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Main Title: Data-independent acquisition improves quantitative cross-linking mass spectrometry
Author(s): Müller, Fränze
Kolbowski, Lars
Bernhardt, Oliver M.
Reiter, Lukas
Rappsilber, Juri
Type: Article
Abstract: Quantitative cross-linking mass spectrometry (QCLMS) reveals structural detail on altered protein states in solution. On its way to becoming a routine technology, QCLMS could benefit from data-independent acquisition (DIA), which generally enables greater reproducibility than data-dependent acquisition (DDA) and increased throughput over targeted methods. Therefore, here we introduce DIA to QCLMS by extending a widely used DIA software, Spectronaut, to also accommodate cross-link data. A mixture of seven proteins cross-linked with bis[sulfosuccinimidyl] suberate (BS3) was used to evaluate this workflow. Out of the 414 identified unique residue pairs, 292 (70%) were quantifiable across triplicates with a coefficient of variation (CV) of 10%, with manual correction of peak selection and boundaries for PSMs in the lower quartile of individual CV values. This compares favorably to DDA where we quantified cross-links across triplicates with a CV of 66%, for a single protein. We found DIA-QCLMS to be capable of detecting changing abundances of cross-linked peptides in complex mixtures, despite the ratio compression encountered when increasing sample complexity through the addition of E. coli cell lysate as matrix. In conclusion, the DIA software Spectronaut can now be used in cross-linking and DIA is indeed able to improve QCLMS.
Subject(s): protein cross-linking
label-free quantification
mass spectrometry
bioinformatics software
data independent acquisition
Issue Date: 1-Apr-2019
Date Available: 4-Mar-2021
Is Part Of: 10.14279/depositonce-9814
Language Code: en
DDC Class: 570 Biowissenschaften; Biologie
Journal Title: Molecular & Cellular Proteomics
Publisher: The American Society for Biochemistry and Molecular Biology
Volume: 18
Issue: 4
Publisher DOI: 10.1074/mcp.TIR118.001276
Page Start: 786
Page End: 795
EISSN: 1535-9484
ISSN: 1535-9476
TU Affiliation(s): Fak. 3 Prozesswissenschaften » Inst. Biotechnologie
Appears in Collections:Technische Universität Berlin » Publications

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