Incorrect modification (TMT) mass detected in the spectrum file

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Incorrect modification (TMT) mass detected in the spectrum file ab  2020-11-25
 
Hi,

I am trying to build a spectra library from a TMT tagged sample to evaluate and select peptides for a PRM experiment. I defined the peptide and transition settings as recommended in Webinar #17 and included the modification information for TMT at K and N-term. When I explore the built library, I see at he N-term modification is marked as [+228.1511?], the precursor m/z is accordingly 1 Da less than what is reported by my peptide search in proteome discoverer (SEQUEST) and therefore I am not able to evaluate results for any of my proteins/peptides of interest. I am wondering why this is the case. I am including an image as an example.

Thank you,
Aparna
 
 
Nick Shulman responded:  2020-11-25
That modification mass is what BiblioSpec found in your peptide search results when building the .blib file.
It sounds like BiblioSpec might be misinterpreting the modifications in your peptide search results, or there might be something else going on.

Can you send us your peptide search results? I guess we will need your .sqt files, your Percolator result file (that might be called "combined-results.xml" or might be something else) and your .mzML files that you searched (or your could send us your .raw files, and we can make the .mzML files ourselves).

If those files are less than 50MB you can attach them to this support request.

Otherwise, you can zip them all up and upload them here:
https://skyline.ms/files.url
-- Nick