Chavez, J. D., Eng, J. K., Schweppe, D. K., Cilia, M., Rivera, K., Zhong, X., Wu, X., Allen, T., Khurgel, M., Kumar, A., Lampropoulos, A., Larsson, M., Maity, S., Morozov, Y., Pathmasiri, W., Perez-Neut, M., Pineyro-Ruiz, C., Polina, E., Post, S., Rider, M., Tokmina-Roszyk, D., Tyson, K., Vieira Parrine Sant'Ana, D., Bruce, J. E. (December 2016) A General Method for Targeted Quantitative Cross-Linking Mass Spectrometry. PLoS One, 11 (12). e0167547. ISSN 1932-6203
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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.
| Item Type: | Paper |
|---|---|
| Subjects: | bioinformatics > genomics and proteomics Investigative techniques and equipment > spectroscopy > mass spectrometry |
| CSHL Authors: | |
| Communities: | CSHL labs > Pappin lab |
| Depositing User: | Matt Covey |
| Date: | 20 December 2016 |
| Date Deposited: | 21 Jul 2017 15:56 |
| Last Modified: | 03 Nov 2017 15:56 |
| PMCID: | PMC5172568 |
| Related URLs: | |
| URI: | https://repository.cshl.edu/id/eprint/35060 |
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