MaxQuant spectral library

MaxQuant spectral library xzhong9  2020-05-20

Hi Skyline Team,
I would firstly like to thank you for enabling Skyline for DIA data analysis.
I have a question about using MaxQuant msms.txt file to construct a spectral library in Skyline. The two samples are labeled with two mass-defect tags with a mass difference of 18 mDa. To construct the spectral library, the mixed samples were acquired in DDA mode, searched in Proteome Discoverer or MaxQuant, and import the .msf or msms.txt file into Skyline. I want to compare the results difference between PD and MaxQuant. I am able to get great results using .msf from PD, but have no clue why Skyline is not able to resolve the light and heavy fragment ions using msms.txt from MaxQuant as shown in the attached files. I would appreciate it if you could help me resolve it.

Thank you,

Nick Shulman responded:  2020-05-20
What exactly do you mean by "resolve the light and heavy fragment ions"?

When Skyline extracts chromatograms from spectra, Skyline sums the intensities across a m/z channel. The width of the channel that Skyline sums across depends on your resolution or mass accuracy settings at:
Settings > Transition Settings > Full Scan

The peptide YAGEVSHDDK++ has m/z 705 in your PD screenshot, and 633 in your MaxQuant screenshot. That difference is probably because there is a modification on the Y residue in the PD screenshot, and no modification on that residue in the MaxQuant screenshot.
It sounds like you might be asking why Skyline is not recognizing the modification on the Y residue in the MaxQuant spectral library.

If you would like to apply a modification to an amino acid yourself, you can right-click on the peptide in the Targets tree and choose the menu item "Modify".

How exactly is that modification defined in your MaxQuant peptide search? I believe that Skyline cannot handle N-terminal MaxQuant modifications. That's what is mentioned in this support request:

We might be able to be more helpful if you send us your MaxQuant search results (msms.txt, and maybe modifications.xml and/or mqpar.xml). You can also send us your Skyline document by using the "File > Share" menu item to create a .zip file.

If those files are less than 50MB you can attach them to this support request. Otherwise, you can upload them here:
-- Nick