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