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Related Concept Videos

Proteomics01:33

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 proteomics...
Protein Networks02:26

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
Peptide Identification Using Tandem Mass Spectrometry01:33

Peptide Identification Using Tandem Mass Spectrometry

Tandem mass spectrometry, also known as MS/MS or MS2, is an analytical technique that employs two mass analyzers. Essentially it is a series of mass spectrometers that helps isolate a particular biomolecule and then helps study its chemical properties.
This technique helps gather information regarding the protein from which the peptide was obtained and to study the peptides’ amino acid sequence. Identifying peptides from a complex mixture is an important component of the growing field of...

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Related Experiment Video

Updated: May 16, 2026

A Clinical Metaproteomics Workflow Implemented within Galaxy Bioinformatics Platform to Analyze Host-Microbiome Interactions Underlying Human Disease
09:52

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

Published on: January 10, 2025

Current methods for global proteome identification.

Marc Vaudel1, Albert Sickmann, Lennart Martens

  • 1Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Dortmund, Germany.

Expert Review of Proteomics
|December 1, 2012
PubMed
Summary
This summary is machine-generated.

Recent advances in shotgun proteomics enable automated identification of entire proteomes, moving beyond single protein analysis. This review covers state-of-the-art methods and free software for this powerful technique.

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Last Updated: May 16, 2026

A Clinical Metaproteomics Workflow Implemented within Galaxy Bioinformatics Platform to Analyze Host-Microbiome Interactions Underlying Human Disease
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The Application of Open Searching-based Approaches for the Identification of Acinetobacter baumannii O-linked Glycopeptides
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Area of Science:

  • Biochemistry
  • Proteomics
  • Bioinformatics

Background:

  • Protein identification has rapidly advanced from single-protein analysis to comprehensive proteome-wide studies.
  • This evolution is driven by peptide-centric, gel-free techniques, notably shotgun proteomics.
  • These methods require sophisticated experimental designs and advanced data processing.

Purpose of the Study:

  • To provide an overview of the current shotgun proteomics identification workflow.
  • To highlight state-of-the-art methods and freely available software tools.
  • To discuss the integration of proteomics data in across-omics studies.

Main Methods:

  • Review of current literature on shotgun proteomics.
  • Identification and categorization of key experimental and data processing methods.
  • Focus on accessible, open-source software solutions.

Main Results:

  • Detailed overview of a typical shotgun proteomics workflow.
  • Compilation of leading methods and associated software.
  • Emphasis on the utility of freely available bioinformatics tools.

Conclusions:

  • Shotgun proteomics offers automated, large-scale protein identification.
  • The workflow relies on advanced experimental and computational approaches.
  • Future directions include integrating proteomics into broader multi-omics research.