Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Proteomics

Proteomics

A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

MegaPX: fast and space-efficient peptide assignment method using IBF-based multi-indexing.

Bioinformatics (Oxford, England)·2026

Same author

The Peptonizer2000: Bringing Confidence to Metaproteomics.

Journal of proteome research·2026

Same author

From Identification to Insight: Making Full Use of the Diagnostic Potential of MS/MS Proteotyping in Clinical Microbiology Using Efficient Bioinformatics.

Journal of proteome research·2025

Same author

The microbiologist's guide to metaproteomics.

iMeta·2025

Same author

MultiStageSearch: An Iterative Workflow for Unbiased Taxonomic Analysis of Pathogens Using Proteogenomics.

Journal of proteome research·2025

Same author

FIORA: Local neighborhood-based prediction of compound mass spectra from single fragmentation events.

Nature communications·2025

Same journal

Mapping the 3D Chromosome Organization of a Biosynthetic Gene Cluster by Capture Hi-C (CHi-C).

Methods in molecular biology (Clifton, N.J.)·2026

Same journal

Mapping the 3D Chromosome Organization of Streptomyces by Hi-C.

Methods in molecular biology (Clifton, N.J.)·2026

Same journal

CUT&Tag Epigenomic Profiling of Biosynthetic Gene Clusters in Arabidopsis thaliana.

Methods in molecular biology (Clifton, N.J.)·2026

Same journal

Rhizobium rhizogenes-Mediated Hairy Root Transformation Protocol for Lotus japonicus and Other Legumes.

Methods in molecular biology (Clifton, N.J.)·2026

Same journal

Characterization of Bioactive Saponins from Sea Cucumbers.

Methods in molecular biology (Clifton, N.J.)·2026

Same journal

Methods for Functional Validation of Terpenoid Metabolic Clusters in Nicotiana benthamiana and Aspergillus oryzae.

Methods in molecular biology (Clifton, N.J.)·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Jun 22, 2025

A Clinical Metaproteomics Workflow Implemented within Galaxy Bioinformatics Platform to Analyze Host-Microbiome Interactions Underlying Human Disease

A Clinical Metaproteomics Workflow Implemented within Galaxy Bioinformatics Platform to Analyze Host-Microbiome Interactions Underlying Human Disease

Published on: January 10, 2025

Bioinformatic Workflows for Metaproteomics.

Tanja Holstein^1,2,3, Thilo Muth^4,5

¹Section eScience (S.3), Federal Institute for Materials Research and Testing, Berlin, Germany.

Methods in Molecular Biology (Clifton, N.J.)

|June 28, 2024

Summary

This summary is machine-generated.

Metaproteomics analyzes microbial community proteins to understand microbiome function and composition. This study reviews essential bioinformatic tools and protocols for accurate metaproteomic analysis.

Keywords:

Bioinformatic workflow Functional assignment Metaproteomics Microbiomes Protein quantification Proteomics Taxonomic assignment

More Related Videos

An Aquatic Microbial Metaproteomics Workflow: From Cells to Tryptic Peptides Suitable for Tandem Mass Spectrometry-based Analysis

An Aquatic Microbial Metaproteomics Workflow: From Cells to Tryptic Peptides Suitable for Tandem Mass Spectrometry-based Analysis

Published on: September 15, 2015

Comprehensive Workflow of Mass Spectrometry-based Shotgun Proteomics of Tissue Samples

Comprehensive Workflow of Mass Spectrometry-based Shotgun Proteomics of Tissue Samples

Published on: November 13, 2021

Related Experiment Videos

Last Updated: Jun 22, 2025

A Clinical Metaproteomics Workflow Implemented within Galaxy Bioinformatics Platform to Analyze Host-Microbiome Interactions Underlying Human Disease

A Clinical Metaproteomics Workflow Implemented within Galaxy Bioinformatics Platform to Analyze Host-Microbiome Interactions Underlying Human Disease

Published on: January 10, 2025

An Aquatic Microbial Metaproteomics Workflow: From Cells to Tryptic Peptides Suitable for Tandem Mass Spectrometry-based Analysis

An Aquatic Microbial Metaproteomics Workflow: From Cells to Tryptic Peptides Suitable for Tandem Mass Spectrometry-based Analysis

Published on: September 15, 2015

Comprehensive Workflow of Mass Spectrometry-based Shotgun Proteomics of Tissue Samples

Comprehensive Workflow of Mass Spectrometry-based Shotgun Proteomics of Tissue Samples

Published on: November 13, 2021

Area of Science:

Microbiology
Bioinformatics
Systems Biology

Background:

Microbiome influence on ecology and human health is increasingly recognized.
Investigating microbial community composition and function requires specialized techniques.
Metaproteomics offers insights into microbial taxonomy, function, and quantity.

Purpose of the Study:

To provide a comprehensive overview of current bioinformatic solutions for metaproteomics.
To detail metaproteomic post-processing steps.
To highlight ten specific bioinformatic software solutions.

Main Methods:

Review of existing bioinformatic software and protocols for metaproteomics.
Explanation of proteomic database search and post-processing.
Focus on software for identification, quantification, and taxonomic/functional assignment.

Main Results:

Identification of ten key bioinformatic software solutions for metaproteomics.
Detailed explanation of database-driven identification and quantification methods.
Coverage of taxonomic and functional assignment strategies.

Conclusions:

Specialized bioinformatic methods are crucial for metaproteomic analysis due to community complexity.
The reviewed software and protocols aid in comprehensive microbiome investigation.
This work serves as a guide to current metaproteomic bioinformatic approaches.