Bioinformatic analysis to investigate metaproteome composition using trans-proteomic pipeline

Steven He; Shoba Ranganathan

doi:10.1002/cpz1.506

Bioinformatic analysis to investigate metaproteome composition using trans-proteomic pipeline

Steven He, Shoba Ranganathan^*

^*Corresponding author for this work

Applied BioSciences

Research output: Contribution to journal › Article › peer-review

1 Citation (Scopus)

112 Downloads (Pure)

Abstract

With evidence emerging that the microbiome has a role in the onset of many human diseases, including cancer, analyzing these microbial communities and their proteins (i.e., the metaproteome) has become a powerful research tool. The Trans-Proteomic Pipeline (TPP) is a free, comprehensive software suite that facilitates the analysis of mass spectrometry (MS) data. By utilizing available microbial proteomes, TPP can identify microbial proteins and species, with an acceptable peptide false-discovery rate (FDR). An application to a publicly available oral cancer dataset is presented as an example to identify the viral metaproteome on the oral cancer invasive tumor front.

Original language	English
Article number	e506
Pages (from-to)	1-25
Number of pages	25
Journal	Current Protocols
Volume	2
Issue number	7
DOIs	https://doi.org/10.1002/cpz1.506
Publication status	Published - 21 Jul 2022

Bibliographical note

Copyright the Author(s) 2022. Version archived for private and non-commercial use with the permission of the author/s and according to publisher conditions. For further rights please contact the publisher.

Keywords

mass spectrometry
metaproteomics
microbial species

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10.1002/cpz1.506

Publisher version (open access)Final published version, 6.48 MBLicence: CC BY-NC-ND

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Bioinformatic analysis to investigate metaproteome composition using trans-proteomic pipeline

Abstract

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Keywords

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