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Nesvilab / FragPipe

A cross-platform Graphical User Interface (GUI) for running MSFragger and Philosopher - powered pipeline for comprehensive analysis of shotgun proteomics data
http://fragpipe.nesvilab.org
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Extracting the intensities of [M+4], [M+5], [M+6] ... isotopes #1480

Closed HijaziHassan closed 4 months ago

HijaziHassan commented 4 months ago

Hello,

In a 13C-glucose labelling experiment, multiple isotopes can emerge especially for heavily modified peptides by acetylation (more than three sites).

Is there an option to extract the AUCs of a user-defined number of isotopes?

Thank you.

anesvi commented 4 months ago

Not sure what to suggest exactly except perhaps you can use skyline?

HijaziHassan commented 4 months ago

Thank you Alexey. Actually I did use Skyline at the very beginning but then I got stuck since as mentioned by the developers:

It is limited to including only isotopes expected to have at least 1% of the total distribution.

But then we found a workaround using Skyline itself suggested in this paper:

To extract the M+0 through M+8 isotopologues for each peptide identified, the results were analyzed as if they were SILAC labeled, considering the M+0 through M+4 isotopologues as the isotope envelope for the “light” peptide (peptide identified by the PD2.1 search) and the M+4 through M+8 isotopologues as the “heavy” peptide (+4.01342 Da was added under the “Isotope Modifications” in the “Peptide Settings” menu to represent the addition of four 13C isotopes).

McDonnell et al