On the reproducibility of label-free quantitative cross-linking/mass spectrometry

dc.contributor.authorMüller, Fränze
dc.contributor.authorFischer, Lutz
dc.contributor.authorChen, Zhuo Angel
dc.contributor.authorAuchynnikava, Tania
dc.contributor.authorRappsilber, Juri
dc.date.accessioned2021-03-04T09:32:42Z
dc.date.available2021-03-04T09:32:42Z
dc.date.issued2017-12-18
dc.description.abstractQuantitative cross-linking/mass spectrometry (QCLMS) is an emerging approach to study conformational changes of proteins and multi-subunit complexes. Distinguishing protein conformations requires reproducibly identifying and quantifying cross-linked peptides. Here we analyzed the variation between multiple cross-linking reactions using bis[sulfosuccinimidyl] suberate (BS3)-cross-linked human serum albumin (HSA) and evaluated how reproducible cross-linked peptides can be identified and quantified by LC-MS analysis. To make QCLMS accessible to a broader research community, we developed a workflow that integrates the established software tools MaxQuant for spectra preprocessing, Xi for cross-linked peptide identification, and finally Skyline for quantification (MS1 filtering). Out of the 221 unique residue pairs identified in our sample, 124 were subsequently quantified across 10 analyses with coefficient of variation (CV) values of 14% (injection replica) and 32% (reaction replica). Thus our results demonstrate that the reproducibility of QCLMS is in line with the reproducibility of general quantitative proteomics and we establish a robust workflow for MS1-based quantitation of cross-linked peptides.en
dc.identifier.eissn1879-1123
dc.identifier.issn1044-0305
dc.identifier.urihttps://depositonce.tu-berlin.de/handle/11303/12719
dc.identifier.urihttp://dx.doi.org/10.14279/depositonce-11519
dc.language.isoenen
dc.relation.ispartof10.14279/depositonce-9814
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/en
dc.subject.ddc530 Physikde
dc.subject.otherquantitationen
dc.subject.othercross-linkingen
dc.subject.otherhuman serum albuminen
dc.subject.otherlabel-freeen
dc.subject.othermass spectrometryen
dc.subject.otherreproducibilityen
dc.titleOn the reproducibility of label-free quantitative cross-linking/mass spectrometryen
dc.typeArticleen
dc.type.versionpublishedVersionen
dcterms.bibliographicCitation.doi10.1021/jasms.8b05754en
dcterms.bibliographicCitation.issue23en
dcterms.bibliographicCitation.journaltitleJournal of the American Society for Mass Spectrometryen
dcterms.bibliographicCitation.originalpublishernameAmerican Chemical Society (ACS)en
dcterms.bibliographicCitation.originalpublisherplaceWashington, DCen
dcterms.bibliographicCitation.pageend412en
dcterms.bibliographicCitation.pagestart405en
dcterms.bibliographicCitation.volume29en
tub.accessrights.dnbfreeen
tub.affiliationFak. 3 Prozesswissenschaften>Inst. Biotechnologiede
tub.affiliation.facultyFak. 3 Prozesswissenschaftende
tub.affiliation.instituteInst. Biotechnologiede
tub.publisher.universityorinstitutionTechnische Universität Berlinen
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