Dataset Information

A differential proteomics pipeline for unsequenced species

ABSTRACT: 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

INSTRUMENT(S): amaZon ETD

ORGANISM(S): Taenia Hydatigena (tapeworm) Escherichia Coli Taenia Solium (pork Tapeworm)

TISSUE(S): Metacestode

SUBMITTER: Sule Yilmaz

LAB HEAD: Lennart Martens

PROVIDER: PXD003625 | Pride | 2016-04-29

REPOSITORIES: pride

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Dataset's files

Source:

			Action	DRS
	130125.LC4.IT4.EC.Standard_1-B2c1_01_3690.d_bad_1.mzXML	Mzxml
	130125.LC4.IT4.EC.Standard_1-B2c1_01_3690.d_good_1.mzXML	Mzxml
	130125.LC4.IT4.EC.Standard_1-B2c1_01_3691.d_bad_2.mzXML	Mzxml
	130125.LC4.IT4.EC.Standard_1-B2c1_01_3691.d_good_2.mzXML	Mzxml
	130125.LC4.IT4.EC.Standard_1-B2c1_01_3793.d_bad_3.mzXML	Mzxml

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Publications

A Pipeline for Differential Proteomics in Unsequenced Species.

Yılmaz Şule Ş Victor Bjorn B Hulstaert Niels N Vandermarliere Elien E Barsnes Harald H Degroeve Sven S Gupta Surya S Sticker Adriaan A Gabriël Sarah S Dorny Pierre P Palmblad Magnus M Martens Lennart L

Journal of proteome research 20160502 6

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. T ...[more]

PMID: 27089233

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