Library Build for SILAC labelled PTM spectra from MetaMorephus mzID and mzML files ERROR No spectra were found for the new library.

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Library Build for SILAC labelled PTM spectra from MetaMorephus mzID and mzML files ERROR No spectra were found for the new library. gwitek  2022-09-21
 

Hello,

I am trying to build a library from my spectra files that contain peptides digested with Pepsin, grown in SILAC media, and that have phosphorylation on S/T/Y (PTM search).
I get mzID and mzML files from MetaMorpheus but I get an error that No spectra were found for the new library.
I tried changing files to lowercase letters mzid and mzml both or each and it does not work.

I did read another request that said PTM searches can cause library build issues and wanted to reach out to you if this might be another issues with PTM or SILAC.

Thank You,
Gabriela

 
 
Nick Shulman responded:  2022-09-21
Sometimes you get that message if BiblioSpec is unable to understand the spectrum identifiers in the peptide search results and cannot figure out which spectrum in the mzml file they are referring to.
I think there might have been a case where if you gave BiblioSpec a .mgf file instead of a .mzML, BiblioSpec could find the spectra.

If you would like, you can send us your files (mzid and mzML) and we can figure out what is going wrong.
Files which are less than 50MB can be attached to this support request.
You can upload larger files here:
https://skyline.ms/files.url
-- Nick
 
gwitek responded:  2022-10-05
Hello,

I have uploaded the files "_GW.zip" please let me know if you have any other questions.

--Gabriela
 
Nick Shulman responded:  2022-10-05
The .mzID file in that zip that you uploaded says that it came from a file named "20220207_FMR_Mosse_C18A1-15_rep1-calib.mzML".
The mzML file in the zip file has a slightly different name "20220207_FMR_C18A1-15_rep1-calib.mzML".

Can you send me the file "20220207_FMR_Mosse_C18A1-15_rep1-calib.mzML"? That's the file that BiblioSpec is going to be looking for spectra in when it is building the spectral library.
-- Nick
 
gwitek responded:  2022-11-10
Hi Nick,

Sorry for not responding earlier.
I uploaded new folder with correct file names, "GabrielaWitek*.zip"

Thank You for your help!
Gabriela
 
Matt Chambers responded:  2022-11-10
Hi Gabriela,

MetaMorpheus's mzIdentML output here is clearly bugged: it's missing the spectrumID attribute for every spectrumIdentificationResult so there's no way to know which spectrum each peptide is associated with. This must be a new bug with MetaMorpheus (the mzid says you're using a non-release, debug version?) because users have been importing its data into Skyline for years. Can you report your data and settings to MetaMorpheus? https://github.com/smith-chem-wisc/MetaMorpheus/issues

Hopefully they can get this fixed pretty quick.
-Matt