| Author | Clasen, Milan Avila | |
| Author | Ruwolt, Max | |
| Author | Wang, Cong | |
| Author | Ruta, Julia | |
| Author | Bogdanow, Boris | |
| Author | Kurt, Louise U | |
| Author | Zhang, Zehong | |
| Author | Wang, Shuai | |
| Author | Gozzo, Fabio C | |
| Author | Chen, Tao | |
| Author | Carvalho, Paulo C | |
| Author | Lima, Diogo Borges | |
| Author | Liu, Fan | |
| Access date | 2024-12-16T11:46:23Z | |
| Available date | 2024-12-16T11:46:23Z | |
| Document date | 2024 | |
| Citation | CLASEN, M.A. et al. Proteome-scale recombinant standards and a robust high-speed search engine to advance cross-linking MS-based interactomics. Nature Methods, v. 21, p.2327–2335, 2024. | en_US |
| ISSN | 1548-7105 | en_US |
| URI | https://www.arca.fiocruz.br/handle/icict/67600 | |
| Language | eng | en_US |
| Publisher | Springer Nature | en_US |
| Rights | open access | en_US |
| Subject in Portuguese | Proteômica | en_US |
| Subject in Portuguese | Interatômica | en_US |
| Title | Proteome-scale recombinant standards and a robust high-speed search engine to advance cross-linking MS-based interactomics | en_US |
| Type | Article | en_US |
| DOI | 10.1038/s41592-024-02478-1 | |
| Abstract | 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 fnd that Scout ofers 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. | en_US |
| Affilliation | Fundação Oswaldo Cruz. Instituto Carlos Chagas. Curitiba, PR, Brasil. | en_US |
| Affilliation | Leibniz-Forschungsinstitut für Molekulare Pharmakologie. Department of Structural Biology. Berlin, Germany. | en_US |
| Affilliation | Leibniz-Forschungsinstitut für Molekulare Pharmakologie. Department of Structural Biology. Berlin, Germany. | en_US |
| Affilliation | Leibniz-Forschungsinstitut für Molekulare Pharmakologie. Department of Structural Biology. Berlin, Germany. | en_US |
| Affilliation | Leibniz-Forschungsinstitut für Molekulare Pharmakologie. Department of Structural Biology. Berlin, Germany. | en_US |
| Affilliation | Fundação Oswaldo Cruz. Instituto Carlos Chagas. Curitiba, PR, Brasil. | en_US |
| Affilliation | Leibniz-Forschungsinstitut für Molekulare Pharmakologie. Department of Structural Biology. Berlin, Germany. | en_US |
| Affilliation | Absea Biotechnology Ltd. ZGC Life Science Park. Beijing, China. | en_US |
| Affilliation | Universidade Estadual de Campinas. Departamento de Química. Campinas, SP, Brasil. | en_US |
| Affilliation | Absea Biotechnology Ltd. ZGC Life Science Park. Beijing, China. | en_US |
| Affilliation | Fundação Oswaldo Cruz. Instituto Carlos Chagas. Curitiba, PR, Brasil. | en_US |
| Affilliation | Leibniz-Forschungsinstitut für Molekulare Pharmakologie. Department of Structural Biology. Berlin, Germany. | en_US |
| Affilliation | Leibniz-Forschungsinstitut für Molekulare Pharmakologie. Department of Structural Biology. Berlin, Germany / Charité Universitätsmedizin Berlin. Berlin, Germany. | en_US |
| Subject | Proteomics | en_US |
| Subject | Interactomics | en_US |
| Subject | Cross-linking mass spectrometry | en_US |
| Subject | XL-MS | en_US |
| DeCS | Espectrometria de Massas | en_US |
| DeCS | Proteômica | en_US |
