No chromatograms for transition ions michael-e-wright  2021-02-26

I wonder why transition ion chromatograms are not available for some peptides? This peptide was quantifiable using TMT across eight different samples. I'm not familiar with MaxQuant pipeline for scoring and quantifying TMT-labeled peptides. But this must be a lousy ID, correct? A lot of sketchy MS/MS spectra filter through .90 to 1 probability cut-off scores using MaxQuant search results. Do MaxQuant peptide scoring filters correlate with PeptideProphet scores? Am I looking at this the wrong way?

Nick Shulman responded:  2021-02-26
One reason that you might see that Chromatogram Information Unavailable thing is that you added the peptides to your document after you extracted chromatograms.

If you change the set of peptides in your Targets tree, you need to tell Skyline to extract chromatograms again by going to:
Edit > Manage Results > Reimport

I can think of other reasons you might be seeing that, but all of my ideas are highly unlikely (e.g. those peptides are outside of the m/z range that you collected data for on your mass spectrometer).

If you send us your Skyline document and one of your raw files we can definitely tell you what happened.

In Skyline you can use the menu item:
File > Share
to create a .zip file containing your Skyline document and supporting files including extracted chromatograms.

If that .zip file is less than 50MB you can attach it to this support request.

Otherwise, you can upload it here:

It would also be helpful if you could send us one of your raw files.
-- Nick