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A pipeline for differential proteomics in unsequenced species

Sule Yilmaz-Rumpf (UGent) , 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
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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.
Keywords
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

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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.
@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},
}

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