Please use this identifier to cite or link to this item: http://dx.doi.org/10.14279/depositonce-11579
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Main Title: A study into the Collision-induced Dissociation (CID) behavior of cross-linked peptides
Author(s): Giese, Sven H.
Fischer, Lutz
Rappsilber, Juri
Type: Article
URI: https://depositonce.tu-berlin.de/handle/11303/12779
http://dx.doi.org/10.14279/depositonce-11579
License: https://creativecommons.org/licenses/by/4.0/
Abstract: Cross-linking/mass spectrometry resolves protein–protein interactions or protein folds by help of distance constraints. Cross-linkers with specific properties such as isotope-labeled or collision-induced dissociation (CID)- cleavable cross-linkers are in frequent use to simplify the identification of cross-linked peptides. Here, we analyzed the mass spectrometric behavior of 910 unique crosslinked peptides in high-resolution MS1 and MS2 from published data and validate the observation by a ninefold larger set from currently unpublished data to explore if detailed understanding of their fragmentation behavior would allow computational delivery of information that otherwise would be obtained via isotope labels or CID cleavage of cross-linkers. Isotope-labeled cross-linkers reveal cross-linked and linear fragments in fragmentation spectra. We show that fragment mass and charge alone provide this information, alleviating the need for isotopelabeling for this purpose. Isotope-labeled cross-linkers also indicate cross-linker-containing, albeit not specifically cross-linked, peptides in MS1. We observed that acquisition can be guided to better than twofold enrich cross-linked peptides with minimal losses based on peptide mass and charge alone. By help of CID-cleavable cross-linkers, individual spectra with only linear fragments can be recorded for each peptide in a cross-link. We show that cross-linked fragments of ordinary crosslinked peptides can be linearized computationally and that a simplified subspectrum can be extracted that is enriched in information on one of the two linked peptides. This allows identifying candidates for this peptide in a simplified database search as we propose in a search strategy here. We conclude that the specific behavior of cross-linked peptides in mass spectrometers can be exploited to relax the requirements on cross-linkers.
Subject(s): crosslinking
proteomics
database
statistics
Issue Date: 1-Mar-2016
Date Available: 11-Mar-2021
Is Part Of: 10.14279/depositonce-12031
Language Code: en
DDC Class: 570 Biowissenschaften; Biologie
Journal Title: Molecular & Cellular Proteomics
Publisher: The American Society for Biochemistry and Molecular Biology
Volume: 15
Issue: 3
Publisher DOI: 10.1074/mcp.M115.049296
Page Start: 1094
Page End: 1104
EISSN: 1535-9484
ISSN: 1535-9476
TU Affiliation(s): Fak. 3 Prozesswissenschaften » Inst. Biotechnologie » FG Bioanalytik
Appears in Collections:Technische Universität Berlin » Publications

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