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Proteome Res."},{"key":"10.1016\/bs.acc.2025.06.008_bib223","doi-asserted-by":"crossref","unstructured":"F. Krause, H. Seelert, Detection and analysis of protein-protein interactions of organellar and prokaryotic proteomes by blue native and colorless native gel electrophoresis. Curr. Protoc. Protein Sci. Chapter 14 (2008) Unit 14.11.","DOI":"10.1002\/0471140864.ps1918s54"},{"key":"10.1016\/bs.acc.2025.06.008_bib224","doi-asserted-by":"crossref","first-page":"5214","DOI":"10.1002\/pmic.200900151","article-title":"Native electrophoretic techniques to identify protein-protein interactions","volume":"9","author":"Wittig","year":"2009","journal-title":"Proteomics"},{"key":"10.1016\/bs.acc.2025.06.008_bib225","doi-asserted-by":"crossref","first-page":"103","DOI":"10.1007\/978-1-0716-1266-8_7","article-title":"Native gel electrophoresis and immunoblotting to analyze electron transport chain complexes","volume":"2276","author":"Beutner","year":"2021","journal-title":"Methods Mol. 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Proteome Res."},{"key":"10.1016\/bs.acc.2025.06.008_bib276","doi-asserted-by":"crossref","first-page":"1821","DOI":"10.1021\/acs.jproteome.5b01136","article-title":"Reproducible tissue homogenization and protein extraction for quantitative proteomics using micropestle-assisted pressure-cycling technology","volume":"15","author":"Shao","year":"2016","journal-title":"J. Proteome Res."},{"key":"10.1016\/bs.acc.2025.06.008_bib277","doi-asserted-by":"crossref","first-page":"1982","DOI":"10.1021\/acs.jproteome.9b00790","article-title":"Accelerated lysis and proteolytic digestion of biopsy-level fresh-frozen and FFPE tissue samples using pressure cycling technology","volume":"19","author":"Gao","year":"2020","journal-title":"J. Proteome Res."},{"key":"10.1016\/bs.acc.2025.06.008_bib278","doi-asserted-by":"crossref","first-page":"2307","DOI":"10.1038\/s41596-022-00727-1","article-title":"High-throughput proteomic sample preparation using pressure cycling technology","volume":"17","author":"Cai","year":"2022","journal-title":"Nat. Protoc."},{"key":"10.1016\/bs.acc.2025.06.008_bib279","doi-asserted-by":"crossref","first-page":"2744","DOI":"10.1021\/acs.jproteome.8b00197","article-title":"Surfactant and chaotropic agent assisted sequential extraction\/on-pellet digestion (SCAD) for enhanced proteomics","volume":"17","author":"Ma","year":"2018","journal-title":"J. Proteome Res."},{"key":"10.1016\/bs.acc.2025.06.008_bib280","doi-asserted-by":"crossref","first-page":"2917","DOI":"10.1021\/acs.jproteome.8b00505","article-title":"S-Trap, an ultrafast sample-preparation approach for shotgun proteomics","volume":"17","author":"HaileMariam","year":"2018","journal-title":"J. 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Proteome Res."},{"key":"10.1016\/bs.acc.2025.06.008_bib286","doi-asserted-by":"crossref","first-page":"2992","DOI":"10.1074\/mcp.M112.025585","article-title":"Quantitative assessment of in-solution digestion efficiency identifies optimal protocols for unbiased protein analysis","volume":"12","author":"Le\u00f3n","year":"2013","journal-title":"Mol. Cell. Proteomics"},{"key":"10.1016\/bs.acc.2025.06.008_bib287","doi-asserted-by":"crossref","first-page":"364","DOI":"10.1039\/D0MO00019A","article-title":"Serial in-solution digestion protocol for mass spectrometry-based glycomics and proteomics analysis","volume":"16","author":"Sethi","year":"2020","journal-title":"mol. 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Chem."},{"key":"10.1016\/bs.acc.2025.06.008_bib321","doi-asserted-by":"crossref","first-page":"4472","DOI":"10.1021\/acs.analchem.8b05222","article-title":"Sequential digestion with trypsin and elastase in cross-linking mass spectrometry","volume":"91","author":"Dau","year":"2019","journal-title":"Anal. Chem."},{"key":"10.1016\/bs.acc.2025.06.008_bib322","doi-asserted-by":"crossref","DOI":"10.1016\/j.isci.2024.109663","article-title":"Sequential trypsin and ProAlanase digestions unearth immunological protein biomarkers shrouded by skeletal collagen","volume":"27","author":"Wilkin","year":"2024","journal-title":"iScience"},{"key":"10.1016\/bs.acc.2025.06.008_bib323","doi-asserted-by":"crossref","first-page":"9523","DOI":"10.1021\/acs.analchem.0c00478","article-title":"Proteomics using protease alternatives to trypsin benefits from sequential digestion with trypsin","volume":"92","author":"Dau","year":"2020","journal-title":"Anal. Chem."},{"key":"10.1016\/bs.acc.2025.06.008_bib324","doi-asserted-by":"crossref","DOI":"10.1155\/2014\/960902","article-title":"In Silico proteome cleavage reveals iterative digestion strategy for high sequence coverage","volume":"2014","author":"Meyer","year":"2014","journal-title":"ISRN Comput. Biol."},{"key":"10.1016\/bs.acc.2025.06.008_bib325","doi-asserted-by":"crossref","DOI":"10.1016\/j.jprot.2024.105109","article-title":"Optimal conditions for carrying out trypsin digestions on complex proteomes: from bulk samples to single cells","volume":"297","author":"Mansuri","year":"2024","journal-title":"J. Proteomics"},{"key":"10.1016\/bs.acc.2025.06.008_bib326","doi-asserted-by":"crossref","first-page":"1183","DOI":"10.1529\/biophysj.104.057158","article-title":"Specificity of trypsin and chymotrypsin: loop-motion-controlled dynamic correlation as a determinant","volume":"89","author":"Ma","year":"2005","journal-title":"Biophys. J."},{"key":"10.1016\/bs.acc.2025.06.008_bib327","doi-asserted-by":"crossref","first-page":"144","DOI":"10.1093\/bfgp\/ell026","article-title":"Enhanced sequence coverage of proteins in human cerebrospinal fluid using multiple enzymatic digestion and linear ion trap LC-MS\/MS","volume":"5","author":"Biringer","year":"2006","journal-title":"Brief. Funct. Genomic. Proteomic"},{"key":"10.1016\/bs.acc.2025.06.008_bib328","doi-asserted-by":"crossref","first-page":"1120","DOI":"10.1002\/jssc.200800596","article-title":"On-line multi-enzymatic approach for improved sequence coverage in protein analysis","volume":"32","author":"Temporini","year":"2009","journal-title":"J. Sep. Sci."},{"key":"10.1016\/bs.acc.2025.06.008_bib329","doi-asserted-by":"crossref","first-page":"3430","DOI":"10.1002\/pmic.201000603","article-title":"New protein isoforms identified within Arabidopsis thaliana seed oil bodies combining chymotrypsin\/trypsin digestion and peptide fragmentation analysis","volume":"11","author":"Vermachova","year":"2011","journal-title":"Proteomics"},{"key":"10.1016\/bs.acc.2025.06.008_bib330","doi-asserted-by":"crossref","first-page":"1006","DOI":"10.1073\/pnas.0409279102","article-title":"Alpha-lytic protease can exist in two separately stable conformations with different His57 mobilities and catalytic activities","volume":"102","author":"Haddad","year":"2005","journal-title":"Proc. Natl. Acad. Sci. USA."},{"key":"10.1016\/bs.acc.2025.06.008_bib331","doi-asserted-by":"crossref","first-page":"1360","DOI":"10.1021\/acs.jproteome.3c00852","article-title":"Accelerating proteomics using broad specificity proteases","volume":"23","author":"Jiang","year":"2024","journal-title":"J. Proteome Res."},{"key":"10.1016\/bs.acc.2025.06.008_bib332","doi-asserted-by":"crossref","DOI":"10.1074\/mcp.M111.013524","article-title":"Use of proteinase K nonspecific digestion for selective and comprehensive identification of interpeptide cross-links: application to prion proteins","volume":"11","author":"Petrotchenko","year":"2012","journal-title":"Mol. Cell. Proteomics"},{"key":"10.1016\/bs.acc.2025.06.008_bib333","doi-asserted-by":"crossref","DOI":"10.1074\/mcp.M110.001479","article-title":"Pressurized pepsin digestion in proteomics: an automatable alternative to trypsin for integrated top-down bottom-up proteomics","volume":"10","author":"L\u00f3pez-Ferrer","year":"2011","journal-title":"Mol. Cell. 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(Camb)"},{"key":"10.1016\/bs.acc.2025.06.008_bib336","doi-asserted-by":"crossref","first-page":"203","DOI":"10.1016\/j.jpba.2016.07.002","article-title":"Fast and efficient non-reduced Lys-C digest using pressure cycling technology for antibody disulfide mapping by LC-MS","volume":"129","author":"Cheng","year":"2016","journal-title":"J. Pharm. Biomed. Anal."},{"key":"10.1016\/bs.acc.2025.06.008_bib337","doi-asserted-by":"crossref","first-page":"405","DOI":"10.1038\/nmeth.1204","article-title":"Straightforward ladder sequencing of peptides using a Lys-N metalloendopeptidase","volume":"5","author":"Taouatas","year":"2008","journal-title":"Nat. Methods"},{"key":"10.1016\/bs.acc.2025.06.008_bib338","doi-asserted-by":"crossref","first-page":"2043","DOI":"10.1002\/jssc.201300118","article-title":"Immobilized endoproteinase Glu-C to magnetic bead cellulose as a tool in proteomic analysis","volume":"36","author":"Prikryl","year":"2013","journal-title":"J. Sep. Sci."},{"key":"10.1016\/bs.acc.2025.06.008_bib339","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1021\/pr0100016","article-title":"Proteolytic 18O labeling for comparative proteomics: evaluation of endoprotease Glu-C as the catalytic agent","volume":"1","author":"Reynolds","year":"2002","journal-title":"J. Proteome Res."},{"key":"10.1016\/bs.acc.2025.06.008_bib340","doi-asserted-by":"crossref","first-page":"1554","DOI":"10.1021\/acs.analchem.7b04410","article-title":"Reversible lysine derivatization enabling improved Arg-C digestion, a highly specific Arg-C digestion using trypsin","volume":"90","author":"Wu","year":"2018","journal-title":"Anal. Chem."},{"key":"10.1016\/bs.acc.2025.06.008_bib341","doi-asserted-by":"crossref","first-page":"2631","DOI":"10.1021\/ac300006b","article-title":"Consecutive proteolytic digestion in an enzyme reactor increases depth of proteomic and phosphoproteomic analysis","volume":"84","author":"Wi\u015bniewski","year":"2012","journal-title":"Anal. Chem."},{"key":"10.1016\/bs.acc.2025.06.008_bib342","doi-asserted-by":"crossref","first-page":"782","DOI":"10.1016\/0076-6879(95)48053-6","article-title":"Peptidyl-Asp metalloendopeptidase","volume":"248","author":"Hagmann","year":"1995","journal-title":"Methods Enzymol."},{"key":"10.1016\/bs.acc.2025.06.008_bib343","doi-asserted-by":"crossref","first-page":"1528","DOI":"10.1016\/0006-291X(89)90848-6","article-title":"Specificity of endoproteinase Asp-N (Pseudomonas fragi): cleavage at glutamyl residues in two proteins","volume":"162","author":"Ingrosso","year":"1989","journal-title":"Biochem. Biophys. Res. Commun."},{"key":"10.1016\/bs.acc.2025.06.008_bib344","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0036980","article-title":"Identification of combinatorial patterns of post-translational modifications on individual histones in the mouse brain","volume":"7","author":"Tweedie-Cullen","year":"2012","journal-title":"PLoS One"},{"key":"10.1016\/bs.acc.2025.06.008_bib345","doi-asserted-by":"crossref","first-page":"2139","DOI":"10.1074\/mcp.TIR120.002129","article-title":"ProAlanase is an effective alternative to trypsin for proteomics applications and disulfide bond mapping","volume":"19","author":"Samodova","year":"2020","journal-title":"Mol. Cell. 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Proteome Res."},{"key":"10.1016\/bs.acc.2025.06.008_bib355","doi-asserted-by":"crossref","first-page":"111","DOI":"10.1016\/bs.apcsb.2019.09.006","article-title":"Mass spectrometric approaches for profiling protein folding and stability","volume":"118","author":"Genereux","year":"2019","journal-title":"Adv. Protein Chem. Struct. Biol."},{"key":"10.1016\/bs.acc.2025.06.008_bib356","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1016\/j.sbi.2019.10.006","article-title":"Mass spectrometry analysis of the structural proteome","volume":"60","author":"de Souza","year":"2020","journal-title":"Curr. Opin. Struct. Biol."},{"key":"10.1016\/bs.acc.2025.06.008_bib357","doi-asserted-by":"crossref","first-page":"2391","DOI":"10.1038\/nprot.2017.100","article-title":"Measuring protein structural changes on a proteome-wide scale using limited proteolysis-coupled mass spectrometry","volume":"12","author":"Schopper","year":"2017","journal-title":"Nat. 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Sci."},{"key":"10.1016\/bs.acc.2025.06.008_bib389","doi-asserted-by":"crossref","first-page":"1390","DOI":"10.1007\/s13361-012-0404-0","article-title":"Charge state coalescence during electrospray ionization improves peptide identification by tandem mass spectrometry","volume":"23","author":"Meyer","year":"2012","journal-title":"J. Am. Soc. Mass Spectrom."},{"key":"10.1016\/bs.acc.2025.06.008_bib390","doi-asserted-by":"crossref","first-page":"898","DOI":"10.1002\/mas.20247","article-title":"Electrospray: from ions in solution to ions in the gas phase, what we know now","volume":"28","author":"Kebarle","year":"2009","journal-title":"Mass Spectrom. Rev."},{"key":"10.1016\/bs.acc.2025.06.008_bib391","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1021\/ac302789c","article-title":"Unraveling the mechanism of electrospray ionization","volume":"85","author":"Konermann","year":"2013","journal-title":"Anal. 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