PXD003880

PXD003880 is an original dataset announced via ProteomeXchange.

Title	Xilmass: a new approach towards the identification of cross-linked peptides
Description	Chemical cross-linking coupled with mass spectrometry plays an important role in unravelling protein interactions, especially weak and transient interactions. Moreover, cross-linking complements several structure determination approaches such as cryo-EM. Although several computational approaches are available for the annotation of spectra obtained from cross-linked peptides, there remains room for improvement. Here, we present Xilmass, a novel algorithm to identify cross-linked peptides that introduces two new concepts: (i) the cross-linked peptides are represented in a novel way in the search database that explicitly encodes cross-linking sites and (ii) the scoring function from the Andromeda algorithm was adapted to score against a theoretical MS spectrum that contains the peaks from all the possible fragment ions of a cross-linked peptide pair. The performance of Xilmass was subsequently evaluated against the recently published Kojak and the popular pLink algorithms on a data set that contains calmodulin-plectin.
HostingRepository	PRIDE
AnnounceDate	2016-09-27
AnnouncementXML	Submission_2016-09-27_03:58:19.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Sule Yilmaz
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2016-03-30 08:05:42	ID requested
⏵ 1	2016-09-27 03:58:21	announced

Y, ı, lmaz Ş, Drepper F, Hulstaert N, Č, erni, č M, Gevaert K, Economou A, Warscheid B, Martens L, Vandermarliere E, Xilmass: A New Approach toward the Identification of Cross-Linked Peptides. Anal Chem, 88(20):9949-9957(2016) [pubmed]

curator keyword: Technical

submitter keyword: human, calmodulin, the actin-binding domain (ABD) of plectin, cross-linking, DSS

Lennart Martens
contact affiliation	Group Leader
contact email	lennart.martens@ugent.be
lab head
Sule Yilmaz
contact affiliation	UGent-VIB
contact email	sule.yilmaz@vib-ugent.be
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/2016/09/PXD003880

PRIDE project URI

• PRIDE
  1. PXD003880
     1. Label: PRIDE project
     2. Name: Xilmass: a new approach towards the identification of cross-linked peptides