The Association of Biomolecular Resource Facilities Proteome Informatics Research Group Study on Metaproteomics (iPRG-2020)

Published

August 7, 2023

Author(s)

Pratik Jagtap, Michael Hoopmann, Ben Neely, Anthony Harvey, Lukas Käll, Yasset Perez-Riverol, Milky Abajorga, Julie Thomas, Susan Weintraub, Magnus Palmblad

Abstract

Metaproteomics research using mass spectrometry data has emerged as a powerful strategy to understand the mechanisms underlying microbiome dynamics and the interaction of microbiomes with their immediate environment. Recent advances in sample preparation, data acquisition, and bioinformatics workflows have greatly contributed to progress in this field. In 2020, the Association of Biomolecular Research Facilities Proteome Informatics Research Group launched a collaborative study to assess the bioinformatics options available for metaproteomics research. The study was conducted in 2 phases. In the first phase, participants were provided with mass spectrometry data files and were asked to identify the taxonomic composition and relative taxa abundances in the samples without supplying any protein sequence databases. The most challenging question asked of the participants was to postulate the nature of any biological phenomena that may have taken place in the samples, such as interactions among taxonomic species. In the second phase, participants were provided a protein sequence database composed of the species present in the sample and were asked to answer the same set of questions as for phase 1. In this report, we summarize the data processing methods and tools used by participants, including database searching and software tools used for taxonomic and functional analysis. This study provides insights into the status of metaproteomics bioinformatics in participating laboratories and core facilities

Citation

The Journal of Biomolecular Techniques

Volume

34

Issue

3

Pub Type

Journals

Download Paper

https://doi.org/10.7171/3fc1f5fe.a058bad4

Local Download

Keywords

metaproteomics, Microbiome, Bioinformatics, Taxonomy, Mass Spectrometry

Citation

Jagtap, P. , Hoopmann, M. , Neely, B. , Harvey, A. , Käll, L. , Perez-Riverol, Y. , Abajorga, M. , Thomas, J. , Weintraub, S. and Palmblad, M. (2023), The Association of Biomolecular Resource Facilities Proteome Informatics Research Group Study on Metaproteomics (iPRG-2020), The Journal of Biomolecular Techniques, [online], https://doi.org/10.7171/3fc1f5fe.a058bad4, https://tsapps.nist.gov/publication/get_pdf.cfm?pub_id=934930 (Accessed October 31, 2024)