Current Progress and Critical Challenges to Overcome in the Bioinformatics of Mass Spectrometry-based Metaproteomics

Overview

Journal Comput Struct Biotechnol J

Specialty Biotechnology

Date 2023 Feb 23

PMID 36817962

Authors

Nobuaki Miura

Shujiro Okuda

Affiliations

Soon will be listed here.

Abstract

Metaproteomics is a relatively young field that has only been studied for approximately 15 years. Nevertheless, it has the potential to play a key role in disease research by elucidating the mechanisms of communication between the human host and the microbiome. Although it has been useful in developing an understanding of various diseases, its analytical strategies remain limited to the extended application of proteomics. The sequence databases in metaproteomics must be large because of the presence of thousands of species in a typical sample, which causes problems unique to large databases. In this review, we demonstrate the usefulness of metaproteomics in disease research through examples from several studies. Additionally, we discuss the challenges of applying metaproteomics to conventional proteomics analysis methods and introduce studies that may provide clues to the solutions. We also discuss the need for a standard false discovery rate control method for metaproteomics to replace common target-decoy search approaches in proteomics and a method to ensure the reliability of peptide spectrum match.

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