References

Protein structure determination by x-ray crystallography

10.1007/978-1-60327-159-2_3 · 2008 · External reference

10.1146/annurev.biochem.73.011303.074004

10.1146/annurev.biochem.73.011303.074004 · External reference

10.1016/j.tibs.2014.10.005

10.1016/j.tibs.2014.10.005 · External reference

10.15252/embj.201694818

10.15252/embj.201694818 · External reference

10.1038/nature01511

10.1038/nature01511 · External reference

10.1038/nchembio736

10.1038/nchembio736 · External reference

10.1038/nbt0303-255

10.1038/nbt0303-255 · External reference

10.1074/mcp.m113.034769

10.1074/mcp.m113.034769 · External reference

Comparative proteomic analysis of eleven common cell lines reveals ubiquitous but varying expression of most proteins

10.1074/mcp.m111.014050 · 2012 · External reference

10.1038/nature22366

10.1038/nature22366 · External reference

10.1126/science.1221483

10.1126/science.1221483 · External reference

10.1038/nature13895

10.1038/nature13895 · External reference

10.1016/j.molcel.2014.10.005

10.1016/j.molcel.2014.10.005 · External reference

10.1021/acs.analchem.6b03058

10.1021/acs.analchem.6b03058 · External reference

Covalent labeling and mass spectrometry reveal subtle higher order structural changes for antibody therapeutics

10.1080/19420862.2019.1565748 · 2019 · External reference

Chaperone Nap1 shields histone surfaces used in a nucleosome and can put H2A–H2B in an unconventional tetrameric form

10.1016/j.molcel.2013.07.015 · 2013 · External reference

10.1126/science.aac7365

10.1126/science.aac7365 · External reference

10.1126/science.aaa4080

10.1126/science.aaa4080 · External reference

10.1039/c5sc04196a

10.1039/c5sc04196a · External reference

The role of mass spectrometry in structural studies of flavin-based electron bifurcating enzymes

10.3389/fmicb.2018.01397 · 2018 · External reference

10.1002/pro.2696

10.1002/pro.2696 · External reference

10.1073/pnas.1303888110

10.1073/pnas.1303888110 · External reference

Comparative higher-order structure analysis of antibody biosimilars using combined bottom-up and top-down hydrogen-deuterium exchange mass spectrometry

10.1016/j.bbapap.2016.08.013 · 2016 · External reference

10.1038/nchem.2908

10.1038/nchem.2908 · External reference

10.1126/science.1228565

10.1126/science.1228565 · External reference

10.1007/s13361-016-1382-4

10.1007/s13361-016-1382-4 · External reference

10.1007/s10858-019-00267-z

10.1007/s10858-019-00267-z · External reference

10.1038/nrm1468

10.1038/nrm1468 · External reference

10.1021/pr101065j

10.1021/pr101065j · External reference

10.1002/pmic.201200439

10.1002/pmic.201200439 · External reference

10.1038/ncomms6277

10.1038/ncomms6277 · External reference

10.1038/nmeth1019

10.1038/nmeth1019 · External reference

10.1038/nmeth1088

10.1038/nmeth1088 · External reference

10.1016/j.jprot.2010.08.009

10.1016/j.jprot.2010.08.009 · External reference

Protein footprinting comes of age: mass spectrometry for biophysical structure assessment

10.1074/mcp.o116.064386 · 2017 · External reference

10.1039/c0cs00113a

10.1039/c0cs00113a · External reference

Bottom-up hydrogen deuterium exchange mass spectrometry: data analysis and interpretation

10.1039/c7an00662d · 2017 · External reference

10.1016/j.aca.2012.01.037

10.1016/j.aca.2012.01.037 · External reference

Measuring the hydrogen/deuterium exchange of proteins at high spatial resolution by mass spectrometry: overcoming gas-phase hydrogen/deuterium scrambling

10.1021/ar500194w · 2014 · External reference

Computational methods and challenges in hydrogen/deuterium exchange mass spectrometry

10.1002/mas.21519 · 2017 · External reference

The Deuterator: software for the determination of backbone amide deuterium levels from H/D exchange MS data

10.1186/1471-2105-8-156 · 2007 · External reference

HD desktop: an integrated platform for the analysis and visualization of H/D exchange data

10.1016/j.jasms.2008.11.019 · 2009 · External reference

10.1007/s13361-012-0419-6

10.1007/s13361-012-0419-6 · External reference

Hydra: software for tailored processing of H/D exchange data from MS or tandem MS analyses

10.1186/1471-2105-10-162 · 2009 · External reference

HDX-analyzer: a novel package for statistical analysis of protein structure dynamics

10.1186/1471-2105-12-s1-s43 · 2011 · External reference

HDXFinder: automated analysis and data reporting of deuterium/hydrogen exchange mass spectrometry

10.1007/s13361-011-0234-5 · 2012 · External reference

Protein hydrogen exchange at residue resolution by proteolytic fragmentation mass spectrometry analysis

10.1073/pnas.1315532110 · 2013 · External reference

ExMS: data analysis for HX-MS experiments

2011 · External reference

10.1016/s1044-0305(01)00301-4

10.1016/s1044-0305(01)00301-4 · External reference

10.1007/s13361-013-0727-5

10.1007/s13361-013-0727-5 · External reference

deMix: decoding deuterated distributions from heterogeneous protein states via HDX-MS

10.1038/s41598-019-39512-8 · 2019 · External reference

Quantitating the statistical distribution of deuterium incorporation to extend the utility of H/D exchange MS data

10.1021/ac050988l · 2006 · External reference

10.1016/s1044-0305(97)82982-0

10.1016/s1044-0305(97)82982-0 · External reference

10.1007/s13361-014-0850-y

10.1007/s13361-014-0850-y · External reference

10.1110/ps.051774906

10.1110/ps.051774906 · External reference

ExMS2: An integrated solution for hydrogen-deuterium exchange mass spectrometry data analysis

10.1021/acs.analchem.9b01682 · 2019 · External reference

H/D exchange centroid monitoring is insufficient to show differences in the behavior of protein states

10.1007/s13361-012-0555-z · 2013 · External reference

10.1016/j.jasms.2006.05.014

10.1016/j.jasms.2006.05.014 · External reference

Probing protein structure by amino acid-specific covalent labeling and mass spectrometry

10.1002/mas.20203 · 2009 · External reference

Covalent labeling-mass spectrometry with non-specific reagents for studying protein structure and interactions

10.1016/j.ymeth.2018.04.002 · 2018 · External reference

10.1002/mas.20256

10.1002/mas.20256 · External reference

Fast photochemical oxidation of proteins (FPOP): A powerful mass spectrometry-based structural proteomics tool

10.1074/jbc.rev119.006218 · 2019 · External reference

10.1042/bst20150130

10.1042/bst20150130 · External reference

Current trends in biotherapeutic higher order structure characterization by irreversible covalent footprinting mass spectrometry

10.2174/0929866526666181128141953 · 2019 · External reference

Quantitative analysis of protein covalent labeling mass spectrometry data in the Mass Spec Studio

10.1021/acs.analchem.9b01625 · 2019 · External reference

PepFoot: a software package for semiautomated processing of protein footprinting data

10.1021/acs.jproteome.9b00238 · 2019 · External reference

Software eyes for protein post-translational modifications

10.1002/mas.21425 · 2015 · External reference

10.1021/cr0682047

10.1021/cr0682047 · External reference

Unrestricted identification of modified proteins using MS/MS

10.1002/pmic.200900502 · 2010 · External reference

Identification of post-translational modifications by blind search of mass spectra

10.1038/nbt1168 · 2005 · External reference

PTMap–a sequence alignment software for unrestricted, accurate, and full-spectrum identification of post-translational modification sites

10.1073/pnas.0811739106 · 2009 · External reference

10.1074/mcp.m800021-mcp200

10.1074/mcp.m800021-mcp200 · External reference

10.1021/pr200153k

10.1021/pr200153k · External reference

Identification of protein modifications using MS/MS de novo sequencing and the OpenSea alignment algorithm

10.1021/pr049781j · 2005 · External reference

TagRecon: high-throughput mutation identification through sequence tagging

10.1021/pr900850m · 2010 · External reference

Unrestrictive identification of multiple post-translational modifications from tandem mass spectrometry using an error-tolerant algorithm based on an extended sequence tag approach

10.1074/mcp.m800101-mcp200 · 2008 · External reference

Fast multi-blind modification search through tandem mass spectrometry

2012 · External reference

ModifiComb, a new proteomic tool for mapping substoichiometric post-translational modifications, finding novel types of modifications, and fingerprinting complex protein mixtures

10.1074/mcp.t500034-mcp200 · 2006 · External reference

Protein identification by spectral networks analysis

10.1073/pnas.0701130104 · 2007 · External reference

10.1021/pr800226w

10.1021/pr800226w · External reference

Multi-species identification of polymorphic peptide variants via propagation in spectral networks

10.1074/mcp.o116.060913 · 2016 · External reference

SpecOMS: a full open modification search method performing all-to-all spectra comparisons within minutes

10.1021/acs.jproteome.7b00308 · 2017 · External reference

Open MS/MS spectral library search to identify unanticipated post-translational modifications and increase spectral identification rate

10.1093/bioinformatics/btq185 · 2010 · External reference

Hunting for unexpected post-translational modifications by spectral library searching with tier-wise scoring

10.1021/pr401006g · 2014 · External reference

The Hybrid Search: a mass spectral library search method for discovery of modifications in proteomics

10.1021/acs.jproteome.6b00988 · 2017 · External reference

10.1038/nbt.3267

10.1038/nbt.3267 · External reference

A novel approach for untargeted post-translational modification identification using integer linear optimization and tandem mass spectrometry

10.1074/mcp.m900487-mcp200 · 2010 · External reference

DeltAMT: a statistical algorithm for fast detection of protein modifications from LC-MS/MS data

2011 · External reference

pFind-Alioth: A novel unrestricted database search algorithm to improve the interpretation of high-resolution MS/MS data

10.1016/j.jprot.2015.05.009 · 2015 · External reference

10.1021/acs.jproteome.7b00873

10.1021/acs.jproteome.7b00873 · External reference

10.1038/nmeth.4256

10.1038/nmeth.4256 · External reference

Unresolved reference

External reference

Lookup peaks: a hybrid of de novo sequencing and database search for protein identification by tandem mass spectrometry

10.1021/ac0617013 · 2007 · External reference

MODplus: Robust and unrestrictive identification of post-translational modifications using mass spectrometry

10.1021/acs.analchem.9b02445 · 2019 · External reference

Elucidating in vivo structural dynamics in integral membrane protein by hydroxyl radical footprinting

10.1074/mcp.m900081-mcp200 · 2009 · External reference

10.1016/j.tibs.2015.10.008

10.1016/j.tibs.2015.10.008 · External reference

10.1021/acs.analchem.7b04431

10.1021/acs.analchem.7b04431 · External reference

10.1016/j.ymeth.2015.06.010

10.1016/j.ymeth.2015.06.010 · External reference

Crosslinking combined with mass spectrometry for structural proteomics

10.1002/mas.20293 · 2010 · External reference

10.1002/pmic.201200305

10.1002/pmic.201200305 · External reference

10.1074/mcp.m700274-mcp200

10.1074/mcp.m700274-mcp200 · External reference

xComb: a cross-linked peptide database approach to protein-protein interaction analysis

10.1021/pr9011816 · 2010 · External reference

10.1021/ac801646f

10.1021/ac801646f · External reference

Finding chimeras: a bioinformatics strategy for identification of cross-linked peptides

10.1074/mcp.m800555-mcp200 · 2010 · External reference

Kojak: efficient analysis of chemically cross-linked protein complexes

10.1021/pr501321h · 2015 · External reference

10.1038/nmeth.2099

10.1038/nmeth.2099 · External reference

Identification of MS-cleavable and noncleavable chemically cross-linked peptides with MetaMorpheus

10.1021/acs.jproteome.8b00141 · 2018 · External reference

Popitam: towards new heuristic strategies to improve protein identification from tandem mass spectrometry data

10.1002/pmic.200300402 · 2003 · External reference

Shotgun cross-linking analysis for studying quaternary and tertiary protein structures

10.1021/pr070234i · 2007 · External reference

Detecting cross-linked peptides by searching against a database of cross-linked peptide pairs

10.1021/pr901163d · 2010 · External reference

Xlink-identifier: an automated data analysis platform for confident identifications of chemically cross-linked peptides using tandem mass spectrometry

10.1021/pr100848a · 2011 · External reference

10.1016/j.jprot.2015.01.013

10.1016/j.jprot.2015.01.013 · External reference

10.1021/acs.analchem.6b01585

10.1021/acs.analchem.6b01585 · External reference

10.1038/nmeth.1192

10.1038/nmeth.1192 · External reference

10.1038/nmeth.3603

10.1038/nmeth.3603 · External reference

10.1007/s13361-014-1001-1

10.1007/s13361-014-1001-1 · External reference

Informatics strategies for large-scale novel cross-linking analysis

10.1021/pr070035z · 2007 · External reference

10.1038/nrm954

10.1038/nrm954 · External reference

10.1016/j.tibs.2011.05.004

10.1016/j.tibs.2011.05.004 · External reference

10.1002/mas.10025

10.1002/mas.10025 · External reference

10.1007/s00216-017-0772-1

10.1007/s00216-017-0772-1 · External reference

10.1021/pr900771r

10.1021/pr900771r · External reference

10.1039/c4mb00688g

10.1039/c4mb00688g · External reference

Facilitating protein disulfide mapping by a combination of pepsin digestion, electron transfer higher energy dissociation (EThcD), and a dedicated search algorithm SlinkS

10.1074/mcp.o114.039057 · 2014 · External reference

Identification and characterization of disulfide bonds in proteins and peptides from tandem MS data by use of the MassMatrix MS/MS search engine

10.1021/pr070363z · 2008 · External reference

10.1074/mcp.r000001-mcp201

10.1074/mcp.r000001-mcp201 · External reference

10.1021/acs.jproteome.6b00004

10.1021/acs.jproteome.6b00004 · External reference

Matching cross-linked peptide spectra: only as good as the worse identification

10.1074/mcp.m113.034009 · 2014 · External reference

10.1038/nmeth.2103

10.1038/nmeth.2103 · External reference

Quirks of error estimation in cross-linking/mass spectrometry

10.1021/acs.analchem.6b03745 · 2017 · External reference

False discovery rate estimation and heterobifunctional cross-linkers

10.1371/journal.pone.0196672 · 2018 · External reference