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MSGFPlus / msgfplus

MS-GF+ (aka MSGF+ or MSGFPlus) performs peptide identification by scoring MS/MS spectra against peptides derived from a protein sequence database.
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(Question) Quantitative output #69

Closed meilumcdermott closed 5 years ago

meilumcdermott commented 5 years ago

After running data with the TMT protocol, I do not have quantitative output. I am assuming that MSGF+ does not output quantification results? What other programs or methods are suggested to use with MSGF+ to get quantification data (eg TMT6plex)? Thanks!

alchemistmatt commented 5 years ago

Correct, MS-GF+ does not quantify TMT reporter ions. We use MASIC, which is available at https://github.com/PNNL-Comp-Mass-Spec/MASIC/releases

That is a Windows application, but it supports command line parameters, allowing it to be run from a batch file. I also have a console version of MASIC that is Linux compatible, including reading both Thermo .Raw files and .mzML files. I am still testing its functionality and working out some issues, but I hope to have it released this week. The new version will be available at https://github.com/PNNL-Comp-Mass-Spec/MASIC/releases

alchemistmatt commented 5 years ago

A related application is https://github.com/PNNL-Comp-Mass-Spec/MASIC-Results-Merger which can combine the results from MS-GF+ and MASIC to create a single file with both sets of data, linked up by scan number. For details, see the MASIC-Results-Merger Readme

meilumcdermott commented 5 years ago

Thanks for your answer!