Hi Skyline Team,
I used skyline-daily to import PD.result files or mzML files from Proteome discoverer to build library on Skyline -Daily, but I keep getting an error message. Please help. Here is my workflow:
Open and save Skyline Daily --> Import FASTA of my protein --> Settings --> Library --> Built --> Data Source "Files" --> Input Files "files.pdResults" OR also Tried "files.mzML" which I learned is not a valid file . For Files.pdResults, the error says MassSpectrumItems table.
Please Help. Below is the error message I get when trying to import the spectra from PD to Skyline.
---------------------------
Skyline-daily
---------------------------
ERROR: This file does not contain q-values. You can set a cut-off score of 0 in order to build a library from it, but this may cause your library to include a lot of false-positives.
ERROR: reading file NfL_DDA_Combined.pdResult
ERROR: no such table: MassSpectrumItems
Command-line: C:\Users\jueun.c.kim\AppData\Local\Apps\2.0\XO3CK2OC.ECG\X7QOLBOA.ELX\skyl..tion_9286511f3362df93_0017.0001_479d187256242aac\BlibBuild -s -A -H -v warn -o -c 0.95 -i NfL_PD_Spectral_20240611 -S "Z:\Jueun Kim\NfL\PD and Skyline\Spectral Library\NfL_PD_Spectral_20240611.redundant202406111144.stdin.txt" "Z:\Jueun Kim\NfL\PD and Skyline\Spectral Library\NfL_PD_Spectral_20240611.redundant.blib"
Working directory: Z:\Jueun Kim\NfL\PD and Skyline\Spectral Library
---------------------------
OK More Info
---------------------------
Skyline-daily (64-bit) 23.1.1.520 (80747de92)
System.IO.IOException: ERROR: This file does not contain q-values. You can set a cut-off score of 0 in order to build a library from it, but this may cause your library to include a lot of false-positives.
ERROR: reading file NfL_DDA_Combined.pdResult
ERROR: no such table: MassSpectrumItems
Command-line: C:\Users\jueun.c.kim\AppData\Local\Apps\2.0\XO3CK2OC.ECG\X7QOLBOA.ELX\skyl..tion_9286511f3362df93_0017.0001_479d187256242aac\BlibBuild -s -A -H -v warn -o -c 0.95 -i NfL_PD_Spectral_20240611 -S "Z:\Jueun Kim\NfL\PD and Skyline\Spectral Library\NfL_PD_Spectral_20240611.redundant202406111144.stdin.txt" "Z:\Jueun Kim\NfL\PD and Skyline\Spectral Library\NfL_PD_Spectral_20240611.redundant.blib"
Working directory: Z:\Jueun Kim\NfL\PD and Skyline\Spectral Library ---> System.IO.IOException: ERROR: This file does not contain q-values. You can set a cut-off score of 0 in order to build a library from it, but this may cause your library to include a lot of false-positives.
ERROR: reading file NfL_DDA_Combined.pdResult
ERROR: no such table: MassSpectrumItems
Command-line: C:\Users\jueun.c.kim\AppData\Local\Apps\2.0\XO3CK2OC.ECG\X7QOLBOA.ELX\skyl..tion_9286511f3362df93_0017.0001_479d187256242aac\BlibBuild -s -A -H -v warn -o -c 0.95 -i NfL_PD_Spectral_20240611 -S "Z:\Jueun Kim\NfL\PD and Skyline\Spectral Library\NfL_PD_Spectral_20240611.redundant202406111144.stdin.txt" "Z:\Jueun Kim\NfL\PD and Skyline\Spectral Library\NfL_PD_Spectral_20240611.redundant.blib"
Working directory: Z:\Jueun Kim\NfL\PD and Skyline\Spectral Library
Output:
Reading results from NfL_DDA_Combined.pdResult.
ERROR: This file does not contain q-values. You can set a cut-off score of 0 in order to build a library from it, but this may cause your library to include a lot of false-positives.
ERROR: reading file NfL_DDA_Combined.pdResult
Reading results from NfL_DDA_Oxi_0530_Labelled.pdResult.
ERROR: no such table: MassSpectrumItems
100%
---> System.IO.IOException: ERROR: This file does not contain q-values. You can set a cut-off score of 0 in order to build a library from it, but this may cause your library to include a lot of false-positives.
ERROR: reading file NfL_DDA_Combined.pdResult
ERROR: no such table: MassSpectrumItems
Command-line: C:\Users\jueun.c.kim\AppData\Local\Apps\2.0\XO3CK2OC.ECG\X7QOLBOA.ELX\skyl..tion_9286511f3362df93_0017.0001_479d187256242aac\BlibBuild -s -A -H -v warn -o -c 0.95 -i NfL_PD_Spectral_20240611 -S "Z:\Jueun Kim\NfL\PD and Skyline\Spectral Library\NfL_PD_Spectral_20240611.redundant202406111144.stdin.txt" "Z:\Jueun Kim\NfL\PD and Skyline\Spectral Library\NfL_PD_Spectral_20240611.redundant.blib"
Working directory: Z:\Jueun Kim\NfL\PD and Skyline\Spectral Library
at pwiz.Common.SystemUtil.ProcessRunner.Run(ProcessStartInfo psi, String stdin, IProgressMonitor progress, IProgressStatus& status, TextWriter writer, ProcessPriorityClass priorityClass, Boolean forceTempfilesCleanup, Func`3 outputAndExitCodeAreGoodFunc, Boolean updateProgressPercentage) in C:\proj\pwiz\pwiz_tools\Shared\CommonUtil\SystemUtil\ProcessRunner.cs:line 203
--- End of inner exception stack trace ---
--- End of inner exception stack trace ---
at pwiz.Common.SystemUtil.ProcessRunner.ThrowExceptionWithOutput(Exception exception, String output) in C:\proj\pwiz\pwiz_tools\Shared\CommonUtil\SystemUtil\ProcessRunner.cs:line 263
at pwiz.Common.SystemUtil.ProcessRunner.Run(ProcessStartInfo psi, String stdin, IProgressMonitor progress, IProgressStatus& status, TextWriter writer, ProcessPriorityClass priorityClass, Boolean forceTempfilesCleanup, Func`3 outputAndExitCodeAreGoodFunc, Boolean updateProgressPercentage) in C:\proj\pwiz\pwiz_tools\Shared\CommonUtil\SystemUtil\ProcessRunner.cs:line 245
at pwiz.BiblioSpec.BlibBuild.BuildLibrary(LibraryBuildAction libraryBuildAction, IProgressMonitor progressMonitor, IProgressStatus& status, String& commandArgs, String& messageLog, String[]& ambiguous) in C:\proj\pwiz\pwiz_tools\Shared\BiblioSpec\BlibBuild.cs:line 445
at pwiz.Skyline.Model.Lib.BiblioSpecLiteBuilder.BuildLibrary(IProgressMonitor progress) in C:\proj\pwiz\pwiz_tools\Skyline\Model\Lib\BiblioSpecLiteBuilder.cs:line 163
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| Nick Shulman responded: |
2024-06-11 12:42 |
I think this will work if you use Skyline-daily instead of Skyline 23.1.
You can install Skyline-daily by clicking the "Skyline-daily (beta)" button on the main Skyline page:
https://skyline.ms/project/home/software/Skyline/begin.view
The error about "MassSpectrumItems" means that this is ProteomeDiscoverer 3.1, which is not supported by Skyline 23.1, but is supported by the current Skyline-daily and will be supported by Skyline 24.1 which we will release later this summer.
-- Nick |
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| jueun c kim responded: |
2024-06-12 08:37 |
Thanks for your response. I did use Skyline-Daily but it is still not working. Any Idea of what I might be doing wrong? |
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| Nick Shulman responded: |
2024-06-12 08:46 |
Are you seeing the same error message or a different error message now?
If you send us your .pdresult files we can probably figure out what is going on.
Files which are less than 50MB can be attached to these support request. If they are bigger than that you can package them up in a zip file and upload them here:
https://skyline.ms/files.url
-- Nick |
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| Nick Shulman responded: |
2024-06-12 08:55 |
In your original post you mentioned a couple of different errors. The error about "MassSpectrumItems" can be solved by upgrading to Skyline-daily.
The other error that you are getting about the file not containing q-values is different.
Skyline is most happy building spectral libraries from .pdresult files that have been fed through something (I think Percolator) which gives the results q-values which represent the false discovery rate.
You can build a spectral library from .pdresult files which do not have q-values but, in order to do that, you need to tell Skyline not to do any filtering of PSMs, which means that you need to set the "Score Threshold" value to "1" (it defaults to 0.05).
-- Nick |
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| jueun c kim responded: |
2024-06-12 09:16 |
I do get the same error over and over again. I just tried to set the score value to 1, but I'm still get the same error. See the error message below.
This results are not fed via percolator, so let me try to reanalyze it on PD and get back to you. Also, one more thing is that my company does not allow to post anything on non-company website although these files are not confidential at all. Is there any way I can send you the files via email?
Thank you~~
---------------------------
Skyline-daily
---------------------------
ERROR: no such table: MassSpectrumItems
ERROR: no such table: MassSpectrumItems
Command-line: C:\Users\jueun.c.kim\AppData\Local\Apps\2.0\XO3CK2OC.ECG\X7QOLBOA.ELX\skyl..tion_9286511f3362df93_0017.0001_479d187256242aac\BlibBuild -s -A -H -v warn -o -i NfL_PDresults_Score1_20240612 -S "Z:\Jueun Kim\NfL\PD and Skyline\Spectral Library\NfL_PDresults_Score1_20240612.redundant202406120900.stdin.txt" "Z:\Jueun Kim\NfL\PD and Skyline\Spectral Library\NfL_PDresults_Score1_20240612.redundant.blib"
Working directory: Z:\Jueun Kim\NfL\PD and Skyline\Spectral Library
---------------------------
OK More Info
---------------------------
Skyline-daily (64-bit) 23.1.1.520 (80747de92)
System.IO.IOException: ERROR: no such table: MassSpectrumItems
ERROR: no such table: MassSpectrumItems
Command-line: C:\Users\jueun.c.kim\AppData\Local\Apps\2.0\XO3CK2OC.ECG\X7QOLBOA.ELX\skyl..tion_9286511f3362df93_0017.0001_479d187256242aac\BlibBuild -s -A -H -v warn -o -i NfL_PDresults_Score1_20240612 -S "Z:\Jueun Kim\NfL\PD and Skyline\Spectral Library\NfL_PDresults_Score1_20240612.redundant202406120900.stdin.txt" "Z:\Jueun Kim\NfL\PD and Skyline\Spectral Library\NfL_PDresults_Score1_20240612.redundant.blib"
Working directory: Z:\Jueun Kim\NfL\PD and Skyline\Spectral Library ---> System.IO.IOException: ERROR: no such table: MassSpectrumItems
ERROR: no such table: MassSpectrumItems
Command-line: C:\Users\jueun.c.kim\AppData\Local\Apps\2.0\XO3CK2OC.ECG\X7QOLBOA.ELX\skyl..tion_9286511f3362df93_0017.0001_479d187256242aac\BlibBuild -s -A -H -v warn -o -i NfL_PDresults_Score1_20240612 -S "Z:\Jueun Kim\NfL\PD and Skyline\Spectral Library\NfL_PDresults_Score1_20240612.redundant202406120900.stdin.txt" "Z:\Jueun Kim\NfL\PD and Skyline\Spectral Library\NfL_PDresults_Score1_20240612.redundant.blib"
Working directory: Z:\Jueun Kim\NfL\PD and Skyline\Spectral Library
Output:
Reading results from NfL_DDA_Combined.pdResult.
ERROR: no such table: MassSpectrumItems
Reading results from NfL_DDA_Oxi_0530_Labelled.pdResult.
ERROR: no such table: MassSpectrumItems
100%
---> System.IO.IOException: ERROR: no such table: MassSpectrumItems
ERROR: no such table: MassSpectrumItems
Command-line: C:\Users\jueun.c.kim\AppData\Local\Apps\2.0\XO3CK2OC.ECG\X7QOLBOA.ELX\skyl..tion_9286511f3362df93_0017.0001_479d187256242aac\BlibBuild -s -A -H -v warn -o -i NfL_PDresults_Score1_20240612 -S "Z:\Jueun Kim\NfL\PD and Skyline\Spectral Library\NfL_PDresults_Score1_20240612.redundant202406120900.stdin.txt" "Z:\Jueun Kim\NfL\PD and Skyline\Spectral Library\NfL_PDresults_Score1_20240612.redundant.blib"
Working directory: Z:\Jueun Kim\NfL\PD and Skyline\Spectral Library
at pwiz.Common.SystemUtil.ProcessRunner.Run(ProcessStartInfo psi, String stdin, IProgressMonitor progress, IProgressStatus& status, TextWriter writer, ProcessPriorityClass priorityClass, Boolean forceTempfilesCleanup, Func`3 outputAndExitCodeAreGoodFunc, Boolean updateProgressPercentage) in C:\proj\pwiz\pwiz_tools\Shared\CommonUtil\SystemUtil\ProcessRunner.cs:line 203
--- End of inner exception stack trace ---
--- End of inner exception stack trace ---
at pwiz.Common.SystemUtil.ProcessRunner.ThrowExceptionWithOutput(Exception exception, String output) in C:\proj\pwiz\pwiz_tools\Shared\CommonUtil\SystemUtil\ProcessRunner.cs:line 263
at pwiz.Common.SystemUtil.ProcessRunner.Run(ProcessStartInfo psi, String stdin, IProgressMonitor progress, IProgressStatus& status, TextWriter writer, ProcessPriorityClass priorityClass, Boolean forceTempfilesCleanup, Func`3 outputAndExitCodeAreGoodFunc, Boolean updateProgressPercentage) in C:\proj\pwiz\pwiz_tools\Shared\CommonUtil\SystemUtil\ProcessRunner.cs:line 245
at pwiz.BiblioSpec.BlibBuild.BuildLibrary(LibraryBuildAction libraryBuildAction, IProgressMonitor progressMonitor, IProgressStatus& status, String& commandArgs, String& messageLog, String[]& ambiguous) in C:\proj\pwiz\pwiz_tools\Shared\BiblioSpec\BlibBuild.cs:line 445
at pwiz.Skyline.Model.Lib.BiblioSpecLiteBuilder.BuildLibrary(IProgressMonitor progress) in C:\proj\pwiz\pwiz_tools\Skyline\Model\Lib\BiblioSpecLiteBuilder.cs:line 163
---------------------------
My company does not allow me to post anything from my work computer. Would it be possible for me to send via an email if possible? Also, |
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| Nick Shulman responded: |
2024-06-12 09:23 |
I will send you an email directly. |
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| jueun c kim responded: |
2024-06-12 12:25 |
Hi Nick,
I was able to upload the file here . The security measure was too high that I couldnt even send via email. Thank you so much for your help. |
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| jueun c kim responded: |
2024-06-12 12:28 |
The file was uploaded in the share folder. Thank you! |
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| Nick Shulman responded: |
2024-06-12 13:01 |
Thank you for uploading those files.
Do you also have files with the filename extension ".pdResultDetails" somewhere?
The way that BiblioSpec decides that a .pdResult file is supposed to be the new format is that it finds "3.1" as the version number in the "SchemaInfo" table, but it also needs to find a file with the same name but the ".pdResultDetails" extension.
Because BiblioSpec is not finding those .pdResultDetails files, BiblioSpec is treating this like a version 3.0 format file.
If you had files named "NfL_DDA_Combined.pdResultDetails" and "NfL_DDA_Oxi_0530_Labelled.pdResultDetails" in the same folder as your two .pdResult files then I think this would work for you.
-- Nick |
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| jueun c kim responded: |
2024-06-13 12:39 |
Hi Nick,
I just tried to add the corresponding .rdResultsDetails files into the same folder as the .pdResults files. I only works when I put the q-value at 1. See the error message-1. If I set the value at setting the q-value to 1 means all the spectra will be selected increasing false positive spectra is that correct?
Also I tried to re-analyze the file via Percolator but it gave the same error as below.
Error Message 1:
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Skyline-daily
---------------------------
ERROR: This file does not contain q-values. You can set a cut-off score of 0 in order to build a library from it, but this may cause your library to include a lot of false-positives.
ERROR: reading file NfL_DDA_Combined.pdResult
Command-line: C:\Users\jueun.c.kim\AppData\Local\Apps\2.0\XO3CK2OC.ECG\X7QOLBOA.ELX\skyl..tion_9286511f3362df93_0017.0001_479d187256242aac\BlibBuild -s -A -H -v warn -o -i NfL_PD_PercolatorTest -S "Z:\Jueun Kim\NfL\PD and Skyline\Spectral Library\PD Research 20240613\NfL_PD_PercolatorTest.redundant202406131237.stdin.txt" "Z:\Jueun Kim\NfL\PD and Skyline\Spectral Library\PD Research 20240613\NfL_PD_PercolatorTest.redundant.blib"
Working directory: Z:\Jueun Kim\NfL\PD and Skyline\Spectral Library\PD Research 20240613
---------------------------
OK More Info
---------------------------
Skyline-daily (64-bit) 23.1.1.520 (80747de92)
System.IO.IOException: ERROR: This file does not contain q-values. You can set a cut-off score of 0 in order to build a library from it, but this may cause your library to include a lot of false-positives.
ERROR: reading file NfL_DDA_Combined.pdResult
Command-line: C:\Users\jueun.c.kim\AppData\Local\Apps\2.0\XO3CK2OC.ECG\X7QOLBOA.ELX\skyl..tion_9286511f3362df93_0017.0001_479d187256242aac\BlibBuild -s -A -H -v warn -o -i NfL_PD_PercolatorTest -S "Z:\Jueun Kim\NfL\PD and Skyline\Spectral Library\PD Research 20240613\NfL_PD_PercolatorTest.redundant202406131237.stdin.txt" "Z:\Jueun Kim\NfL\PD and Skyline\Spectral Library\PD Research 20240613\NfL_PD_PercolatorTest.redundant.blib"
Working directory: Z:\Jueun Kim\NfL\PD and Skyline\Spectral Library\PD Research 20240613 ---> System.IO.IOException: ERROR: This file does not contain q-values. You can set a cut-off score of 0 in order to build a library from it, but this may cause your library to include a lot of false-positives.
ERROR: reading file NfL_DDA_Combined.pdResult
Command-line: C:\Users\jueun.c.kim\AppData\Local\Apps\2.0\XO3CK2OC.ECG\X7QOLBOA.ELX\skyl..tion_9286511f3362df93_0017.0001_479d187256242aac\BlibBuild -s -A -H -v warn -o -i NfL_PD_PercolatorTest -S "Z:\Jueun Kim\NfL\PD and Skyline\Spectral Library\PD Research 20240613\NfL_PD_PercolatorTest.redundant202406131237.stdin.txt" "Z:\Jueun Kim\NfL\PD and Skyline\Spectral Library\PD Research 20240613\NfL_PD_PercolatorTest.redundant.blib"
Working directory: Z:\Jueun Kim\NfL\PD and Skyline\Spectral Library\PD Research 20240613
Output:
Reading results from NfL_DDA_Combined.pdResult.
ERROR: This file does not contain q-values. You can set a cut-off score of 0 in order to build a library from it, but this may cause your library to include a lot of false-positives.
ERROR: reading file NfL_DDA_Combined.pdResult
100%
---> System.IO.IOException: ERROR: This file does not contain q-values. You can set a cut-off score of 0 in order to build a library from it, but this may cause your library to include a lot of false-positives.
ERROR: reading file NfL_DDA_Combined.pdResult
Command-line: C:\Users\jueun.c.kim\AppData\Local\Apps\2.0\XO3CK2OC.ECG\X7QOLBOA.ELX\skyl..tion_9286511f3362df93_0017.0001_479d187256242aac\BlibBuild -s -A -H -v warn -o -i NfL_PD_PercolatorTest -S "Z:\Jueun Kim\NfL\PD and Skyline\Spectral Library\PD Research 20240613\NfL_PD_PercolatorTest.redundant202406131237.stdin.txt" "Z:\Jueun Kim\NfL\PD and Skyline\Spectral Library\PD Research 20240613\NfL_PD_PercolatorTest.redundant.blib"
Working directory: Z:\Jueun Kim\NfL\PD and Skyline\Spectral Library\PD Research 20240613
at pwiz.Common.SystemUtil.ProcessRunner.Run(ProcessStartInfo psi, String stdin, IProgressMonitor progress, IProgressStatus& status, TextWriter writer, ProcessPriorityClass priorityClass, Boolean forceTempfilesCleanup, Func`3 outputAndExitCodeAreGoodFunc, Boolean updateProgressPercentage) in C:\proj\pwiz\pwiz_tools\Shared\CommonUtil\SystemUtil\ProcessRunner.cs:line 203
--- End of inner exception stack trace ---
--- End of inner exception stack trace ---
at pwiz.Common.SystemUtil.ProcessRunner.ThrowExceptionWithOutput(Exception exception, String output) in C:\proj\pwiz\pwiz_tools\Shared\CommonUtil\SystemUtil\ProcessRunner.cs:line 263
at pwiz.Common.SystemUtil.ProcessRunner.Run(ProcessStartInfo psi, String stdin, IProgressMonitor progress, IProgressStatus& status, TextWriter writer, ProcessPriorityClass priorityClass, Boolean forceTempfilesCleanup, Func`3 outputAndExitCodeAreGoodFunc, Boolean updateProgressPercentage) in C:\proj\pwiz\pwiz_tools\Shared\CommonUtil\SystemUtil\ProcessRunner.cs:line 245
at pwiz.BiblioSpec.BlibBuild.BuildLibrary(LibraryBuildAction libraryBuildAction, IProgressMonitor progressMonitor, IProgressStatus& status, String& commandArgs, String& messageLog, String[]& ambiguous) in C:\proj\pwiz\pwiz_tools\Shared\BiblioSpec\BlibBuild.cs:line 445
at pwiz.Skyline.Model.Lib.BiblioSpecLiteBuilder.BuildLibrary(IProgressMonitor progress) in C:\proj\pwiz\pwiz_tools\Skyline\Model\Lib\BiblioSpecLiteBuilder.cs:line 163
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| Nick Shulman responded: |
2024-06-13 12:59 |
Can you send me your .pdResultDetails files? |
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| jueun c kim responded: |
2024-06-27 09:51 |
Hi Nick. I apologize for the delay. Thank you for your help. Let me upload the files. The file is called JueunKim_DDA. Thank you! |
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| Nick Shulman responded: |
2024-06-27 10:27 |
Thank you for sending that .pdResult and .pdResultDetails files.
I think there really might not be any q-values in there that BiblioSpec knows how to read.
BlibBuild.exe is a command line program that Skyline executes to build a spectral library.
If you run BlibBuild.exe yourself, you can always add in the extra parameter "-v debug" to tell BiblioSpec to output more verbose information.
When I do this:
BlibBuild.exe -v debug NfL_DDA_Combined.pdResult myLibrary.redundant.blib
I see the following output:
DEBUG: Schema version is 3 (3.1.0.638)
DEBUG: Searched in table 'TargetPeptideGroups' for column 'Qvalityqvalue', not found
DEBUG: Searched in table 'TargetPsms' for column 'PercolatorqValue', not found
DEBUG: Searched in table 'TargetPsms' for column 'qValue', not found
DEBUG: Searched in table 'TargetPsms' for column 'ExpectationValue', not found
ERROR: This file does not contain q-values. You can set a cut-off score of 0 in order to build a library from it, but this may cause your library to include a lot of false-positives.
I think your only option really is to specify a q-value cutoff of 100% which will include lots of false positives.
Do you have some reason to believe that BiblioSpec should be finding something that it could use to control for false discovery rates? Do you think there is something else that BiblioSpec could be looking at when it has to decide whether to include a particular PSM or peptide?
-- Nick
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| jueun c kim responded: |
2024-06-28 13:51 |
Hi Nick,
Thank you for looking into this issue. I cant understand why this file has no q-values. PD results files should have q-values right? And the FDR for ID'ed peptides is already calculated in the analysis process in PD right?
I have other files that was fed via Percolator. Would you like to try that? I can send both results and detail files. Do all PD result files have this issue? or is it just me?
Also to your question: I have no idea.. but..
Do you have some reason to believe that BiblioSpec should be finding something that it could use to control for false discovery rates?
- what controls do you suggest that I can use?
Do you think there is something else that BiblioSpec could be looking at when it has to decide whether to include a particular PSM or peptide?
-This is probably beyond what I can comprehend. I would think BiblioSpec should look at both the interference % and also the best score compared to different scoring engines..??? What do you think?
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