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A generic solution for quantifying cross-linked peptides using software Skyline

2018; Springer Nature; Linguagem: Inglês

10.1038/protex.2018.001

2043-0116

Zhuo Chen, Zhuo Chen, Juri Rappsilber,

Machine Learning in Bioinformatics

Quantitative cross-linking/mass spectrometry \(QCLMS) probes protein conformational dynamics in solution.It compares different conformers by quantifying cross-linked peptides obtained by digesting the proteins after them having been cross-linked in solution in their native fold, conserving structural details that may be inaccessible by alternative technologies.Computational solutions that automate quantitation of cross-linking data would promote applications to a wider range of users, beyond the technical development eld.Here we present a strategy for quantifying cross-linking data using a wellestablished quantitation proteomics software, Skyline.Our approach can be applied to label-free quantitation, SILAC based quantitation and quantitation using isotope labelled cross-linkers.The work ow can be adapted to extend across a wide range of existing computational pipeline, from identi cation to quantitation of cross-linked peptides.