Skyline MS1 Quant of glycopeptides

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Skyline MS1 Quant of glycopeptides mstokes  2018-11-19
 

Hello, we are trying to use Skyline for MS1 quant of peptides with N-linked glyco groups. We are having some trouble building the library from these as we have many hundreds of different added masses, and some identical added masses for structural isomers. Wondering if there is a way to build a library for quant that incorporates the glyco information in addition to peptide backbone sequence. Thanks!