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A pipeline for differential proteomics in unsequenced species

Sule Yilmaz-Rumpf, Bjorn Victor, Niels Hulstaert UGent, Elien Vandermarliere UGent, Harald Barsnes, Sven Degroeve UGent, Surya Gupta UGent, Adriaan Sticker UGent, Sarah Gabriël UGent, Pierre Dorny UGent, et al. (2016) JOURNAL OF PROTEOME RESEARCH. 15(6). p.1963-1970
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. To perform such an analysis in the absence of a database, we here propose a novel, generic pipeline comprising an adapted 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 two parasitic tapeworms: Taenia solium and Taenia hydatigena, of which only the former poses a threat to humans. Furthermore, because the genome of T. solium recently became available, we were able to prove the effectiveness and reliability of our pipeline a posteriori.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
mass spectrometry, unsequenced species, SPECTROMETRY-BASED PROTEOMICS, differential proteomics, unique spectrum, TANDEM MASS-SPECTRA, FREE SHOTGUN PROTEOMICS, TAENIA-SOLIUM, DATA SETS, COMPUTATIONAL ANALYSIS, MS/MS SPECTRA, PROTEIN, IDENTIFICATION, PEPTIDE
journal title
JOURNAL OF PROTEOME RESEARCH
J. Proteome Res.
volume
15
issue
6
pages
1963 - 1970
Web of Science type
Article
Web of Science id
000377319200020
JCR category
BIOCHEMICAL RESEARCH METHODS
JCR impact factor
4.268 (2016)
JCR rank
14/77 (2016)
JCR quartile
1 (2016)
ISSN
1535-3893
DOI
10.1021/acs.jproteome.6b00140
language
English
UGent publication?
yes
classification
A1
copyright statement
I have transferred the copyright for this publication to the publisher
id
7902724
handle
http://hdl.handle.net/1854/LU-7902724
date created
2016-06-30 20:56:19
date last changed
2017-03-06 11:27:07
@article{7902724,
  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. To perform such an analysis in the absence of a database, we here propose a novel, generic pipeline comprising an adapted 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 two parasitic tapeworms: Taenia solium and Taenia hydatigena, of which only the former poses a threat to humans. Furthermore, because the genome of T. solium recently became available, we were able to prove the effectiveness and reliability of our pipeline a posteriori.},
  author       = {Yilmaz-Rumpf, Sule and Victor, Bjorn and Hulstaert, Niels and Vandermarliere, Elien and Barsnes, Harald and Degroeve, Sven and Gupta, Surya and Sticker, Adriaan and Gabri{\"e}l, Sarah and Dorny, Pierre and Palmblad, Magnus and Martens, Lennart},
  issn         = {1535-3893},
  journal      = {JOURNAL OF PROTEOME RESEARCH},
  keyword      = {mass spectrometry,unsequenced species,SPECTROMETRY-BASED PROTEOMICS,differential proteomics,unique spectrum,TANDEM MASS-SPECTRA,FREE SHOTGUN PROTEOMICS,TAENIA-SOLIUM,DATA SETS,COMPUTATIONAL ANALYSIS,MS/MS SPECTRA,PROTEIN,IDENTIFICATION,PEPTIDE},
  language     = {eng},
  number       = {6},
  pages        = {1963--1970},
  title        = {A pipeline for differential proteomics in unsequenced species},
  url          = {http://dx.doi.org/10.1021/acs.jproteome.6b00140},
  volume       = {15},
  year         = {2016},
}

Chicago
Yilmaz-Rumpf, Sule, Bjorn Victor, Niels Hulstaert, Elien Vandermarliere, Harald Barsnes, Sven Degroeve, Surya Gupta, et al. 2016. “A Pipeline for Differential Proteomics in Unsequenced Species.” Journal of Proteome Research 15 (6): 1963–1970.
APA
Yilmaz-Rumpf, S., Victor, B., Hulstaert, N., Vandermarliere, E., Barsnes, H., Degroeve, S., Gupta, S., et al. (2016). A pipeline for differential proteomics in unsequenced species. JOURNAL OF PROTEOME RESEARCH, 15(6), 1963–1970.
Vancouver
1.
Yilmaz-Rumpf S, Victor B, Hulstaert N, Vandermarliere E, Barsnes H, Degroeve S, et al. A pipeline for differential proteomics in unsequenced species. JOURNAL OF PROTEOME RESEARCH. 2016;15(6):1963–70.
MLA
Yilmaz-Rumpf, Sule, Bjorn Victor, Niels Hulstaert, et al. “A Pipeline for Differential Proteomics in Unsequenced Species.” JOURNAL OF PROTEOME RESEARCH 15.6 (2016): 1963–1970. Print.