MS2-dependent MS1 chromatogram extraction

MS2-dependent MS1 chromatogram extraction megamatt  2018-11-05

We use IP2 software to generate mzIdent files. We import those files into skyline to analyze SILAC and other various ratios. The situation: we import two datasets where the peptide/protein of interest is identified by IP2 from its MS2 spectra in run 1 but not in run 2. Our understanding of skyline is that it extracts chromatograms for the peptide in both runs even though it was only identified from one of them. Our question: is there a way to have skyline only extract a chromatogram when either the heavy or light peptide was identified in that run?

Nick Shulman responded:  2018-11-06
Normally you would not want your peak integration to be dependent on whether there was an MS2 identification. That is, there are many reasons that a peptide might not have been identified in a particular run, and you still should integrate the chromatogram over the time range where the peptide is expected to be, in order to quantify it.

Skyline does not give you a way to prevent chromatograms from being extracted from particular runs based on the presence of IDs.
Skyline will tell you whether there was an ID in that particular run which overlaps in time with the peak boundaries. This value "Integrated" is available in the Document Grid on the column:
Proteins > Peptides > Precursors > Precursor Results > Identified

If you want to know more about how to use the Document Grid, you should take a look at the Custom Reports tutorial:

-- Nick
Brendan MacLean responded:  2018-11-06

You should be able to find the peaks that have been integrated by "alignment" only of IDs in other runs, i.e. no IDs for either label type, by using the Precursor Results.Identified column in a report. The values should be "TRUE", "FALSE", "ALIGNED". It sounds like you want only ALIGNED. Would just having this column in a report be enough for you to calculate your statistics, or do you truly need to remove the peak integration for these peaks so that Skyline would use #N/A for all of the peak statistics?

So far, we don't have an easy way to remove peaks in the Document Grid. So, you would need to use linked columns in the document grid to navigate to the peaks and then right-click > Remove Peak, which is probably prohibitively manual.

I just spoke with Nick, and he said he would think about a way to allow you to remove peaks for any set of PrecursorResults you can select in the Document Grid.

Sorry, we don't have a better answer for you at the moment.