Problem in building of spectral library

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Problem in building of spectral library arvindverma0078  2020-09-29
 

Dear Skyline team,

Recently I used Skyline to build a spectral library from .mgf files. However, I want to convert .mgf file to blib format, because skyline do not accept .mgf file. If a direct conversion is not possible, perhaps there is a way to convert the library to an intermediate format that you are aware of?
Moreover, it is very helpful to me. If you assist me to building of spectral library from my data generated from Thermo Scientific Orbitrap Fusion MS platform.

Best regards,
Arivnd

 
 
Nick Shulman responded:  2020-09-29
Arivnd,

This page has a list of file formats that you can build a .blib file from:
https://skyline.ms/wiki/home/software/BiblioSpec/page.view?name=BlibBuild

You build BiblioSpec files from peptide search results. Do you maybe have some .mzid or .pepXML files?

My understanding is that .mgf is a spectrum format, and holds the data that was collected by the mass spectrometer, but does not have any information about what sort of peptides are there. You can use .mgf files as part of the process of building a spectral library, but you also need to have some other files which say which peptides were found in which spectra.

By the way, if you want to convert your .mgf file to a different format, such as .mzML, you can use ProteoWizard MSConvert.
-- Nick