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Comparison of OpenPepXL and xQuest on a Labeled Cross-Linking MS dataset

ABSTRACT: These data sets are part of a large study aimed at the comparison of experimental and computational workflows used in chemical cross-linking coupled to mass spectrometry. Bovine serum albumin (BSA) was used as a model protein. Two different cross-linking chemistries were used: disuccinimidyl suberate (DSS) and a combination of pimelic acid dihydrazide (PDH) and the coupling reagent, DMTMM. See related publication: Iacobucci et al., First Community-Wide, Comparative Cross-Linking Mass Spectrometry Study, Analytical Chemistry, 91 (2019) 6953-6961, DOI: 10.1021/acs.analchem.9b00658 This project is a reanalysis of these datasets with the two Labeled Cross-Linking MS identification tools OpenPepXL and xQuest.

INSTRUMENT(S): Orbitrap Fusion Lumos, LTQ Orbitrap Elite

ORGANISM(S): Bos Taurus (bovine)

SUBMITTER: Eugen Netz

LAB HEAD: Alexander Leitner

PROVIDER: PXD014523 | 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

Publication: 1/2

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