Prideapplication/xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/11/PXD021648/checksum.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/11/PXD021648/QExHFX4_RSLC3_BSA_DSBU.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/11/PXD021648/BSA-only.fastaftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/11/PXD021648/BSA-10000prot-human.fastaftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/11/PXD021648/BSA-10prot-human.fastaftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/11/PXD021648/BSA-1000prot-human.fastaftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/11/PXD021648/BSA-100prot-human.fastaftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/11/PXD021648/QExHFX4_RSLC3_BSA_DSBU.mgfftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/11/PXD021648/review_revision_BSA100prot_minscore0_5perFDR_stiegerpaper_allstepped_XlinkX.pdResultftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/11/PXD021648/BSAonly_Rise.zhrmftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/11/PXD021648/review_revision_BSA1prot_minscore0_5perFDR_stiegerpaper_allstepped_XlinkX.pdResultftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/11/PXD021648/BSAonly_protwide.zhrmftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/11/PXD021648/BSA_1000Prot_protwide.zhrmftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/11/PXD021648/RiseUP-Mode_5perFDR.mxfftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/11/PXD021648/BSA_10000Prot_RiseUP.zhrmftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/11/PXD021648/BSA_10000Prot_protwide.zhrmftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/11/PXD021648/review_revision_BSA10prot_minscore0_5perFDR_stiegerpaper_allstepped_XlinkX.pdResultftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/11/PXD021648/BSA_1000Prot_RiseUP.zhrmftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/11/PXD021648/review_revision_BSA10000prot_minscore0_5perFDR_stiegerpaper_allstepped_XlinkX.pdResultftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/11/PXD021648/Rise-Mode_5perFDR.mxfftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/11/PXD021648/BSA_10000prot_Rise.zhrmftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/11/PXD021648/BSA_100Prot_protwide.zhrmftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/11/PXD021648/BSAonly_RiseUP.zhrmftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/11/PXD021648/review_revision_BSA1000prot_minscore0_5perFDR_stiegerpaper_allstepped_XlinkX.pdResultftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/11/PXD021648/BSA_1000Prot_Rise.zhrmftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/11/PXD021648/BSA_10Prot_protwide.zhrmftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/11/PXD021648/BSA_100Prot_Rise.zhrmftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/11/PXD021648/BSA_100Prot_RiseUP.zhrmftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/11/PXD021648/Proteomewide-Mode_5perFDR.mxfftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/11/PXD021648/BSA_10Prot_RiseUP.zhrmftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/11/PXD021648/BSA_10Prot_Rise.zhrmprimaryOK200karl.mechtler@imp.ac.atManuel MatzingerMass SpectrometryChemical cross-linking coupled with mass spectrometry proteomicsProteome DiscovererBsaDsbuMass-spectromertyCrosslinkingXlinkxMeroxhttp://www.ebi.ac.uk/pride/archive/projects/PXD021648BSA was cross-linked using DSBU, reduced (DTT), alkylated (IAA) and digested (trypsin). The digested protein was analyzed on an Orbitrap using a stepped collisional HCD method.PrideNot availableiodoacetamide derivatized residuemonohydroxylated residueThermo raw files were processed directly via XlinkX within Proteome Discoverer 2.4. For analysis using MeroX (v2.0.1.4) raw files were converted to mgf using MSConvertGUI (v3.0.20119-8768fab3c) without any filters. Data was analyzed against a fasta file containing BSA plus an increasing number of human proteins.ProteomicsKarl MechtlerQ Exactive HFPARTIAL1Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, AustriaBos Taurus (bovine)33151691 Matzinger M, Mechtler K. Cleavable Cross-Linkers and Mass Spectrometry for the Ultimate Task of Profiling Protein-Protein Interaction Networks <i>in Vivo</i>. J Proteome Res. 2021 20(1):78-93 10.1021/acs.jproteome.0c00583manuel.matzinger@imp.ac.atEpic-xsIMP / University of ViennaAustriaCross-linking mass spectrometry (XL-MS) has matured into a potent tool to identify protein-protein interactions or to uncover protein structures in living cells, tissues, or organelles. The unique ability to investigate the interplay of proteins within their native environment delivers valuable complementary information to other advanced structural biology techniques. This Review gives a comprehensive overview of the current possible applications as well as the remaining limitations of the technique, focusing on cross-linking in highly complex biological systems like cells, organelles, or tissues. Thanks to the commercial availability of most reagents and advances in user-friendly data analysis, validation, and visualization tools, studies using XL-MS can, in theory, now also be utilized by nonexpert laboratories.Cleavable Cross-Linkers and Mass Spectrometry for the Ultimate Task of Profiling Protein-Protein Interaction Networks <i>in Vivo</i>.Matzinger Manuel M, Mechtler Karl Ksmall, 1H-indol-3-ylacetic acid, underdeveloped, protein complex, beta-Trypsin, hypoplasia, 3-Indolylessigsaeure, Tripcellim, Indoleacetic acid, proteins, 2-(indol-3-yl)ethanoic acid, protein, decreased number, protein-containing complex, beta Trypsin, plan specification, Trypure, Indole-3-acetic acid, protein polypeptide chains, method, (Indol-3-yl)acetate, decreased, heteroauxin, IAA, (indol-3-yl)acetic acid, native protein, HCD, method used in an experiment., reduced, natural protein, polypeptide chain, subnumerary, Protein, tiny, IES, protein aggregate, present in fewer numbers in organismMass Spectrum Analysis, Mass Spectrum, PPH4, Analyses, OAT1, Protein., protein complex, Spectrometry, proteins, protein, Spectrum Analyses, protein-containing complex, Spectrum Analysis, Spectroscopy, K2p3.1, TASK, protein polypeptide chains, TBAK1, native protein, natural protein, polypeptide chain, Protein, Mass, Analysis, TASK-1, protein aggregate, Mass Spectrum Analyses, Mass SpectroscopyIGF-I, Bru, data, steel factor, Clo, human being, Raw, determination, Slf, SLF, hematopoietic growth factor KL, Proteins, Somatomedin-C, number, somatomedin, Gene, FPH2, extra or missing physical or functional parts, IBP1, contrasted, sKITLG, mereological quality, mechano growth factor, chemical analysis, Protein, Gene Products, Del(8)44H, Igf-1, Svc, SHEP7, Col4a-1, mast cell growth factor, Protein., Stem cell factor, somatomedin-C, SF, Kitl, proteins, number of, STAT5, man, Mast cell growth factor, human, Protein Gene Products, Gene Proteins, stem cell factor, Con, Kitlg, KL-1, IGF1, MGF, Mgf, c-Kit ligand, cardinality, has or lacks parts of type, Mechano growth factor, blz, KITLG, assay, Soluble KIT ligand, SCF, Sl, GbData Set., Data Basevisualization, advanced, Laboratory., protein complex, Proteins, Gene, protein, Spectrum Analyses, Organelle, protein-containing complex, Spectrum Analysis, Cell, limitations, Impact, Spectroscopy, Environmental, protein polypeptide chains, Review Literature, native protein, natural protein, polypeptide chain, Protein, Mass, Gene Products, precocious, Impacts, Analysis, Environmental Impacts, protein aggregate, study limitations, Mass Spectrum Analyses, Mass Spectroscopy, Mass Spectrum Analysis, Multicase, Mass Spectrum, Analyses, pre-mortem, Review, Academic, availability, Tissue, Spectrometry, proteins, early, Protein Gene Products, Gene Proteins, Environmental Impact, living, data encoding as image, Data, Environments, Review of Reported Cases, Data AnalysesData Analyses., Analysis, Data, AnalysesfalseXL-MS data analysis with MeroX and XlinkXComparison of MeroX in different modes and XlinkX upon variation of database size based on DSBU linked BSA as 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