Proteomics

Dataset Information

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Cross-linking mass spectrometry analysis of trimeric complex of CRM1, SNP1 and RanGTP cross-linked with BS3

ABSTRACT: An X-ray crystallography structure of the trimeric nuclear export complex of CRM1, SNP1 and RanGTP is available on the PDB database with the ID 3GJX. To get an XL-MS dataset of a clean sample of a stable protein complex for benchmarking purposes, another sample from the protein expression, purification and complex assembly employed in the crystallography study was also cross-linked and analyzed by mass spectrometry. The tools OpenPepXL, pLink 2, Kojak, StavroX, XiSearch and xQuest were used to analyze this dataset with comparable search settings.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Escherichia Coli

SUBMITTER: Eugen Netz  

LAB HEAD: Oliver Kohlbacher

PROVIDER: PXD014359 | Pride | 2020-10-20

REPOSITORIES: Pride

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Dataset's files

Source:
Action DRS
CRM_Kojak_PeptideProphet_interact.pep.txt Txt
CRM_OpenPepXL_filtered_PSM.csv Csv
CRM_StavroX.csv Csv
CRM_XiSearch_xiFDR_PSM.csv Csv
CRM_pLink2_filtered_cross-linked_spectra.csv Csv
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Publications

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]

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