We are analyzing samples of recombinant protein which were incubated with small molecules that attach covalently to cysteine. The objective is to identify the positions of modification and extract the chromatograms of the labeled peptides for characterization. Essentially I define the molecule's formula in MaxQuant (saved in the modifications.xml file) and define both the molecule and carbamidomethyl as variable modifications. The analysis by MaxQuant clearly identifies peptides containing the molecule as well as their sequence and the exact labeling site (including if there are two cysteines in the same peptide). My objective was to import the peptide search into skyline to build a spectra library and to extract the chromatograms of the carbamidomethyl and molecule-bound peptides. However, the peptides with the bound molecule are never added to the library - only carbamidomethyl peptides are. This is even though MaxQuant clearly identifies the modified peptides and they are defined in the same way.
Is there anything you can recommend to help in this problem?
Details: Windows server R2 enterprise 64 bit
Skyline 64 bit 18.104.22.16805
I attach the screenshot from skyline. Cysteine containing peptides are added to the library (carbamidomethyl containing) and some are not (molecule-labeled).
I also attach the screen shot from the MaxQuant output showing the identification of the molecule-labeled peptide.