Harmonizing structural mass spectrometry analyses in the mass spec studio

Majumdar, 2015, Hydrogen-deuterium exchange mass spectrometry as an emerging analytical tool for stabilization and formulation development of therapeutic monoclonal antibodies, J. Pharm. Sci., 104, 327, 10.1002/jps.24224 Lagerström, 2008, Structural diversity of G protein-coupled receptors and significance for drug discovery, Nat. Rev. Drug Discov., 7, 339, 10.1038/nrd2518 Wells, 1987, Recruitment of substrate-specificity properties from one enzyme into a related one by protein engineering, Proc. Natl. Acad. Sci. U. S. A., 84, 5167, 10.1073/pnas.84.15.5167 Murphy, 2009, Alteration of enzyme specificity by computational loop remodeling and design, Proc. Natl. Acad. Sci. U. S. A., 106, 9215, 10.1073/pnas.0811070106 Hura, 2009, Robust, high-throughput solution structural analyses by small angle X-ray scattering (SAXS), Nat. Methods, 6, 606, 10.1038/nmeth.1353 Muench, 2019, The expanding toolkit for structural biology: synchrotrons, X-ray lasers and cryoEM, IUCrJ., 6, 167, 10.1107/S2052252519002422 Liu, 2005, Recent developments in structural proteomics for protein structure determination, Proteomics., 5, 2056, 10.1002/pmic.200401104 Wuthrich, 1990, Protein structure determination in solution by NMR spectroscopy, J. Biol. Chem., 265, 22059, 10.1016/S0021-9258(18)45665-7 Guo, 2018, In Situ Structure of Neuronal C9orf72 Poly-GA Aggregates Reveals Proteasome Recruitment, Cell, 172, 696, 10.1016/j.cell.2017.12.030 Schmidt, 2017, Combining cryo-electron microscopy (cryo-EM) and cross-linking mass spectrometry (CX-MS) for structural elucidation of large protein assemblies, Curr. Opin. Struct. Biol., 46, 157, 10.1016/j.sbi.2017.10.005 Bertram, 2017, Cryo-EM structure of a Pre-catalytic human spliceosome primed for activation, Cell, 170, 701, 10.1016/j.cell.2017.07.011 Donnarumma, 2016, The role of structural proteomics in vaccine development: recent advances and future prospects, Expert Rev. Proteomics., 13, 55, 10.1586/14789450.2016.1121113 Politis, 2014, A mass spectrometry-based hybrid method for structural modeling of protein complexes, Nat. Methods, 11, 403, 10.1038/nmeth.2841 Konermann, 2008, Protein structure and dynamics studied by mass spectrometry: H/D exchange, hydroxyl radical labeling, and related approaches, J. Mass Spectrom., 43, 1021, 10.1002/jms.1435 Sharon, 2007, The role of mass spectrometry in structure elucidation of dynamic protein complexes, Annu. Rev. Biochem., 76, 167, 10.1146/annurev.biochem.76.061005.090816 Lössl, 2016, The diverse and expanding role of mass spectrometry in structural and molecular biology, EMBO J, 35, 2634, 10.15252/embj.201694818 O’Reilly, 2018, Cross-linking mass spectrometry: methods and applications in structural, molecular and systems biology, Nat. Struct. Mol. Biol., 25, 10.1038/s41594-018-0147-0 Chavez, 2016, In vivo conformational dynamics of Hsp90 and its interactors, Cell Chem. Biol., 23, 716, 10.1016/j.chembiol.2016.05.012 Trinkle-Mulcahy, 2019, Recent advances in proximity-based labeling methods for interactome mapping, F1000Research, 8, 135, 10.12688/f1000research.16903.1 Gingras, 2019, Getting to know the neighborhood: using proximity-dependent biotinylation to characterize protein complexes and map organelles, Curr. Opin. Chem. Biol., 48, 44, 10.1016/j.cbpa.2018.10.017 Branon, 2018, Efficient proximity labeling in living cells and organisms with TurboID, Nat. Biotechnol., 36, 880, 10.1038/nbt.4201 Ben-Nissan, 2018, The application of ion-mobility mass spectrometry for structure/function investigation of protein complexes, Curr. Opin. Chem. Biol., 42, 25, 10.1016/j.cbpa.2017.10.026 Kelly, 2005, How to study proteins by circular dichroism, Biochim. Biophys. Acta, 1751, 119, 10.1016/j.bbapap.2005.06.005 Harvey, 2019, Relative interfacial cleavage energetics of protein complexes revealed by surface collisions, Proc. Natl. Acad. Sci. U. S. A., 116, 8143, 10.1073/pnas.1817632116 Bullock, 2018, Modeling protein complexes using restraints from crosslinking mass spectrometry, Structure., 1 Filella-Merce, 2019, Quantitative Structural Interpretation of Protein Crosslinks, Structure, 1 Makarov, 2019, Lamin A molecular compression and sliding as mechanisms behind nucleoskeleton elasticity, Nat. Commun., 10, 1, 10.1038/s41467-019-11063-6 Chen, 2018, Protein dynamics in solution by quantitative crosslinking/mass spectrometry, Trends Biochem. Sci., 43, 908, 10.1016/j.tibs.2018.09.003 Konermann, 2011, Hydrogen exchange mass spectrometry for studying protein structure and dynamics, Chem. Soc. Rev., 40, 1224, 10.1039/C0CS00113A Percy, 2012, Probing protein interactions with hydrogen/deuterium exchange and mass spectrometry-a review, Anal. Chim. Acta, 721, 7, 10.1016/j.aca.2012.01.037 Schmidt, 2017, Surface accessibility and dynamics of macromolecular assemblies probed by covalent labeling mass spectrometry and integrative modeling, Anal. Chem., 89, 1459, 10.1021/acs.analchem.6b02875 Xie, 2017, Quantitative protein topography measurements by high resolution hydroxyl radical protein footprinting enable accurate molecular model selection, Sci. Rep., 7, 4552, 10.1038/s41598-017-04689-3 Limpikirati, 2018, Covalent labeling-mass spectrometry with non-specific reagents for studying protein structure and interactions, Methods., 144, 79, 10.1016/j.ymeth.2018.04.002 Aprahamian, 2018, Rosetta protein structure prediction from hydroxyl radical protein Footprinting mass spectrometry data, Anal. Chem., 90, 7721, 10.1021/acs.analchem.8b01624 Ryu, 2014 Perez-Riverol, 2014, Open source libraries and frameworks for mass spectrometry based proteomics: a developer’s perspective, Biochim. Biophys. Acta - Proteins Proteomics., 1844, 63, 10.1016/j.bbapap.2013.02.032 Claesen, 2017, Computational methods and challenges in hydrogen/deuterium exchange mass spectrometry, Mass Spectrom. Rev., 36, 649, 10.1002/mas.21519 Iacobucci, 2017, To be or not to be? Five guidelines to avoid Misassignments in cross-linking/mass spectrometry, Anal. Chem., 89, 7832, 10.1021/acs.analchem.7b02316 Tsiamis, 2019, One thousand and one software for proteomics: Tales of the toolmakers of science, J. Proteome Res., 18, 3580, 10.1021/acs.jproteome.9b00219 Hoopmann, 2015, Kojak: efficient analysis of chemically cross-linked protein complexes, J. Proteome Res., 14, 2190, 10.1021/pr501321h Liu, 2017, Optimized fragmentation schemes and data analysis strategies for proteome-wide cross-link identification, Nat. Commun., 8 Iacobucci, 2018, A cross-linking/mass spectrometry workflow based on MS-cleavable cross-linkers and the MeroX software for studying protein structures and protein–protein interactions, Nat. Protoc., 13, 10.1038/s41596-018-0068-8 Mendes, 2019, An integrated workflow for crosslinking mass spectrometry, Mol. Syst. Biol., 15, 1, 10.15252/msb.20198994 Z.-L. Chen, J.-M. Meng, Y. Cao, J.-L. Yin, R.-Q. Fang, S.-B. Fan, C. Liu, W.-F. Zeng, Y.-H. Ding, D. Tan, L. Wu, W.-J. Zhou, H. Chi, R.-X. Sun, M.-Q. Dong, S.-M. He, A high-speed search engine pLink 2 with systematic evaluation for proteome-scale identification of cross-linked peptides, Nat. Commun. 10 (2019). doi:https://doi.org/10.1038/s41467-019-11337-z. Lima, 2014, SIM-XL: a powerful and user-friendly tool for peptide cross-linking analysis, J. Proteome, 129, 51, 10.1016/j.jprot.2015.01.013 Lu, 2018, Identification of MS-cleavable and noncleavable chemically cross-linked peptides with MetaMorpheus, J. Proteome Res., 17, 2370, 10.1021/acs.jproteome.8b00141 Trnka, 2014, Matching cross-linked peptide spectra: only as good as the worse identification, Mol. Cell. Proteomics, 13, 420, 10.1074/mcp.M113.034009 Pascal, 2012, HDXWorkbench: software for the analysis of H/D exchange MS data, J. Am. Soc. Mass Spectrom., 23, 1512, 10.1007/s13361-012-0419-6 Kan, 2019, ExMS2: an integrated solution for hydrogen-deuterium exchange mass spectrometry data analysis, Anal. Chem., 91, 7474, 10.1021/acs.analchem.9b01682 Guttman, 2013, Analysis of overlapped and noisy hydrogen/deuterium exchange mass spectra, J. Am. Soc. Mass Spectrom., 24, 1906, 10.1007/s13361-013-0727-5 Fellers, 2015, ProSight lite: graphical software to analyze top-down mass spectrometry data, Proteomics., 15, 1235, 10.1002/pmic.201400313 Marty, 2015, Bayesian deconvolution of mass and ion mobility spectra: from binary interactions to polydisperse ensembles, Anal. Chem., 87, 4370, 10.1021/acs.analchem.5b00140 Allison, 2015, Quantifying the stabilizing effects of protein-ligand interactions in the gas phase, Nat. Commun., 6, 10.1038/ncomms9551 Schweppe, 2016, XLinkDB 2.0: Integrated, large-scale structural analysis of protein crosslinking data, Bioinformatics, 32, 2716, 10.1093/bioinformatics/btw232 Webb, 2018, Integrative structure modeling with the integrative modeling platform, Protein Sci., 27, 245, 10.1002/pro.3311 Rey, 2014, Mass spec studio for integrative structural biology, Structure., 22, 1538, 10.1016/j.str.2014.08.013 Van Rossum Van Der Walt, 2011, The NumPy array: a structure for efficient numerical computation, Comput. Sci. Eng., 13, 22, 10.1109/MCSE.2011.37 P. Virtanen, R. Gommers, T.E. Oliphant, M. Haberland, T. Reddy, D. Cournapeau, E. Burovski, P. Peterson, W. Weckesser, J. Bright, S.J. van der Walt, M. Brett, J. Wilson, K.J. Millman, N. Mayorov, A.R.J. Nelson, E. Jones, R. Kern, E. Larson, C. Carey, İ. Polat, Y. Feng, E.W. Moore, J. VanderPlas, D. Laxalde, J. Perktold, R. Cimrman, I. Henriksen, E.A. Quintero, C.R. Harris, A.M. Archibald, A.H. Ribeiro, F. Pedregosa, P. van Mulbregt, S. 1. 0 Contributors, SciPy 1.0--Fundamental Algorithms for Scientific Computing in Python, (2019) 1–22. http://arxiv.org/abs/1907.10121. Röst, 2014, pyOpenMS: A Python-based interface to the OpenMS mass-spectrometry algorithm library, Proteomics, 14, 74, 10.1002/pmic.201300246 Sarpe, 2017, Supporting metabolomics with adaptable software: design architectures for the end-user, Curr. Opin. Biotechnol., 43, 110, 10.1016/j.copbio.2016.11.001 MacLean, 2010, Skyline: an open source document editor for creating and analyzing targeted proteomics experiments, Bioinformatics., 26, 966, 10.1093/bioinformatics/btq054 Pluskal, 2010, MZmine 2: modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data, BMC Bioinformatics., 11, 395, 10.1186/1471-2105-11-395 Tyanova, 2016, The Perseus computational platform for comprehensive analysis of (prote)omics data, Nat. Methods, 13, 731, 10.1038/nmeth.3901 Kim, 2014, MS-GF+ makes progress towards a universal database search tool for proteomics, Nat. Commun., 5, 5277, 10.1038/ncomms6277 Alka, 2019 Walzthoeni, 2012, False discovery rate estimation for cross-linked peptides identified by mass spectrometry, Nat. Methods, 9, 901, 10.1038/nmeth.2103 Pettersen, 2004, UCSF chimera - a visualization system for exploratory research and analysis, J. Comput. Chem., 25, 1605, 10.1002/jcc.20084 Sarpe, 2016, High sensitivity crosslink detection coupled with integrative structure modeling in the mass spec studio, Mol. Cell. Proteomics, 15, 3071, 10.1074/mcp.O116.058685 Sinz, 2006, Chemical cross-linking and mass spectrometry to map three-dimensional protein structures and protein-protein interactions, Mass Spectrom. Rev., 25, 663, 10.1002/mas.20082 Fioramonte, 2018, XPlex: an effective, multiplex cross-linking chemistry for acidic residues, Anal. Chem., 90, 6043, 10.1021/acs.analchem.7b05135 Rappsilber, 2011, The beginning of a beautiful friendship: cross-linking/mass spectrometry and modelling of proteins and multi-protein complexes, J. Struct. Biol., 173, 530, 10.1016/j.jsb.2010.10.014 Giese, 2016, Optimized fragmentation regime for diazirine photo-cross-linked peptides, Anal. Chem., 88, 8239, 10.1021/acs.analchem.6b02082 Ziemianowicz, 2019, Photo-cross-linking mass spectrometry and integrative modeling enables rapid screening of antigen interactions involving bacterial transferrin receptors, J. Proteome Res., 18, 934, 10.1021/acs.jproteome.8b00629 Engen, 2009, Analysis of protein conformation and dynamics by hydrogen/deuterium exchange MS, Anal. Chem., 81, 7870, 10.1021/ac901154s Konermann, 2011, Hydrogen exchange mass spectrometry for studying protein structure and dynamics, Chem. Soc. Rev., 40, 1224, 10.1039/C0CS00113A Oganesyan, 2018, Contemporary hydrogen deuterium exchange mass spectrometry, Methods., 144, 27, 10.1016/j.ymeth.2018.04.023 Chalmers, 2011, Differential hydrogen/deuterium exchange mass spectrometry analysis of protein-ligand interactions, Expert Rev. Proteomics., 8, 43, 10.1586/epr.10.109 Engen, 2015, Analytical aspects of hydrogen exchange mass spectrometry, Annu. Rev. Anal. Chem., 8, 127, 10.1146/annurev-anchem-062011-143113 Slysz, 2008, Restraining expansion of the peak envelope in H/D exchange-MS and its application in detecting perturbations of protein structure/dynamics, Anal. Chem., 80, 7004, 10.1021/ac800897q Hotchko, 2006, Automated extraction of backbone deuteration levels from amide H/2H mass spectrometry experiments, Protein Sci., 15, 583, 10.1110/ps.051774906 Ziemianowicz, 2017, Amino acid insertion frequencies arising from photoproducts generated using aliphatic Diazirines, J. Am. Soc. Mass Spectrom., 28, 2011, 10.1007/s13361-017-1730-z Ziemianowicz, 2019, Quantitative analysis of protein covalent labeling mass spectrometry data in the mass spec studio, Anal. Chem., 91, 8492, 10.1021/acs.analchem.9b01625 Jumper, 2012, High-resolution mapping of carbene-based protein footprints, Anal. Chem., 84, 4411, 10.1021/ac300120z Van Zundert, 2016, The HADDOCK2.2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes, J. Mol. Biol., 428, 720, 10.1016/j.jmb.2015.09.014 Rout, 2019, Principles for integrative structural biology studies, Cell., 177, 1384, 10.1016/j.cell.2019.05.016 M.J. Trnka, R. Pellarin, P.J. Robinson, Role of integrative structural biology in understanding transcriptional initiation, Methods. (2019) 1–19. doi:https://doi.org/10.1016/j.ymeth.2019.03.009. Robinson, 2015, Molecular architecture of the yeast mediator complex, Elife., 4, 1, 10.7554/eLife.08719 Erzberger, 2014, Molecular architecture of the 40S · eIF1 · eIF3 translation initiation complex, Cell., 158, 1123, 10.1016/j.cell.2014.07.044 Burley, 2017, PDB-dev: a prototype system for depositing integrative/hybrid structural models, Structure., 25, 1317, 10.1016/j.str.2017.08.001 Vallat, 2018, Development of a Prototype System for Archiving Integrative/Hybrid Structure Models of Biological Macromolecules, Structure, 26, 894, 10.1016/j.str.2018.03.011 Robinson, 2017, From molecular chaperones to membrane motors: through the lens of a mass spectrometrist, Biochem. Soc. Trans., 45, 251, 10.1042/BST20160395 Masson, 2019, Recommendations for performing, interpreting and reporting hydrogen deuterium exchange mass spectrometry (HDX-MS) experiments., Nature Methods, 16, 595, 10.1038/s41592-019-0459-y