PXD052022 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Dataset used to guide the development of Scout and bechmark XL-MS search engines |
Description | This submission includes the raw data analyzed and search results described in our manuscript “Proteome-Scale Recombinant Standards And A Robust High-Speed Search Engine To Advance Cross-Linking MS-Based Interactomics”. In this study, we develop a strategy to generate a well-controlled XL-MS standard by systematically mixing and cross-linking recombinant proteins. The standard can be split into independent datasets, each of which has the MS2-level complexity of a typical proteome-wide XL-MS experiment. The raw datasets included in this submission were used to (1) guide the development of Scout, a machine learning-based search engine for XL-MS with MS-cleavable cross-linkers (batch 1), test different LC-MS acquisition methods (batch 2), and directly compare Scout to widely used XL-MS search engines (batches 3 and 4). |
HostingRepository | PRIDE |
AnnounceDate | 2025-03-18 |
AnnouncementXML | Submission_2025-03-18_08:44:39.936.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Max Ruwolt |
SpeciesList | scientific name: Homo sapiens (Human); NCBI TaxID: 9606; |
ModificationList | monohydroxylated residue; iodoacetamide derivatized residue |
Instrument | Orbitrap Fusion Lumos |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2024-05-06 09:09:47 | ID requested | |
1 | 2024-08-03 12:26:58 | announced | |
2 | 2024-10-22 06:52:25 | announced | 2024-10-22: Updated project metadata. |
⏵ 3 | 2025-03-18 08:44:40 | announced | 2025-03-18: Updated project metadata. |
Publication List
Clasen MA, Ruwolt M, Wang C, Ruta J, Bogdanow B, Kurt LU, Zhang Z, Wang S, Gozzo FC, Chen T, Carvalho PC, Lima DB, Liu F, Proteome-scale recombinant standards and a robust high-speed search engine to advance cross-linking MS-based interactomics. Nat Methods, 21(12):2327-2335(2024) [pubmed] |
10.1038/s41592-024-02478-1; |
Keyword List
submitter keyword: search engine,cross-linking, PPI, benchmarking, XL-MS, FDR |
Contact List
Fan Liu |
contact affiliation | Leibniz-Forschungsinstitut fuer Molekulare Pharmakologie |
contact email | Fliu@fmp-berlin.de |
lab head | |
Max Ruwolt |
contact affiliation | Leibniz-Forschungsinstitut for Molecular Pharmacology |
contact email | ruwolt@fmp-berlin.de |
dataset submitter | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD052022
- Label: PRIDE project
- Name: Dataset used to guide the development of Scout and bechmark XL-MS search engines