Isotopologues at high resolution

Isotopologues at high resolution Yasin  2018-11-29


I have a question regarding the masses of isotopologues calculated by Skyline for high resolution mass spectrometry. Apparently Skyline is making some kind of average over several isotopologues. Is it somehow possible to calculate isotopologues according to the resolution used as in the envipat package?

Thanks a lot in advance!

Nick Shulman responded:  2018-11-29
I am not sure I understand your question. How high of resolution are you talking about?
I know that there is a .01 amu difference between the 13C2 peak and the 34S1 peak. Are you saying that you might want to see separate chromatograms for those two things?

Which peptide or chemical formula are you thinking of? Which numbers are getting averaged?
-- Nick
Yasin responded:  2018-11-30
E.g. with a chemical formula of C5H8N2O5 measured as [M-H] at a resolution of 120000 at 200 mz I would expect an M+1 isotopologue of 176.0394 mz. However Skyline is extracting an M+1 of 176.0388. With my usual mass window of 5 ppm I am missing several scans of my chromatographic peaks because of it. However, when I make my window bigger that would lead to more potential interferences.

Thanks a lot for your time and effort
Yasin responded:  2018-11-30
Here I have also a file with two examples
Nick Shulman responded:  2018-11-30
Can you send us your raw data file too? If that .raw file is less than 50MB then you can attach it to this support request. Otherwise, you can upload it here:

We have always anticipated that someone might want to differentiate the peaks of different isotopes that have the same nominal mass, but you are the first person to ask for it.
I am not sure how we should implement support for this in Skyline but it would be very helpful to look at your raw data and see what those spectra look like.
-- Nick
Yasin responded:  2018-12-02
I uploaded the mzML file with the description "Isotopologues at high resolution"
Thank you for your help.