PXD003625-1

PXD003625 is an original dataset announced via ProteomeXchange.

Title	A differential proteomics pipeline for unsequenced species
Description	Shotgun proteomics experiments often take the form of a differential analysis, where two or more samples are compared against each other. The objective is to identify proteins that are either unique to a specific sample or a set of samples (qualitative differential proteomics), or that are significantly differentially expressed in one or more samples (quantitative differential proteomics). However, the success depends on the availability of a reliable protein sequence database for each sample. In order to perform such an analysis in the absence of a database, we here propose a novel, generic pipeline comprising a modified spectral similarity score derived from database search algorithms that compares samples at the spectrum level to detect unique spectra. We applied our pipeline to compare the two parasitic tapeworms: Taenia solium and Taenia hydatigena, of which only the former poses a threat to humans. Furthermore, because the genome of Taenia solium recently became available, we were able to prove the effectiveness and reliability of our pipeline a posteriori
HostingRepository	PRIDE
AnnounceDate	2016-04-29
AnnouncementXML	Submission_2016-04-29_00:41:23.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Sule Yilmaz
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562; scientific name: Taenia solium (Pork tapeworm); NCBI TaxID: 6204; scientific name: Taenia hydatigena (Tapeworm); NCBI TaxID: 85431;
ModificationList	2-pyrrolidone-5-carboxylic acid (Gln); monohydroxylated residue; iodoacetamide derivatized residue
Instrument	amaZon ETD

Revision	Datetime	Status	ChangeLog Entry
0	2016-02-12 03:35:20	ID requested
⏵ 1	2016-04-29 00:41:24	announced
2	2024-10-22 04:10:09	announced	2024-10-22: Updated project metadata.

Y, ı, lmaz Ş, Victor B, Hulstaert N, Vandermarliere E, Barsnes H, Degroeve S, Gupta S, Sticker A, Gabri, ë, l S, Dorny P, Palmblad M, Martens L, A Pipeline for Differential Proteomics in Unsequenced Species. J Proteome Res, 15(6):1963-70(2016) [pubmed]

curator keyword: Biomedical

submitter keyword: Taenia solium, Taenia hydatigena, Escherichia coli

Lennart Martens
contact affiliation	VIB-Ghent University
contact email	lennart.martens@vib-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/2016/04/PXD003625

PRIDE project URI

• PRIDE
  1. PXD003625
     1. Label: PRIDE project
     2. Name: A differential proteomics pipeline for unsequenced species