Wrong scans extracted when building spectral library from MaxQuant results danielz  2019-10-22

Hi Skyline Team,

Tools used: Skyline and MaxQuant 1.6.5

I realized (after hours of questioning my sanity :-) ) that there is a bug when using this new feature where Skyline takes the MaxQuant result and goes back to the raw file to extract the raw scan (great feature, by the way).

When one uses the MaxQuant msms.txt as is, the scans that are extracted by Skyline look nothing like they should look like, because the wrong scan is extracted. I tested this on multiple instances, however not MaxQuant versions (will follow). What happens is, that Skyline always takes the scan subsequent to the actual scan-number (ScanNr + 1) it should extract. Probably an indexing error or the difference between the scan number and the internal counting when accessing the raw file?

A working quick-fix for this issue is to edit the scan number column of the msms.txt in Excel and subtract 1 (ScanNr - 1) from the respective scan number. Skyline will then extract the correct scan.

Can you reproduce this or is my MQ version bogus? I will try an older one tonight.

matt.chambers42 responded:  2019-10-22

Hi Daniel,

This was fixed in Skyline-daily A patch to fix it in 19.1 release will be coming soon. Sorry for the inconvenience and head scratching!

danielz responded:  2019-10-22

Hi Matt,

glad to hear that, thanks.