Proteome-scale recombinant standards and a robust high-speed search engine to advance cross-linking MS-based interactomics.
Journal
Nature methods
ISSN: 1548-7105
Titre abrégé: Nat Methods
Pays: United States
ID NLM: 101215604
Informations de publication
Date de publication:
31 Oct 2024
31 Oct 2024
Historique:
received:
23
10
2023
accepted:
19
09
2024
medline:
1
11
2024
pubmed:
1
11
2024
entrez:
1
11
2024
Statut:
aheadofprint
Résumé
Advancing data analysis tools for proteome-wide cross-linking mass spectrometry (XL-MS) requires ground-truth standards that mimic biological complexity. Here we develop well-controlled XL-MS standards comprising hundreds of recombinant proteins that are systematically mixed for cross-linking. We use one standard dataset to guide the development of Scout, a search engine for XL-MS with MS-cleavable cross-linkers. Using other, independent standard datasets and published datasets, we benchmark the performance of Scout and existing XL-MS software. We find that Scout offers an excellent combination of speed, sensitivity and false discovery rate control. The results illustrate how our large recombinant standard can support the development of XL-MS analysis tools and evaluation of XL-MS results.
Identifiants
pubmed: 39482464
doi: 10.1038/s41592-024-02478-1
pii: 10.1038/s41592-024-02478-1
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Subventions
Organisme : Deutsche Forschungsgemeinschaft (German Research Foundation)
ID : DFG Project LI 3260/6-1
Organisme : Leibniz-Gemeinschaft (Leibniz Association)
ID : Leibniz-Wettbewerb P70/2018
Informations de copyright
© 2024. The Author(s).
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