Mass Spec Studio for Integrative Structural Biology

Martial Rey; Vladimir Sarpe; Kyle M. Burns; Joshua Buse; Charles A. H. Baker; Marc van Dijk; Linda Wordeman; Alexandre M. J. J. Bonvin; David C. Schriemer

doi:10.1016/j.str.2014.08.013

Mass Spec Studio for Integrative Structural Biology

Martial Rey, Vladimir Sarpe, Kyle M. Burns, Joshua Buse, Charles A. H. Baker, Marc van Dijk, Linda Wordeman, Alexandre M. J. J. Bonvin, David C. Schriemer^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › Academic › peer-review

Abstract

The integration of biophysical data from multiple sources is critical for developing accurate structural models of large multiprotein systems and their regulators. Mass spectrometry (MS) can be used to measure the insertion location for a wide range of topographically sensitive chemical probes, and such insertion data provide a rich, but disparate set of modeling restraints. We have developed a software platform that integrates the analysis of label-based MS and tandem MS (MS 2) data with protein modeling activities (Mass Spec Studio). Analysis packages can mine any labeling data from any mass spectrometer in a proteomics-grade manner, and link labeling methods with data-directed protein interaction modeling using HADDOCK. Support is provided for hydrogen/deuterium exchange (HX) and covalent labeling chemistries, including novel acquisition strategies such as targeted HX-MS 2 and data-independent HX-MS 2. The latter permits the modeling of highly complex systems, which we demonstrate by the analysis of microtubule interactions.

Original language	English
Pages (from-to)	1538-1548
Number of pages	11
Journal	Structure
Volume	22
Issue number	10
DOIs	https://doi.org/10.1016/j.str.2014.08.013
Publication status	Published - 7 Oct 2014

Funding

This work was supported by the Natural Sciences and Engineering Research Council (DS) and the University of Calgary through grants to D.C.S. It was also supported by the Dutch Foundation for Scientific Research through a VICI grant (no. 700.56.442) to A.M.J.J.B. and by the WeNMR project (European FP7 e-Infrastructure grant, contract no. 261572, http://www.wenmr.eu). We present the "Woods plot" as a useful designation for a pairwise comparison of deuteration levels across linear sequence, in recognition of Virgil Woods, Jr., a pioneer in HX-MS who presented it, and who recently passed away.

Keywords

CENTROMERE-ASSOCIATED KINESIN
MOLECULAR ARCHITECTURE
PROTEIN-STRUCTURE
SPECTROMETRY
COMPLEX
DOCKING
CRYSTALLOGRAPHY
IDENTIFICATION
LAULIMALIDE
INFORMATION

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title = "Mass Spec Studio for Integrative Structural Biology",

abstract = "The integration of biophysical data from multiple sources is critical for developing accurate structural models of large multiprotein systems and their regulators. Mass spectrometry (MS) can be used to measure the insertion location for a wide range of topographically sensitive chemical probes, and such insertion data provide a rich, but disparate set of modeling restraints. We have developed a software platform that integrates the analysis of label-based MS and tandem MS (MS 2) data with protein modeling activities (Mass Spec Studio). Analysis packages can mine any labeling data from any mass spectrometer in a proteomics-grade manner, and link labeling methods with data-directed protein interaction modeling using HADDOCK. Support is provided for hydrogen/deuterium exchange (HX) and covalent labeling chemistries, including novel acquisition strategies such as targeted HX-MS 2 and data-independent HX-MS 2. The latter permits the modeling of highly complex systems, which we demonstrate by the analysis of microtubule interactions.",

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author = "Martial Rey and Vladimir Sarpe and Burns, {Kyle M.} and Joshua Buse and Baker, {Charles A. H.} and {van Dijk}, Marc and Linda Wordeman and Bonvin, {Alexandre M. J. J.} and Schriemer, {David C.}",

year = "2014",

month = oct,

day = "7",

doi = "10.1016/j.str.2014.08.013",

language = "English",

volume = "22",

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journal = "Structure",

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publisher = "Cell Press",

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AU - Rey, Martial

AU - Sarpe, Vladimir

AU - Burns, Kyle M.

AU - Buse, Joshua

AU - Baker, Charles A. H.

AU - van Dijk, Marc

AU - Wordeman, Linda

AU - Bonvin, Alexandre M. J. J.

AU - Schriemer, David C.

PY - 2014/10/7

Y1 - 2014/10/7

N2 - The integration of biophysical data from multiple sources is critical for developing accurate structural models of large multiprotein systems and their regulators. Mass spectrometry (MS) can be used to measure the insertion location for a wide range of topographically sensitive chemical probes, and such insertion data provide a rich, but disparate set of modeling restraints. We have developed a software platform that integrates the analysis of label-based MS and tandem MS (MS 2) data with protein modeling activities (Mass Spec Studio). Analysis packages can mine any labeling data from any mass spectrometer in a proteomics-grade manner, and link labeling methods with data-directed protein interaction modeling using HADDOCK. Support is provided for hydrogen/deuterium exchange (HX) and covalent labeling chemistries, including novel acquisition strategies such as targeted HX-MS 2 and data-independent HX-MS 2. The latter permits the modeling of highly complex systems, which we demonstrate by the analysis of microtubule interactions.

AB - The integration of biophysical data from multiple sources is critical for developing accurate structural models of large multiprotein systems and their regulators. Mass spectrometry (MS) can be used to measure the insertion location for a wide range of topographically sensitive chemical probes, and such insertion data provide a rich, but disparate set of modeling restraints. We have developed a software platform that integrates the analysis of label-based MS and tandem MS (MS 2) data with protein modeling activities (Mass Spec Studio). Analysis packages can mine any labeling data from any mass spectrometer in a proteomics-grade manner, and link labeling methods with data-directed protein interaction modeling using HADDOCK. Support is provided for hydrogen/deuterium exchange (HX) and covalent labeling chemistries, including novel acquisition strategies such as targeted HX-MS 2 and data-independent HX-MS 2. The latter permits the modeling of highly complex systems, which we demonstrate by the analysis of microtubule interactions.

KW - CENTROMERE-ASSOCIATED KINESIN

KW - MOLECULAR ARCHITECTURE

KW - PROTEIN-STRUCTURE

KW - SPECTROMETRY

KW - COMPLEX

KW - DOCKING

KW - CRYSTALLOGRAPHY

KW - IDENTIFICATION

KW - LAULIMALIDE

KW - INFORMATION

U2 - 10.1016/j.str.2014.08.013

DO - 10.1016/j.str.2014.08.013

M3 - Article

SN - 0969-2126

VL - 22

SP - 1538

EP - 1548

JO - Structure

JF - Structure

IS - 10

ER -

Mass Spec Studio for Integrative Structural Biology

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Keywords

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