Preprint: Please note that this article has not completed peer review.

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

Juri Rappsilber, Zhuo Chen
DOI: 10.1038/protex.2018.001

Abstract

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 field. Here we present a strategy for quantifying cross-linking data using a well-established quantitation proteomics software, Skyline. Our approach can be applied to label-free quantitation, SILAC based quantitation and quantitation using isotope labelled cross-linkers. The workflow can be adapted to extend across a wide range of existing computational pipeline, from identification to quantitation of cross-linked peptides.

Keywords
quantitation, cross-linking/mass spectrometry, protein conformationanl changes, automated data process, software Skyline, label-free, isotope-labelling

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Preprint: Please note that this article has not completed peer review.

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

Juri Rappsilber, Zhuo Chen

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Abstract

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 field. Here we present a strategy for quantifying cross-linking data using a well-established quantitation proteomics software, Skyline. Our approach can be applied to label-free quantitation, SILAC based quantitation and quantitation using isotope labelled cross-linkers. The workflow can be adapted to extend across a wide range of existing computational pipeline, from identification to quantitation of cross-linked peptides.

Figures

Introduction

Equipment

Procedure

Timing

Troubleshooting

References

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