1;1;1;1;1;1;1;1;1;1;1;1;1;1;1;1;1;1;1 4;1;1;1;1;1;1;1;1;1;1;1;1;1;1;1;1;1;1;1;1 3;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0 gCAM_K|JHW 21 4 4 3 4 3 4 1 2 0 1 1 1 4 3 4 1 2 0 1 1 1 3 3 3 1 2 0 1 1 1 36 36 24 16.567 150 150;144;146;147;147;146;146;146;146;146;146;145;145;145;145;145;145;145;145;145;152 0 323.31 By MS/MS By MS/MS By MS/MS By matching By matching None By matching By matching By matching 36 24 36 7.3 18 0 7.3 7.3 7.3 17751000 1299100 10839000 3037900 524420 432440 0 675770 496220 445420 2116500 1777200 1632300 0 329710 0 0 0 0 4 2 5 0 0 0 0 0 0 11 FSGSGSGTDFTLEISR;SSQSLVYSDGR;TVAAPSVFIFPPSDEQLK;TYLNWFQQR 38 992;2875;3138;3146 True;True;True;True 1005;2912;3177;3185 5911;5912;5913;5914;5915;5916;5917;5918;5919;5920;5921;5922;5923;5924;16618;16619;16620;16621;16622;16623;16624;16625;16626;18112;18113;18150;18151;18152;18153;18154;18155 1882;1883;1884;1885;1886;1887;5209;5210;5697;5709;5710 1882;5210;5697;5709 -1;-1;-1;-1;-1;-1;-1;-1;-1;-1;-1;-1;-1;-1;-1;-1;-1;-1;-1;-1;-1 ;;;;;;;;;;;;;;;;;;;; Lambda|JHW;P0DOY2;P0DOY3;B9A064;P0CG04;P0DOX8;P0CF74 Lambda|JHW;P0DOY2;P0DOY3;B9A064;P0CG04;P0DOX8 8;8;7;4;4;4;3 7;7;6;3;3;3;3 5;5;5;1;1;1;1 Immunoglobulin lambda constant 2;Immunoglobulin lambda constant 3;Immunoglobulin lambda-like polypeptide 5;Immunoglobulin lambda constant 1;Immunoglobulin lambda-1 light chain IGLC2;IGLC3;IGLL5;IGLC1 Lambda|JHW;sp|P0DOY2|IGLC2_HUMAN Immunoglobulin lambda constant 2 OS=Homo sapiens OX=9606 GN=IGLC2 PE=1 SV=1;sp|P0DOY3|IGLC3_HUMAN Immunoglobulin lambda constant 3 OS=Homo sapiens OX=9606 GN=IGLC3 PE=1 SV=1;sp|B9A064|IGLL5_HUMAN Immunoglobulin lambda-like 7 8 7 5 1 0 0 6 5 4 6 8 7 1 0 0 5 4 3 5 7 6 0 0 0 4 3 2 4 5 4 70.8 70.8 53.8 11.293 106 106;106;106;214;106;216;106 0 323.31 By matching None None By matching By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 14.2 0 0 67.9 67.9 61.3 67.9 70.8 70.8 19912000 18299 0 0 3233100 1228100 2789600 4547100 4392800 3703200 0 0 0 684880 285410 408180 561290 417460 544160 0 0 0 0 1 2 2 4 5 14 ADSSPVKAGVETTTPSK;ADSSPVKAGVETTTPSKQSNNK;AGVETTTPSKQSNNK;ATLVCLISDFYPGAVTVAWK;ATLVCLISDFYPGAVTVAWKADSSPVK;SYSCQVTHEGSTVEK;YAASSYLSLTPEQWK;YAASSYLSLTPEQWKSHR 39 29;30;97;277;278;2922;3674;3675 True;True;True;False;True;True;True;True 30;31;99;281;282;2959;3716;3717 208;209;210;211;212;213;590;591;592;593;594;595;1546;1547;1548;1549;1550;1551;1552;1553;1554;1555;1556;1557;1558;1559;1560;1561;1562;1563;1564;1565;1566;1567;1568;1569;1570;1571;1572;1573;1574;1575;1576;1577;1578;1579;1580;1581;1582;1583;1584;1585;1586;1587;1588;1589;1590;1591;1592;1593;1594;1595;1596;1597;1598;1599;1600;1601;1602;1603;1604;16903;16904;16905;16906;16907;16908;16909;16910;16911;16912;16913;16914;16915;16916;16917;16918;16919;16920;16921;16922;21213;21214;21215;21216;21217;21218;21219;21220;21221 76;77;78;209;520;521;522;523;524;525;526;527;528;529;530;531;532;533;534;5298;5299;5300;5301;5302;5303;5304;6664;6665 76;78;209;523;534;5301;6664;6665 -1;-1;-1;-1;-1;-1;-1 ;;;;;; NA2_H|JHW;P0DP02;P01767;A0A0C4DH42;P01772;A0A075B6Q5 NA2_H|JHW;P0DP02 6;3;1;1;1;1 4;3;1;1;1;1 2;1;0;0;0;1 Immunoglobulin heavy variable 3-30-3 IGHV3-30-3 NA2_H|JHW;sp|P0DP02|HVC33_HUMAN Immunoglobulin heavy variable 3-30-3 OS=Homo sapiens OX=9606 GN=IGHV3-30-3 PE=3 SV=1 6 6 4 2 3 2 2 6 6 5 2 2 3 1 0 0 4 4 3 0 0 1 1 0 0 2 2 2 0 0 0 63.7 45.9 28.1 15.49 146 146;117;116;116;117;118 0 323.31 By matching By matching By matching By MS/MS By MS/MS By MS/MS By matching By matching By MS/MS 32.9 17.8 17.8 63.7 63.7 56.2 17.8 17.8 25.3 55702000 6100.7 0 0 18322000 19626000 13517000 0 0 4231000 0 0 0 2589700 4015100 3353700 0 0 0 0 0 0 1 22 11 0 0 1 35 DLDGMDVWGQGTTVTVSSASTK;GLEWVAVISYDGSNK;GPSVFPLAPSSK;LSCAASGFTFSSYAMHWVR;NTLYLQMNSLR;STSGGTAALGCLVK 40 457;1173;1201;2065;2450;2892 True;True;False;True;True;False 465;1187;1217;2087;2484;2929 2573;2574;2575;2576;2577;2578;2579;2580;2581;2582;2583;2584;2585;2586;2587;2588;2589;2590;2591;2592;2593;2594;6938;6939;6940;6941;6942;6943;6944;6945;6946;6947;6948;6949;6950;6951;6952;6953;6954;6955;6956;6957;6958;6959;6960;6961;6962;6963;6964;6965;6966;6967;6968;6969;6970;6971;6972;6973;6974;6975;6976;6977;6978;6979;6980;6981;6982;6983;7178;7179;7180;7181;7182;7183;7184;7185;7186;7187;12165;12166;12167;12168;12169;14405;14406;14407;16725;16726;16727;16728;16729;16730;16731;16732;16733;16734;16735;16736;16737;16738;16739;16740;16741;16742;16743;16744;16745 833;834;835;836;837;838;839;840;841;842;2232;2233;2234;2235;2236;2237;2238;2239;2240;2241;2242;2243;2244;2245;2246;2247;2248;2249;2250;2251;2252;2318;2319;3842;3843;3844;4537;5240;5241;5242;5243;5244 837;2243;2319;3843;4537;5243 -1;-1;-1;-1;-1;-1 ;;;;; NA2_L|JHW;P01700 NA2_L|JHW 3;1 2;1 2;1 NA2_L|JHW 2 3 2 2 0 0 0 3 3 2 1 1 1 0 0 0 2 2 1 0 0 0 0 0 0 2 2 1 0 0 0 28.8 15.7 15.7 16.143 153 153;117 0 38.347 None None None By matching By MS/MS By MS/MS By matching By matching By matching 0 0 0 28.8 28.8 20.3 13.1 13.1 13.1 6624700 0 0 0 2812900 2206100 1605700 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 2 ATLVCLISDFYPGAVTVAWK;NNQRPSGVPDR;SGTSASLAISGLR 41 277;2408;2767 False;True;True 281;2441;2804 1546;1547;1548;1549;1550;1551;1552;1553;1554;1555;1556;1557;1558;1559;1560;1561;1562;1563;1564;1565;1566;1567;1568;1569;1570;1571;1572;1573;1574;1575;1576;1577;1578;1579;1580;1581;1582;1583;1584;1585;1586;1587;1588;1589;1590;1591;1592;1593;1594;1595;1596;1597;1598;1599;1600;14163;14164;14165;16116;16117 520;521;522;523;524;525;526;527;528;529;530;531;532;533;4464;5044 523;4464;5044 -1;-1 ; NR1_H|JHW;P01782;P0DP04;P01780;P01763;P01762;A0A0C4DH32;A0A0B4J1V1;P01766;A0A0B4J1X8 NR1_H|JHW 10;4;3;2;2;2;2;2;1;1 8;4;3;2;2;2;2;2;1;1 7;3;3;1;1;1;1;1;1;1 NR1_H|JHW 10 10 8 7 5 5 2 3 2 4 9 10 9 3 3 0 1 0 2 7 8 7 3 3 0 1 0 2 7 7 6 95.4 78.3 72.4 16.135 152 152;118;118;117;117;117;117;117;116;118 0 323.31 By matching By matching By matching By matching By matching By matching By MS/MS By MS/MS By MS/MS 59.2 49.3 17.1 24.3 17.1 36.8 89.5 95.4 88.2 117090000 1287000 242530 0 36744 0 96770 30035000 36478000 48916000 285710 35405 0 0 0 82274 3869600 5119400 4500700 0 0 0 0 0 0 15 21 37 73 AEDTALYYCAK;ASSWYAYGMDVWGQGTLVTVSSASTK;EVQLVESGGGLVQPGR;FTISRDNAK;GLEWVSGISWSSGSIGYADSVK;GPSVFPLAPSSK;LSCAASGFTFDDYAMHWVR;NSLYLQMNSLR;QVPGKGLEWVSGISWSSGSIGYADSVK;STSGGTAALGCLVK 42 40;258;838;1013;1174;1201;2064;2441;2638;2892 True;True;True;True;True;False;True;True;True;False 41;262;848;849;1026;1188;1217;2085;2086;2475;2672;2929 258;259;260;261;1448;1449;1450;1451;1452;1453;1454;1455;1456;4838;4839;4840;4841;4842;4843;4844;4845;4846;4847;4848;4849;4850;4851;4852;4853;4854;4855;4856;4857;4858;4859;4860;4861;4862;4863;4864;4865;4866;4867;4868;4869;4870;4871;4872;4873;4874;4875;4876;4877;4878;4879;4880;4881;4882;4883;4884;4885;4886;4887;4888;4889;6044;6045;6984;6985;6986;6987;6988;6989;6990;6991;6992;6993;6994;6995;6996;6997;6998;6999;7000;7001;7002;7003;7004;7005;7006;7007;7008;7009;7010;7011;7012;7178;7179;7180;7181;7182;7183;7184;7185;7186;7187;12104;12105;12106;12107;12108;12109;12110;12111;12112;12113;12114;12115;12116;12117;12118;12119;12120;12121;12122;12123;12124;12125;12126;12127;12128;12129;12130;12131;12132;12133;12134;12135;12136;12137;12138;12139;12140;12141;12142;12143;12144;12145;12146;12147;12148;12149;12150;12151;12152;12153;12154;12155;12156;12157;12158;12159;12160;12161;12162;12163;12164;14355;14356;14357;14358;14359;15442;15443;15444;15445;16725;16726;16727;16728;16729;16730;16731;16732;16733;16734;16735;16736;16737;16738;16739;16740;16741;16742;16743;16744;16745 94;95;96;483;484;485;1506;1507;1508;1509;1510;1511;1512;1513;1514;1515;1516;1517;1518;1519;1520;1521;1522;1523;1524;1525;1526;1527;1528;1529;1530;1531;1532;1937;2253;2254;2255;2256;2257;2258;2259;2260;2261;2262;2263;2318;2319;3817;3818;3819;3820;3821;3822;3823;3824;3825;3826;3827;3828;3829;3830;3831;3832;3833;3834;3835;3836;3837;3838;3839;3840;3841;4525;4842;4843;5240;5241;5242;5243;5244 94;485;1506;1937;2253;2319;3837;4525;4842;5243 15 34 -1;-1;-1;-1;-1;-1;-1;-1;-1;-1 ;;;;;;;;; NR1_L|JHW NR1_L|JHW 8 8 7 NR1_L|JHW 1 8 8 7 0 0 2 3 2 2 6 8 7 0 0 2 3 2 2 6 8 7 0 0 2 2 1 1 5 7 6 77.2 77.2 63.8 15.92 149 149 0 323.31 None None By matching By matching By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 0 0 21.5 34.9 24.2 24.2 67.1 77.2 77.2 102460000 0 0 28538 1099600 769970 633750 33075000 30673000 36182000 0 0 79093 572950 393270 347110 2427700 2170000 6788300 0 0 0 0 6 2 4 7 25 44 ATLVCLISDFYPGAVTVAWK;FSGSIDSSSNSASLIISGLK;FSGSIDSSSNSASLIISGLKTEDEADYYCQSTR;NFMLTQPHSVSESPGK;PGSSPTTVIYDDNQR;SSGSIASNYVQWYQQR;TEDEADYYCQSTR;VFGGGTKLTVLGQPK 43 277;994;995;2349;2492;2867;2963;3226 True;True;True;True;True;True;True;True 281;1007;1008;2379;2380;2381;2526;2904;3000;3265 1546;1547;1548;1549;1550;1551;1552;1553;1554;1555;1556;1557;1558;1559;1560;1561;1562;1563;1564;1565;1566;1567;1568;1569;1570;1571;1572;1573;1574;1575;1576;1577;1578;1579;1580;1581;1582;1583;1584;1585;1586;1587;1588;1589;1590;1591;1592;1593;1594;1595;1596;1597;1598;1599;1600;5927;5928;5929;5930;5931;5932;5933;5934;5935;5936;5937;5938;5939;5940;5941;5942;5943;5944;5945;5946;5947;5948;5949;5950;5951;5952;5953;5954;5955;13760;13761;13762;13763;13764;13765;13766;13767;13768;13769;13770;13771;14710;14711;16573;16574;16575;16576;16577;16578;16579;16580;16581;16582;17136;18578;18579;18580;18581;18582 520;521;522;523;524;525;526;527;528;529;530;531;532;533;1889;1890;1891;1892;1893;1894;1895;1896;1897;1898;1899;1900;1901;1902;1903;4344;4345;4346;4347;4348;4349;4634;5188;5189;5190;5377;5842;5843;5844;5845 523;1891;1903;4349;4634;5188;5377;5842 16 3 -1
O00151 O00151 2 2 2 PDZ and LIM domain protein 1 PDLIM1 sp|O00151|PDLI1_HUMAN PDZ and LIM domain protein 1 OS=Homo sapiens OX=9606 GN=PDLIM1 PE=1 SV=4 1 2 2 2 0 1 0 2 1 1 2 1 2 0 1 0 2 1 1 2 1 2 0 1 0 2 1 1 2 1 2 8.5 8.5 8.5 36.071 329 329 0 81.831 None By matching None By matching By matching By matching By MS/MS By MS/MS By MS/MS 0 4 0 8.5 4 4 8.5 4 8.5 1208500 0 10367 0 194030 207300 141700 219670 127320 308140 0 0 0 40491 0 0 52335 0 71729 0 0 0 0 0 0 1 1 2 4 GHFFVEDQIYCEK;VTPPEGYEVVTVFPK 44 1131;3411 True;True 1145;3452 6686;6687;6688;6689;6690;6691;6692;6693;19652;19653;19654 2149;2150;2151;6190 2151;6190 -1
O00154 O00154 2 2 2 Cytosolic acyl coenzyme A thioester hydrolase ACOT7 sp|O00154|BACH_HUMAN Cytosolic acyl coenzyme A thioester hydrolase OS=Homo sapiens OX=9606 GN=ACOT7 PE=1 SV=3 1 2 2 2 1 1 1 2 2 2 2 2 2 1 1 1 2 2 2 2 2 2 1 1 1 2 2 2 2 2 2 9.5 9.5 9.5 41.796 380 380 0 323.31 By matching By matching By matching By matching By MS/MS By MS/MS By matching By MS/MS By MS/MS 5.3 5.3 5.3 9.5 9.5 9.5 9.5 9.5 9.5 4761700 157930 245770 81761 699300 891620 877620 616650 599410 591630 0 0 0 0 140970 171450 0 129810 131410 0 0 0 0 1 1 0 1 1 4 IMRPDDANVAGNVHGGTILK;TNIVTASVDAINFHDK 45 1564;3060 True;True 1582;3099 9239;9240;9241;9242;9243;9244;9245;9246;9247;17672;17673;17674;17675;17676;17677 2967;5560;5561;5562 2967;5560 -1
O00170 O00170 1 1 1 AH receptor-interacting protein AIP sp|O00170|AIP_HUMAN AH receptor-interacting protein OS=Homo sapiens OX=9606 GN=AIP PE=1 SV=2 1 1 1 1 0 0 1 1 1 1 1 1 0 0 0 1 1 1 1 1 1 0 0 0 1 1 1 1 1 1 0 5.8 5.8 5.8 37.636 330 330 0.0092166 5.6543 None None By matching By MS/MS By matching By matching By matching By matching None 0 0 5.8 5.8 5.8 5.8 5.8 5.8 0 590190 0 0 40512 99260 106030 137850 92299 114250 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 VESPGTYQQDPWAMTDEEK 46 3215 True 3254 18519;18520;18521;18522;18523;18524 5827 5827 -1
O00178 O00178 2 2 2 GTP-binding protein 1 GTPBP1 sp|O00178|GTPB1_HUMAN GTP-binding protein 1 OS=Homo sapiens OX=9606 GN=GTPBP1 PE=1 SV=3 1 2 2 2 0 1 1 0 0 2 2 1 2 0 1 1 0 0 2 2 1 2 0 1 1 0 0 2 2 1 2 5.7 5.7 5.7 72.453 669 669 0 12.378 None By matching By matching None None By MS/MS By matching By matching By matching 0 2.8 2.8 0 0 5.7 5.7 2.8 5.7 799040 0 83101 47544 0 0 265190 207670 66421 129120 0 0 0 0 0 51791 65601 0 45293 0 0 0 0 0 2 0 0 0 2 EHLGLALALNVPVFVVVTK;MCPIFQISNVTGENLDLLK 47 678;2165 True;True 687;2187 3975;3976;3977;3978;12670;12671;12672;12673;12674 1249;4005 1249;4005 -1
O00192 O00192 1 1 1 Splicing regulator ARVCF ARVCF sp|O00192|ARVC_HUMAN Armadillo repeat protein deleted in velo-cardio-facial syndrome OS=Homo sapiens OX=9606 GN=ARVCF PE=1 SV=1 1 1 1 1 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 2 2 2 104.64 962 962 0.0015649 6.4585 None By MS/MS None None None None None None None 0 2 0 0 0 0 0 0 0 17189 0 17189 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 ECEGLVDALLHALQSAVGR 48 605 True 613 3585 1125 1125 -1
O00203 O00203 1 1 1 AP-3 complex subunit beta-1 AP3B1 sp|O00203|AP3B1_HUMAN AP-3 complex subunit beta-1 OS=Homo sapiens OX=9606 GN=AP3B1 PE=1 SV=3 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1.6 1.6 1.6 121.32 1094 1094 0 318.39 By matching By matching None By matching By matching By matching By matching By matching By MS/MS 1.6 1.6 0 1.6 1.6 1.6 1.6 1.6 1.6 500120 118220 31368 0 66866 50293 45665 44957 75979 66770 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 LEILTNLANEANISTLLR 49 1825 True 1844 10706;10707;10708;10709;10710;10711;10712;10713 3403 3403 -1
O00231 O00231 5 5 5 26S proteasome non-ATPase regulatory subunit 11 PSMD11 sp|O00231|PSD11_HUMAN 26S proteasome non-ATPase regulatory subunit 11 OS=Homo sapiens OX=9606 GN=PSMD11 PE=1 SV=3 1 5 5 5 1 3 3 4 2 5 5 3 5 1 3 3 4 2 5 5 3 5 1 3 3 4 2 5 5 3 5 18.2 18.2 18.2 47.463 422 422 0 323.31 By matching By MS/MS By MS/MS By matching By matching By matching By MS/MS By matching By MS/MS 6.6 12.1 12.1 15.4 10 18.2 18.2 12.1 18.2 6027500 25526 612370 351790 924750 423010 1606200 601960 715820 766110 0 218030 224860 161470 161400 127140 46275 148300 70125 0 1 2 0 0 0 3 0 3 9 DDPIISTHLAK;EASIDILHSIVK;SLLDLFLDMEAATGQEVELCLECIEWAK;TGQAAELGGLLK;TYEAALETIQNMSK 50 384;602;2804;2998;3143 True;True;True;True;True 391;610;2841;3036;3182 2184;2185;2186;2187;2188;2189;2190;3569;3570;3571;3572;3573;16291;16292;16293;16294;16295;16296;16297;16298;16299;17302;17303;17304;17305;17306;18137;18138;18139;18140;18141 719;1120;5096;5097;5098;5438;5439;5702;5703 719;1120;5096;5438;5702 -1
O00232 O00232 5 5 5 26S proteasome non-ATPase regulatory subunit 12 PSMD12 sp|O00232|PSD12_HUMAN 26S proteasome non-ATPase regulatory subunit 12 OS=Homo sapiens OX=9606 GN=PSMD12 PE=1 SV=3 1 5 5 5 3 2 3 5 4 4 4 3 5 3 2 3 5 4 4 4 3 5 3 2 3 5 4 4 4 3 5 15.6 15.6 15.6 52.904 456 456 0 323.31 By matching By MS/MS By MS/MS By MS/MS By MS/MS By matching By MS/MS By MS/MS By MS/MS 7.2 5.3 7.2 15.6 11.2 12.9 11.2 8.6 15.6 7018500 79855 252150 83947 1207100 1220100 1166000 1134300 880300 994620 59580 0 56195 163030 156120 151520 177030 169850 178500 0 1 1 1 1 0 3 3 3 13 DPNNLLNDWSQK;FFQEENTEK;MEVDYSATVDQR;MVQQCCTYVEEITDLPIK;YYNLMIQLDQHEGSYLSICK 51 505;914;2205;2295;3670 True;True;True;True;True 513;925;2231;2324;3711 2869;2870;2871;2872;2873;2874;2875;2876;2877;5327;5328;5329;5330;5331;5332;5333;5334;5335;5336;12897;12898;12899;12900;12901;12902;12903;12904;12905;12906;12907;12908;12909;12910;13467;13468;13469;13470;13471;13472;21169;21170;21171 918;919;920;1692;1693;1694;1695;1696;4090;4091;4256;4257;6651 919;1696;4090;4256;6651 -1
O00267 O00267 1 1 1 Transcription elongation factor SPT5 SUPT5H sp|O00267|SPT5H_HUMAN Transcription elongation factor SPT5 OS=Homo sapiens OX=9606 GN=SUPT5H PE=1 SV=1 1 1 1 1 0 0 0 1 1 0 1 0 1 0 0 0 1 1 0 1 0 1 0 0 0 1 1 0 1 0 1 1.1 1.1 1.1 121 1087 1087 0 260.8 None None None By matching By matching None By MS/MS None By MS/MS 0 0 0 1.1 1.1 0 1.1 0 1.1 171460 0 0 0 19246 19625 0 38429 0 94165 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 2 LGYWNQQMVPIK 52 1896 True 1916 11099;11100;11101;11102 3522;3523 3522 -1
O00291 O00291 2 2 2 Huntingtin-interacting protein 1 HIP1 sp|O00291|HIP1_HUMAN Huntingtin-interacting protein 1 OS=Homo sapiens OX=9606 GN=HIP1 PE=1 SV=5 1 2 2 2 1 1 2 2 1 2 1 1 1 1 1 2 2 1 2 1 1 1 1 1 2 2 1 2 1 1 1 4.1 4.1 4.1 116.22 1037 1037 0 177.03 By matching By matching By matching By matching By MS/MS By MS/MS By matching By MS/MS By matching 1.6 1.6 4.1 4.1 1.6 4.1 1.6 1.6 2.4 406810 18994 11885 52142 111030 25605 117100 20339 23465 26258 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1 0 3 GHVSELEADLAEQQHLR;QEELGDLVDKEMAATSAAIETATAR 53 1140;2542 True;True 1154;2576 6729;6730;6731;6732;6733;6734;6735;6736;14951;14952;14953;14954 2163;2164;4702 2163;4702 -1
O75610;O00292 O75610;O00292 1;1 1;1 1;1 Left-right determination factor 1;Left-right determination factor 2 LEFTY1;LEFTY2 sp|O75610|LFTY1_HUMAN Left-right determination factor 1 OS=Homo sapiens OX=9606 GN=LEFTY1 PE=2 SV=1;sp|O00292|LFTY2_HUMAN Left-right determination factor 2 OS=Homo sapiens OX=9606 GN=LEFTY2 PE=1 SV=2 2 1 1 1 0 0 0 1 1 1 1 1 1 0 0 0 1 1 1 1 1 1 0 0 0 1 1 1 1 1 1 4.4 4.4 4.4 40.88 366 366;366 0 30.231 None None None By matching By matching By matching By MS/MS By MS/MS By MS/MS 0 0 0 4.4 4.4 4.4 4.4 4.4 4.4 762240 0 0 0 53476 58099 85313 135800 220810 208740 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 3 AFDVTEAVNFWQQLSR 54 67 True 69 410;411;412;413;414;415 154;155;156 156 -1;-1 ; O00299 O00299 3 3 3 Chloride intracellular channel protein 1 CLIC1 sp|O00299|CLIC1_HUMAN Chloride intracellular channel protein 1 OS=Homo sapiens OX=9606 GN=CLIC1 PE=1 SV=4 1 3 3 3 0 0 0 3 2 2 3 2 3 0 0 0 3 2 2 3 2 3 0 0 0 3 2 2 3 2 3 16.6 16.6 16.6 26.922 241 241 0 308.97 None None None By matching By MS/MS By MS/MS By matching By MS/MS By MS/MS 0 0 0 16.6 12.9 11.2 16.6 12.9 16.6 32516000 0 0 0 4884600 5417500 5043900 5793600 5472000 5904800 0 0 0 1278700 1186700 0 1758500 3402800 1654000 0 0 0 0 2 1 0 1 3 7 IEEFLEAVLCPPR;LHIVQVVCK;LAALNPESNTAGLDIFAK 55 1447;1900;2149 True;True;True 1464;1920;2171 8569;8570;8571;8572;8573;11128;11129;11130;11131;11132;12603;12604;12605;12606;12607;12608 2751;2752;3532;3533;3975;3976;3977 2752;3533;3976 -1
O00303 O00303 2 2 2 Eukaryotic translation initiation factor 3 subunit F EIF3F sp|O00303|EIF3F_HUMAN Eukaryotic translation initiation factor 3 subunit F OS=Homo sapiens OX=9606 GN=EIF3F PE=1 SV=1 1 2 2 2 1 2 1 1 2 2 2 2 2 1 2 1 1 2 2 2 2 2 1 2 1 1 2 2 2 2 2 10.1 10.1 10.1 37.563 357 357 0 323.31 By matching By MS/MS By MS/MS By matching By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 5.3 10.1 5.3 4.8 10.1 10.1 10.1 10.1 10.1 10209000 642900 655460 592890 910520 1611700 2020500 1349000 1147900 1277900 0 156070 0 0 293190 359670 330850 291500 406710 0 1 1 0 1 1 1 1 2 8 IQDALSTVLQYAEDVLSGK;VIGLSSDLQQVGGASAR 56 1582;3272 True;True 1600;3311 9348;9349;9350;9351;9352;9353;9354;9355;18834;18835;18836;18837;18838;18839;18840 3009;3010;3011;3012;3013;3014;3015;5927 3009;5927 -1
O00330 O00330 1 1 1 Pyruvate dehydrogenase protein X component, mitochondrial PDHX sp|O00330|ODPX_HUMAN Pyruvate dehydrogenase protein X component, mitochondrial OS=Homo sapiens OX=9606 GN=PDHX PE=1 SV=3 1 1 1 1 0 1 1 0 1 0 0 0 0 0 1 1 0 1 0 0 0 0 0 1 1 0 1 0 0 0 0 3.2 3.2 3.2 54.122 501 501 0.0022814 6.2226 None By matching By matching None By MS/MS None None None None 0 3.2 3.2 0 3.2 0 0 0 0 226650 0 154960 42182 0 29509 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 1 LGSLIGLIVEEGEDWK 57 1889 True 1909 11064;11065;11066 3508 3508 -1
O00391 O00391 1 1 1 Sulfhydryl oxidase 1 QSOX1 sp|O00391|QSOX1_HUMAN Sulfhydryl oxidase 1 OS=Homo sapiens OX=9606 GN=QSOX1 PE=1 SV=3 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2.1 2.1 2.1 82.577 747 747 0 74.481 By matching By matching By matching By matching By matching By matching By matching By matching By MS/MS 2.1 2.1 2.1 2.1 2.1 2.1 2.1 2.1 2.1 734650 26239 27215 22464 111850 69525 124090 123940 112530 116790 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 DCASHFEQMAAASMHR 58 371 True 376 2100;2101;2102;2103;2104;2105;2106;2107;2108 696 696 -1
O00408 O00408 1 1 1 cGMP-dependent 3,5-cyclic phosphodiesterase PDE2A sp|O00408|PDE2A_HUMAN cGMP-dependent 3,5-cyclic phosphodiesterase OS=Homo sapiens OX=9606 GN=PDE2A PE=1 SV=1 1 1 1 1 0 0 1 1 1 0 0 1 0 0 0 1 1 1 0 0 1 0 0 0 1 1 1 0 0 1 0 1.6 1.6 1.6 105.72 941 941 0 7.3405 None None By matching By matching By MS/MS None None By matching None 0 0 1.6 1.6 1.6 0 0 1.6 0 460070 0 0 5110.3 76170 364880 0 0 13905 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 1 VFDGGVVDDESYEIR 59 3220 True 3259 18546;18547;18548;18549 5833 5833 -1
O00410 O00410 11 11 11 Importin-5 IPO5 sp|O00410|IPO5_HUMAN Importin-5 OS=Homo sapiens OX=9606 GN=IPO5 PE=1 SV=4 1 11 11 11 7 7 6 7 8 7 10 8 9 7 7 6 7 8 7 10 8 9 7 7 6 7 8 7 10 8 9 15.2 15.2 15.2 123.63 1097 1097 0 323.31 By matching By matching By MS/MS By matching By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 9.8 9.8 8.4 9.5 10.4 9.5 14.1 11 12.9 19792000 3368100 711150 1197200 1479200 1427700 1949400 3437100 3645500 2576500 633900 474270 615620 719800 598030 561970 1027300 914630 1043200 0 0 1 0 3 2 5 5 5 21 EFQQYLPVVMGPLMK;FMQDASDVMQLLLK;IFSIIAEGEMHEAIK;LCGDTSLNNMQR;LVLEQVVTSIASVADTAEEK;MLVQCMQDQEHPSIR;QAEETYENIPGQSK;QLALEVIVTLSETAAAMLR;STACQMLVCYAK;VIAALLQTMEDQGNQR;YLRPHLEATLQLSLK 60 645;959;1479;1773;2115;2247;2520;2575;2883;3285;3601 True;True;True;True;True;True;True;True;True;True;True 653;972;1496;1792;2137;2274;2554;2609;2920;3324;3642 3805;3806;3807;3808;3809;3810;3811;3812;5581;5582;5583;8729;8730;8731;8732;8733;8734;8735;8736;8737;10383;10384;10385;10386;10387;10388;10389;10390;12423;12424;13209;13210;13211;13212;13213;13214;13215;13216;13217;14844;14845;15123;15124;15125;15126;15127;15128;15129;15130;16668;16669;16670;16671;18907;18908;18909;18910;18911;18912;18913;18914;18915;20818;20819;20820;20821;20822;20823;20824;20825;20826 1194;1195;1784;2797;2798;2799;2800;3310;3311;3312;3313;3915;4182;4183;4672;4750;4751;5221;5951;5952;6535 1194;1784;2799;3311;3915;4183;4672;4750;5221;5952;6535 -1
O00429 O00429 7 7 7 Dynamin-1-like protein DNM1L sp|O00429|DNM1L_HUMAN Dynamin-1-like protein OS=Homo sapiens OX=9606 GN=DNM1L PE=1 SV=2 1 7 7 7 2 3 3 5 5 3 2 4 2 2 3 3 5 5 3 2 4 2 2 3 3 5 5 3 2 4 2 16 16 16 81.876 736 736 0 316.14 By matching By MS/MS By MS/MS By matching By MS/MS By MS/MS By MS/MS By MS/MS By MS/MS 4.9 7.2 7.2 12.4 12.4 7.3 5.2 8.4 3.4 9587800 229350 1598700 992500 1153400 1816600 1520600 518370 1030800 727580 187360 259830 251230 175830 204890 235620 293020 236560 365860 0 1 1 0 4 1 1 3 2 13 FATEYCNTIEGTAK;LYTDFDEIRQEIENETER;MEALIPVINK;PALFVPEVSFELLVK;RLPVTNEMVHNLVAIELAYINTK;SSLLDDLLTESEDMAQR;TLESVDPLGGLNTIDILTAIR 61 876;2145;2184;2486;2666;2869;3030 True;True;True;True;True;True;True 887;2167;2209;2520;2701;2906;3068 5081;5082;5083;12588;12589;12590;12800;12801;14668;14669;14670;14671;14672;14673;14674;14675;14676;15612;15613;15614;15615;16587;16588;17505;17506;17507;17508;17509;17510 1600;1601;3971;4047;4048;4620;4621;4622;4623;4624;4890;5192;5512 1600;3971;4048;4620;4890;5192;5512 -1
O00442 O00442 1 1 1 RNA 3-terminal phosphate cyclase RTCA sp|O00442|RTCA_HUMAN RNA 3-terminal phosphate cyclase OS=Homo sapiens OX=9606 GN=RTCA PE=1 SV=1 1 1 1 1 0 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 3.8 3.8 3.8 39.336 366 366 0 46.78 None By matching By matching By matching By matching By matching By matching By matching By MS/MS 0 3.8 3.8 3.8 3.8 3.8 3.8 3.8 3.8 3416400 0 1512100 564770 90849 454780 188140 211970 222160 171590 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 VGIEAAEMLLANLR 62 3250 True 3289 18693;18694;18695;18696;18697;18698;18699;18700 5880 5880 -1
O00468 O00468 3 3 3 Agrin;Agrin N-terminal 110 kDa subunit;Agrin C-terminal 110 kDa subunit;Agrin C-terminal 90 kDa fragment;Agrin C-terminal 22 kDa fragment AGRN sp|O00468|AGRIN_HUMAN Agrin OS=Homo sapiens OX=9606 GN=AGRN PE=1 SV=6 1 3 3 3 1 0 0 1

Johanhw-ms commented 2 months ago

Hello,

Following up on that last e-mail: I now ran the analysis on the newest MaxQuant with only the UniProt database, and do get ca. 200 more proteins than before (ca 1700 in total). However, that is still ca 1300 less than when we used the old version. Are you sure you got ca 3300 hits with the "split protein groups by taxonomy ID" turned off?

Best regards, Johanna

From: Johanna Henny Wagnerberger Sent: 09 September 2024 09:25:57 To: cox-labs/CoxLab_Bug_Reporting; cox-labs/CoxLab_Bug_Reporting Cc: Author Subject: Re: [cox-labs/CoxLab_Bug_Reporting] Different MaxQuant versions identify vastly different number of Protein groups via MS/MS in the same sample (Issue #110)

Hello Jinqiu,

I tried this on our PC now, but I still got about 1500 hits.

See attached mqpar and the resulting proteingroups file (I unchecked "split protein groups by taxonomy ID" and changed the identifier for my homemade fasta file to ">.") This time, I ran MQ v.2.6.4.0 with .NET 8.0.302.

But I also don't understand how trouble with identifying taxonomy IDs can lead to the loss of so many protein hits. My homemade fasta only contains 54 sequences, and they are all IgG, so they should only group with immunoglobulin sequences in the UniProt file.

Thank you for looking into this!

Best regards,

Johanna

From: JinqiuXiao @.***> Sent: 05 September 2024 10:46:54 To: cox-labs/CoxLab_Bug_Reporting Cc: Johanna Henny Wagnerberger; Author Subject: Re: [cox-labs/CoxLab_Bug_Reporting] Different MaxQuant versions identify vastly different number of Protein groups via MS/MS in the same sample (Issue #110)

Hi Johanna,

This is Jinqiu, I'm Walter's colleague. He's still on holiday and I took over this issue. We didn't change much for DDA analysis for the past releases, so I tried some parameters and found out what's going on there. In MaxQuant there's a parameter called "Split protein groups by taxonomy ID" (as shown in the screenshot), you can find it in "Global parameters->Identification". In multi species dataset, if you take proteomes from uniprot, the taxonomy ID will be automatically assigned to each species, then during the identification, the protein from different species will not be combined into protein groups.

image.png (view on web)https://github.com/user-attachments/assets/bf810966-986d-404e-b754-f49f2205a3bd

For 2.4.7 it was off by default, but we switch it on for the NET7 and NET8 version. Your dataset was kind of special, since you have two database from homo sampiens, and one of them is not from uniprot, so the taxonomy id was not recognized properly, it made some confusion during some identification. So for your dataset you can switch it off. I tried to run latest MQ version with default settings, and like you mentioned, I only identified around 1500 protein groups, but by switch this parameter off I identified 3300 protein groups. You can try to switch it off and run it again, please let us know how it works :)

We'll look into this issue afterwards, thank you for letting us know about it!

Best, Jinqiu

— Reply to this email directly, view it on GitHubhttps://github.com/cox-labs/CoxLab_Bug_Reporting/issues/110#issuecomment-2330956371, or unsubscribehttps://github.com/notifications/unsubscribe-auth/BKSQETK6KYPCILYIWA65ECLZVAK75AVCNFSM6AAAAABMUIYZYOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGMZQHE2TMMZXGE. You are receiving this because you authored the thread.Message ID: @.***>

JinqiuXiao commented 2 months ago

Hi Johanna,

Sorry for the late reply, we were busy with the MaxQuant summer school lasst week. I did the test with your dataset with the MQ 2.6.3 (2.6.4 was not released by that time). I unchecked the split by taxonomy and get around 3300 protein groups, and I checked split by taxonomy and that was the only change I made, and I identified 1500 proteins.

You can see my results and corresponding mqpar files in this link. The password is the full name of your raw file "gC*****_3290". You can compare two mqpar files, the only difference is True or False for "splitProteinGroupsByTaxonomy".

One thing you can try is before you rerun the test, delete all intermediate files (folders that have same names as your raw files that include n0, p0 folders, and also the .index files), which were created during database search. Because when you start the db search, MQ will look for these intermediate files and will skip some steps to save time. So when you rerun the db search it's always good to remove them.

Best, Jinqiu

JinqiuXiao commented 6 hours ago

Hi Johanna,

Can you please try it out with the latest MaxQuant 2.6.6.0? We fixed a bug in mass recalibration that could reduce the number of identification in timstof dda data, which was introduced between the MQ 2.4.14 and MQ 2.5.0.0.

We regained proper number of identification with yours and another dataset that also show reduced identification in post 2.4 MaxQuant.

Thank you very much for your patience! Hope it works for you.

Best, Jinqiu