PXD052022

PXD052022 is an original dataset announced via ProteomeXchange.

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

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.

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;

submitter keyword: search engine,cross-linking, PPI, benchmarking, XL-MS, FDR

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

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2024/08/PXD052022

PRIDE project URI

• PRIDE
  1. PXD052022
     1. Label: PRIDE project
     2. Name: Dataset used to guide the development of Scout and bechmark XL-MS search engines