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Reanalysis of a synthetic cross-linked peptide library with OpenPepXL for benchmarking purposes

ABSTRACT: Reanalysis of a synthetic crosslinked peptide library dataset. The three replicates of the XL-MS experiment with the non-cleavable cross-linker DSS from the dataset published in Beveridge et al., Nature Commun., 2020 (PRIDE project PXD014337) were searched with the XL-MS identification tool OpenPepXL for benchmarking purposes.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Streptococcus Pyogenes Abc020006030

SUBMITTER: Eugen Netz

LAB HEAD: Oliver Kohlbacher

PROVIDER: PXD021417 | Pride | 2020-10-20

REPOSITORIES: Pride

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OpenPepXL: An Open-Source Tool for Sensitive Identification of Cross-Linked Peptides in XL-MS.

Netz Eugen E Dijkstra Tjeerd M H TMH Sachsenberg Timo T Zimmermann Lukas L Walzer Mathias M Monecke Thomas T Ficner Ralf R Dybkov Olexandr O Urlaub Henning H Kohlbacher Oliver O

Molecular & cellular proteomics : MCP 20201016 12

Cross-linking MS (XL-MS) has been recognized as an effective source of information about protein structures and interactions. In contrast to regular peptide identification, XL-MS has to deal with a quadratic search space, where peptides from every protein could potentially be cross-linked to any other protein. To cope with this search space, most tools apply different heuristics for search space reduction. We introduce a new open-source XL-MS database search algorithm, OpenPepXL, which offers in ...[more]

PMID: 33067342

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