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PXD052022

PXD052022 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleDataset used to guide the development of Scout and bechmark XL-MS search engines
DescriptionThis 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).
HostingRepositoryPRIDE
AnnounceDate2025-03-18
AnnouncementXMLSubmission_2025-03-18_08:44:39.936.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterMax Ruwolt
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListmonohydroxylated residue; iodoacetamide derivatized residue
InstrumentOrbitrap Fusion Lumos
Dataset History
RevisionDatetimeStatusChangeLog Entry
02024-05-06 09:09:47ID requested
12024-08-03 12:26:58announced
22024-10-22 06:52:25announced2024-10-22: Updated project metadata.
32025-03-18 08:44:40announced2025-03-18: 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 affiliationLeibniz-Forschungsinstitut fuer Molekulare Pharmakologie
contact emailFliu@fmp-berlin.de
lab head
Max Ruwolt
contact affiliationLeibniz-Forschungsinstitut for Molecular Pharmacology
contact emailruwolt@fmp-berlin.de
dataset submitter
Full Dataset Link List
Dataset FTP location
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Repository Record List
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