PXD001677

PXD001677 is an original dataset announced via ProteomeXchange.

Title	SIM-XL: a powerful and user-friendly tool for peptide cross-linking analysis
Description	Chemical cross-linking has emerged as a powerful approach for the structural characterization of proteins and protein complexes. However, the correct identification of covalently linked (cross-linked) peptides analyzed by tandem mass spectrometry is still an open challenge. Here we present SIM-XL, a software tool that can analyze data generated through commonly used cross-linkers (e.g., BS3/DSS, etc.). Our software introduces a new paradigm for search-space reduction, which ultimately accounts for its increase in speed and sensitivity. Moreover, our search engine is the first to capitalize on reporter ions for selecting tandem mass spectra derived from cross-linked peptides. It also makes available a 2D interaction map and a spectrum-annotation tool unmatched by any of its kind. We show SIM-XL to be more sensitive and faster than a competing tool when analyzing a dataset obtained from the human HSP90. The software is freely available for academic use at http://patternlabforproteomics.org/sim-xl.
HostingRepository	PRIDE
AnnounceDate	2017-01-17
AnnouncementXML	Submission_2017-01-17_07:27:51.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD001677
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Diogo Borges Lima
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	DSS; Disuccinimidyl Suberate - DSS
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2015-01-14 06:33:02	ID requested
1	2015-02-02 03:04:31	announced
2	2015-02-02 03:07:42	announced	Updated publication reference for PubMed record(s): 25638023.
⏵ 3	2017-01-17 07:27:53	announced	Updated project metadata.

Lima DB, de Lima TB, Balbuena TS, Neves-Ferreira AGC, Barbosa VC, Gozzo FC, Carvalho PC, SIM-XL: A powerful and user-friendly tool for peptide cross-linking analysis. J Proteomics, 129():51-55(2015) [pubmed]

curator keyword: Technical

submitter keyword: cross-linked peptides, search engine, cross-linking

Paulo Costa Carvalho
contact affiliation	Carlos Chagas Institute - Fiocruz - Brazil
contact email	paulo@pcarvalho.com
lab head
Diogo Borges Lima
contact affiliation	Fiocruz - Brazil
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/2015/02/PXD001677

PRIDE project URI

• PRIDE
  1. PXD001677
     1. Label: PRIDE project
     2. Name: SIM-XL: a powerful and user-friendly tool for peptide cross-linking analysis