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error message for the impro diletta piana  2022-01-20 06:35
 
I downloaded from Peaks the peptides in a format readable by skyline, but once attached I get the error message that I report below and attached.
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Skyline
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ERROR: While searching for spectrum file for the search results file 'peptides.pep.xml', could not find matches for the following basename with any of the supported file extensions (.mz5, .mz5, .mzML, .mzXML, .raw, .wiff, .wiff2, .d, .lcd, .ms2, .cms2, .bms2, .pms2):
ERROR: Sample1BIS_RUN1(180919)
ERROR:
ERROR: In any of the following directories:
ERROR: D:\Diletta\SKYLINE
ERROR: D:\Diletta
ERROR: D:\
ERROR:
ERROR: While searching for spectrum file for the search results file 'peptides_1_1_0.mzid', could not find matches for the following basename with any of the supported file extensions (.MGF, .MGF, .mzXML, .mzML, .mz5, .raw, .wiff, .wiff2, .d, .lcd):
ERROR: Sample11_RUN1(180919)_VUS
ERROR:
ERROR: In any of the following directories:
ERROR: D:\Diletta\SKYLINE
ERROR:

Command-line: C:\Users\Urbani\AppData\Local\Apps\2.0\TTENHC55.79M\37MD986X.ZC4\skyl..tion_e4141a2a22107248_0015.0002_b6130d78fa8ea9a3\BlibBuild -s -A -H -o -c 0.99 -i DDAtoMS1_prova1_190122 -S "C:\Users\Urbani\AppData\Local\Temp\tmp3650.tmp" "C:\Users\Urbani\Documents\DdaSearchMs1Filtering (1)\DdaSearchMS1Filtering\DDAtoMS1_prova1_190122.redundant.blib"
Working directory: D:\Diletta\SKYLINE
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OK More Info
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System.IO.IOException: ERROR: While searching for spectrum file for the search results file 'peptides.pep.xml', could not find matches for the following basename with any of the supported file extensions (.mz5, .mz5, .mzML, .mzXML, .raw, .wiff, .wiff2, .d, .lcd, .ms2, .cms2, .bms2, .pms2):
ERROR: Sample1BIS_RUN1(180919)
ERROR:
ERROR: In any of the following directories:
ERROR: D:\Diletta\SKYLINE
ERROR: D:\Diletta
ERROR: D:\
ERROR:
ERROR: While searching for spectrum file for the search results file 'peptides_1_1_0.mzid', could not find matches for the following basename with any of the supported file extensions (.MGF, .MGF, .mzXML, .mzML, .mz5, .raw, .wiff, .wiff2, .d, .lcd):
ERROR: Sample11_RUN1(180919)_VUS
ERROR:
ERROR: In any of the following directories:
ERROR: D:\Diletta\SKYLINE
ERROR:

Command-line: C:\Users\Urbani\AppData\Local\Apps\2.0\TTENHC55.79M\37MD986X.ZC4\skyl..tion_e4141a2a22107248_0015.0002_b6130d78fa8ea9a3\BlibBuild -s -A -H -o -c 0.99 -i DDAtoMS1_prova1_190122 -S "C:\Users\Urbani\AppData\Local\Temp\tmp3650.tmp" "C:\Users\Urbani\Documents\DdaSearchMs1Filtering (1)\DdaSearchMS1Filtering\DDAtoMS1_prova1_190122.redundant.blib"
Working directory: D:\Diletta\SKYLINE
   at pwiz.Common.SystemUtil.ProcessRunner.Run(ProcessStartInfo psi, String stdin, IProgressMonitor progress, IProgressStatus& status, TextWriter writer, ProcessPriorityClass priorityClass) in C:\proj\skyline_21_2_x64\pwiz_tools\Shared\Common\SystemUtil\ProcessRunner.cs:line 149
   at pwiz.BiblioSpec.BlibBuild.BuildLibrary(LibraryBuildAction libraryBuildAction, IProgressMonitor progressMonitor, IProgressStatus& status, String& commandArgs, String& messageLog, String[]& ambiguous) in C:\proj\skyline_21_2_x64\pwiz_tools\Shared\BiblioSpec\BlibBuild.cs:line 201
   at pwiz.Skyline.Model.Lib.BiblioSpecLiteBuilder.BuildLibrary(IProgressMonitor progress) in C:\proj\skyline_21_2_x64\pwiz_tools\Skyline\Model\Lib\BiblioSpecLiteBuilder.cs:line 157
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I was wondering how I could read my library of peptides to make a DDA search to MS1.
I tried to save the files in mz5 format but at the end it gives me the error that it doesn't read or doesn't find the corresponding match.
 
 
Nick Shulman responded:  2022-01-20 11:53
Do you have the original .mzML, or .mzXML files which your peptide search engine used when it created those pep.xml files?
The error message that you are seeing says that it was trying to find a file called maybe "peptides_1_1_0.mzML" or "peptides_1_1_0.raw".
If you put a file with that name in the same folder as the "peptides_1_1_0.mzid" that you have, then it would probably work.

Here is the web page which says, for each different type of peptide search engine, what files to provide:
https://skyline.ms/wiki/home/software/BiblioSpec/page.view?name=BlibBuild

It's a little strange that you are trying to use both a "pep.xml" file and a ".mzid" file. You certainly can do something like that if you want, especially if you are trying to create a library which has peptide search results from two different peptide search engines, but it's typically not done.
-- Nick
 
diletta piana responded:  2022-01-21 06:31
thank you very much,
At the end re-downloaded the files in mzxml format before reading the answer.
I got an identification but some proteins were not recognized...
I clicked on the view and then on spectral view to search for a specific peptide of a protein. I entered the m/z ratio of interest and found the peptide but when I clicked on "associate protein" I got a message saying: "this peptide does not match with current filter settings".

I'm trying to figure out what I can change in the peptide settings do you recommend anything in particular? should I adjust the peptides settings or transition settings?
Is it possible to change and redo the analysis in the same document or do I have to create a new document?

Thank you again and waiting for your kind reply I wish you a good day,

Diletta
 
Nick Shulman responded:  2022-01-21 08:12
I believe that "peptide does not match the current filter settings" usually means that, if Skyline were to add that peptide to your document, the peptide would not end up having either any precursors or transitions.

I believe you can tell Skyline to add the peptide to your document anyway, and you can then right-click on the peptide and choose "Pick Children" to add precursors.

You can also go to the settings at:
Settings > Transition Settings > Filter
and add some more numbers to the list of allowed precursor and product charges.

You might also be able to do something about this by going to:
Settings > Peptide Settings > Filter
or maybe
Settings > Peptide Settings > Library

If you send us your Skyline document I could probably figure out what is going on and what to do about it.
In Skyline you can use the menu item:
File > Share
to create a .zip file containing your Skyline document and supporting files including spectral libraries.

If that .zip file is less than 50MB you can attach it to this support request. You can upload larger files here:
https://skyline.ms/files.url

-- Nick