Proteome-scale recombinant standards and a robust high-speed search engine to advance cross-linking MS-based interactomics
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.
Authors
- Diogo Borges Lima (ORCID: https://orcid.org/0000-0001-6056-0825)
- Louise Ulrich Kurt (ORCID: https://orcid.org/0000-0002-9703-7226)
- Boris Bogdanow (ORCID: https://orcid.org/0000-0002-9634-7353)
- Fábio C. Gozzo (ORCID: https://orcid.org/0000-0002-5270-4427)
- Paulo C. Carvalho (ORCID: https://orcid.org/0000-0001-6530-3350)
- Zehong Zhang (ORCID: https://orcid.org/0000-0003-1309-4395)
- Max Ruwolt (ORCID: https://orcid.org/0009-0000-7220-406X)
- Milan Avila Clasen (ORCID: https://orcid.org/0000-0002-9118-7581)
- Julia Ruta (ORCID: https://orcid.org/0009-0007-0524-6885)
- Fan Liu (ORCID: https://orcid.org/0000-0002-2358-549X)
- Cong Wang
- Tao Chen (ORCID: https://orcid.org/0000-0001-9047-3343)
- Shuai Wang (ORCID: https://orcid.org/0009-0002-7506-5426)
Institutions
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (DE)
- Hospital de Clínicas da Unicamp (BR)
- Fundação Carlos Chagas (BR)
- Charité - Universitätsmedizin Berlin (DE)
Publication Details
- Journal
- Nature Methods
- Published
- 2024-10-31
- DOI
- https://doi.org/10.1038/s41592-024-02478-1
- Citations
- 33
- Primary Topic
- Advanced Proteomics Techniques and Applications
- Type
- article
- Field-Weighted Citation Impact
- 7.94
Funders
- Deutsche Forschungsgemeinschaft
- Conselho Nacional de Desenvolvimento Científico e Tecnológico
- Fundação Araucária
- Instituto Nacional de Ciência e Tecnologia de Bioanalítica
- Leibniz-Gemeinschaft