PXD042173-1

PXD042173 is an original dataset announced via ProteomeXchange.

Title	Proteome-scale recombinant standard datasets for XL-MS
Description	This submission includes the complete set of raw data generated from the analytical standard, the concept of which is 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. This submission includes 5 raw datasets (batches 1-5), each comprising 64 randomly selected human proteins engaging in up to 224 allowed protein-protein interactions per dataset. The data were searched with Scout (v. 1.4.14, https://github.com/diogobor/Scout) and results are reported in mzIdentML 1.2.0 format. For the specific results reported in our original publication, please refer to PXD042173.
HostingRepository	PRIDE
AnnounceDate	2024-08-06
AnnouncementXML	Submission_2024-08-06_02:38:24.060.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD042173
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Diogo Borges Lima
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2023-05-12 04:25:22	ID requested
⏵ 1	2024-08-06 02:38:24	announced

10.6019/PXD042173;

submitter keyword: crosslinking mass spectrometry, search engine, bioinformatics

Fan Liu
contact affiliation	Leibniz-Forschungsinstitut für Molekulare Pharmakologie
contact email	fliu@fmp-berlin.de
lab head
Diogo Borges Lima
contact affiliation	Leibniz-Forschungsinstitut für Molekulare Pharmakologie
contact email	diogobor@gmail.com
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/PXD042173

PRIDE project URI

• PRIDE
  1. PXD042173
     1. Label: PRIDE project
     2. Name: Proteome-scale recombinant standard datasets for XL-MS