Bioinformatic analysis to investigate metaproteome composition using trans-proteomic pipeline

Steven He, Shoba Ranganathan*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

1 Citation (Scopus)
63 Downloads (Pure)


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 languageEnglish
Article numbere506
Pages (from-to)1-25
Number of pages25
JournalCurrent Protocols
Issue number7
Publication statusPublished - 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.


  • mass spectrometry
  • metaproteomics
  • microbial species


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