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PLoS One. 2016 Dec 20;11(12):e0167547. doi: 10.1371/journal.pone.0167547. eCollection 2016.

A General Method for Targeted Quantitative Cross-Linking Mass Spectrometry.

Author information

1
Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, United States of America.
2
Boyce Thompson Institute for Plant Research, Ithaca, NY, United States of America.
3
USDA-Agricultural Research Service, Ithaca, NY, United States of America.
4
Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY, United States of America.
5
Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States of America.
6
Cold Spring Harbor Laboratory Proteomics Course 2016, Cold Spring Harbor, NY, United States of America.

Abstract

Chemical cross-linking mass spectrometry (XL-MS) provides protein structural information by identifying covalently linked proximal amino acid residues on protein surfaces. The information gained by this technique is complementary to other structural biology methods such as x-ray crystallography, NMR and cryo-electron microscopy[1]. The extension of traditional quantitative proteomics methods with chemical cross-linking can provide information on the structural dynamics of protein structures and protein complexes. The identification and quantitation of cross-linked peptides remains challenging for the general community, requiring specialized expertise ultimately limiting more widespread adoption of the technique. We describe a general method for targeted quantitative mass spectrometric analysis of cross-linked peptide pairs. We report the adaptation of the widely used, open source software package Skyline, for the analysis of quantitative XL-MS data as a means for data analysis and sharing of methods. We demonstrate the utility and robustness of the method with a cross-laboratory study and present data that is supported by and validates previously published data on quantified cross-linked peptide pairs. This advance provides an easy to use resource so that any lab with access to a LC-MS system capable of performing targeted quantitative analysis can quickly and accurately measure dynamic changes in protein structure and protein interactions.

PMID:
27997545
PMCID:
PMC5172568
DOI:
10.1371/journal.pone.0167547
[Indexed for MEDLINE]
Free PMC Article

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