With data like this, where there are only MS1 chromatograms, I believe the only thing that Skyline pays attention to is the whether the peak areas of the M, M+1, M+2 etc match the expected isotope distribution based on the chemical formula of the peptide. If you have already imported results, then the chromatograms might show up immediately (you told Skyline to extract MS1, but since the transitions did not exist in the Targets tree, Skyline did not show them to you). If you expand the precursors, you will see that Skyline has given you a few precursor transitions ('M' for the monoisotopic precursor, 'M+1' for the isotope that is one Dalton heavier, etc). If you expand one of those peptides in the Targets tree, you will see at one level the precursors for the different charge states.

If you wanted your chromatograms extracted from MS1 and MS2, you might make that 'y, p' or 'y, b, p', but, since you only want the precursors, then you can just make that 'p'.Īfter you change the ion types, Skyline will change the set of transitions that are in your Targets tree. The next thing that you need to do is tell Skyline that you want to extract precursors (from the MS1 scans).Īnd under 'Ion Types' change it to 'p' for 'precursor'. Waters has probably given you a better tool for looking at mass spec data than what SeeMS.exe is, but SeeMS.exe has the ability to look at multiple different formats of mass spec raw files.ĭo you have a list of peptides you want to analyze? If you just want to browse the spectra in a Waters file, then you can use a program called 'SeeMS.exe' which is part of ProteoWizard. Skyline does not have the ability to just open a mass spec file and show you the spectra, etc. If you have a list of peptides that you want to analyze, then you can tell Skyline about them by using the menu item: If you have peptide search results, then the MS1 full scan filtering tutorial will show you how to start from those search results and analyze your data. However, before you tell Skyline to extract chromatograms, you need to tell Skyline which peptides or molecules you are interested in.

The way that you tell Skyline to extract chromatograms from these. I believe Waters raw files are actually entire directories, and all of the files inside of the directory are important.

Dat file converter