Please use this identifier to cite or link to this item: http://dx.doi.org/10.14279/depositonce-11519
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Main Title: On the reproducibility of label-free quantitative cross-linking/mass spectrometry
Author(s): Müller, Fränze
Fischer, Lutz
Chen, Zhuo Angel
Auchynnikava, Tania
Rappsilber, Juri
Type: Article
URI: https://depositonce.tu-berlin.de/handle/11303/12719
http://dx.doi.org/10.14279/depositonce-11519
License: https://creativecommons.org/licenses/by/4.0/
Abstract: Quantitative 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.
Subject(s): quantitation
cross-linking
human serum albumin
label-free
mass spectrometry
reproducibility
Issue Date: 18-Dec-2017
Date Available: 4-Mar-2021
Is Part Of: 10.14279/depositonce-9814
Language Code: en
DDC Class: 530 Physik
Journal Title: Journal of the American Society for Mass Spectrometry
Publisher: American Chemical Society (ACS)
Volume: 29
Issue: 23
Publisher DOI: 10.1021/jasms.8b05754
Page Start: 405
Page End: 412
EISSN: 1879-1123
ISSN: 1044-0305
TU Affiliation(s): Fak. 3 Prozesswissenschaften » Inst. Biotechnologie
Appears in Collections:Technische Universität Berlin » Publications

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