Navigating through metaproteomics data: A logbook of database searching

Proteomics
Thilo MuthLennart Martens

Abstract

Metaproteomic research involves various computational challenges during the identification of fragmentation spectra acquired from the proteome of a complex microbiome. These issues are manifold and range from the construction of customized sequence databases, the optimal setting of search parameters to limitations in the identification search algorithms themselves. In order to assess the importance of these individual factors, we studied the effect of strategies to combine different search algorithms, explored the influence of chosen database search settings, and investigated the impact of the size of the protein sequence database used for identification. Furthermore, we applied de novo sequencing as a complementary approach to classic database searching. All evaluations were performed on a human intestinal metaproteome dataset. Pyrococcus furiosus proteome data were used to contrast database searching of metaproteomic data to a classic proteomic experiment. Searching against subsets of metaproteome databases and the use of multiple search engines increased the number of identifications. The integration of P. furiosus sequences in a metaproteomic sequence database showcased the limitation of the target-decoy-controlled false di...Continue Reading

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Citations

Dec 22, 2015·Expert Review of Proteomics·Jonathan M Blackburn, Lennart Martens
Nov 13, 2015·Analytical Chemistry·Janice MayneDaniel Figeys
Sep 30, 2015·Proteomics·Joseph A Christie-Oleza, Jean Armengaud
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Aug 19, 2016·Frontiers in Microbiology·David A RussoJagroop Pandhal
Aug 12, 2016·Translational Research : the Journal of Laboratory and Clinical Medicine·Cecilia NoeckerElhanan Borenstein
Oct 19, 2016·Analytical Chemistry·Şule YılmazElien Vandermarliere
Jul 15, 2017·Journal of Proteomics·Xu ZhangDaniel Figeys
Jul 28, 2017·Analytical Chemistry·Xu ZhangDaniel Figeys
Nov 15, 2017·Nature Communications·Kerstin ScheubertSebastian Böcker
Dec 1, 2017·Briefings in Bioinformatics·Aitor Blanco-MíguezAnália Lourenço
May 28, 2019·Nature Methods·Siegfried GessulatMathias Wilhelm
Jul 20, 2019·Proteomics·Danielle L PetersDaniel Figeys
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Jul 5, 2016·Expert Review of Proteomics·Thilo MuthLennart Martens
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Feb 3, 2021·Journal of Proteome Research·Ariane BassignaniCatherine Juste
Feb 15, 2021·Journal of Proteomics·Robert StarkeFelipe Bastida
May 24, 2021·Cell Systems·Hugo B C KleikampMartin Pabst

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