Optimization Workflow for the Analysis of Cross-Linked Peptides Using a Quadrupole Time-of-Flight Mass Spectrometer

被引：7
作者：
James, Juliette M. B. [1 ]
Cryar, Adam [1 ,2 ]
Thalassinos, Konstantinos [1 ,3 ]
机构：
[1] UCL, Dept Struct & Mol Biol, Inst Struct & Mol Biol, Gower St, London WC1E 6BT, England
[2] LGC Grp, Queens Rd, Teddington TW11 0LY, Middx, England
[3] Birkbeck Univ London, Dept Biol Sci, Inst Struct & Mol Biol, London WC1E 7HX, England
来源：
ANALYTICAL CHEMISTRY | 2019年 / 91卷 / 03期
基金：
英国惠康基金;
关键词：
COLLISION-INDUCED DISSOCIATION; LINKING; IDENTIFICATION; FRAGMENTATION; PROTEINS;
D O I：
10.1021/acs.analchem.8b02319
中图分类号：
O65 [分析化学];
学科分类号：
070302 ; 081704 ;
摘要：
Cross-linking mass spectrometry is an emerging structural biology technique. Almost exclusively, the analyzer of choice for such an experiment has been the Orbitrap. We present an optimized protocol for the use of a Synapt G2-Si for the analysis of cross-linked peptides. We first tested six different energy ramps and analyzed the fragmentation behavior of cross -inked peptides identified by xQuest. By combining the most successful energy ramps, cross-link yield can be increased by up to 40%. When compared to previously published Orbitrap data, the Synapt G2-Si also offers improved fragmentation of the beta peptide. In order to improve cross-link quality control we have also developed ValidateXL, a programmatic solution that works with existing cross-linking software to improve cross-link quality control.
引用
收藏
页码：1808 / 1814
页数：7
相关论文
共 31 条
[1]   A new crosslinker for mass spectrometric analysis of the quaternary structure of protein complexes [J].
Back, JW ;
Hartog, AF ;
Dekker, HL ;
Muijsers, AO ;
de Koning, LJ ;
de Jong, L .
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY, 2001, 12 (02) :222-227
[2]   The Impact II, a Very High-Resolution Quadrupole Time-of-Flight Instrument (QTOF) for Deep Shotgun Proteomics [J].
Beck, Scarlet ;
Michalski, Annette ;
Raether, Oliver ;
Lubeck, Markus ;
Kaspar, Stephanie ;
Goedecke, Niels ;
Baessmann, Carsten ;
Hornburg, Daniel ;
Meier, Florian ;
Paron, Igor ;
Kulak, Nils A. ;
Cox, Juergen ;
Mann, Matthias .
MOLECULAR & CELLULAR PROTEOMICS, 2015, 14 (07) :2014-2029
[3]   Solving protein structures using short-distance cross-linking constraints as a guide for discrete molecular dynamics simulations [J].
Brodie, Nicholas I. ;
Popov, Konstantin I. ;
Petrotchenko, Evgeniy V. ;
Dokholyan, Nikolay V. ;
Borchers, Christoph H. .
SCIENCE ADVANCES, 2017, 3 (07)
[4]   The Importance of Non-accessible Crosslinks and Solvent Accessible Surface Distance in Modeling Proteins with Restraints From Crosslinking Mass Spectrometry [J].
Bullock, Joshua Matthew Allen ;
Schwab, Jannik ;
Thalassinos, Konstantinos ;
Topf, Maya .
MOLECULAR & CELLULAR PROTEOMICS, 2016, 15 (07) :2491-2500
[5]   Accommodating Protein Dynamics in the Modeling of Chemical Crosslinks [J].
Degiacomi, Matteo T. ;
Schmidt, Carla ;
Baldwin, Andrew J. ;
Benesch, Justin L. P. .
STRUCTURE, 2017, 25 (11) :1751-+
[6]   Optimized Fragmentation Regime for Diazirine Photo-Cross-Linked Peptides [J].
Giese, Sven H. ;
Belsom, Adam ;
Rappsilber, Juri .
ANALYTICAL CHEMISTRY, 2016, 88 (16) :8239-8247
[7]   A Study into the Collision-induced Dissociation (CID) Behavior of Cross-Linked Peptides [J].
Giese, Sven H. ;
Fischer, Lutz ;
Rappsilber, Juri .
MOLECULAR & CELLULAR PROTEOMICS, 2016, 15 (03) :1094-1104
[8]   The First Zero-Length Mass Spectrometry-Cleavable Cross-Linker for Protein Structure Analysis [J].
Hage, Christoph ;
Iacobucci, Claudio ;
Rehkamp, Anne ;
Arlt, Christian ;
Sinz, Andrea .
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, 2017, 56 (46) :14551-14555
[9]   To Be or Not to Be? Five Guidelines to Avoid Misassignments in Cross-Linking/Mass Spectrometry [J].
Iacobucci, Claudio ;
Sinz, Andrea .
ANALYTICAL CHEMISTRY, 2017, 89 (15) :7832-7835
[10]   Collision-Induced Dissociation of Lys-Lys Intramolecular Crosslinked Peptides [J].
Iglesias, Amadeu H. ;
Santos, Luiz F. A. ;
Gozzo, Fabio C. .
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY, 2009, 20 (04) :557-566
1234