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 proteomics...

Peptide Identification Using Tandem Mass Spectrometry

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...

You might also read

Related Articles

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

Sort by

Same author

Paradoxical non-catalytic kinase functions are driven by inhibitor-induced displacement of autoinhibitory domains.

Molecular systems biology·2026

Same author

The environmental stress response regulates biophysics of the cytoplasm and survival in quiescence.

The Journal of cell biology·2026

Same author

Structural alterations in PPP1R13L, SAE1, ATP5A1 and PCK2 disrupt NF-κB signalling and mitochondrial metabolism in primary dermal fibroblasts in systemic sclerosis.

Rheumatology (Oxford, England)·2026

Same author

Structure-function relationship of alpha-synuclein fibrillar polymorphs derived from distinct synucleinopathies.

Molecular systems biology·2026

Same author

3D Proteomics: Structural, Functional, Chemical and Biomarker Discovery Proteomics With LiP-MS.

Molecular & cellular proteomics : MCP·2026

Same author

What questions currently beyond reach do you hope systems approaches will enable addressing in the next decade?

Cell systems·2026

Search research articles

Related Experiment Video

Updated: Jul 14, 2026

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

The implications of proteolytic background for shotgun proteomics.

Paola Picotti¹, Ruedi Aebersold, Bruno Domon

¹Institute of Molecular Systems Biology, ETH Zürich, CH-8093, Zürich, Switzerland.

Molecular & Cellular Proteomics : MCP

|May 30, 2007

Summary

Proteomics analysis reveals that proteins generate far more peptides than previously assumed. This complexity challenges current methods and necessitates new strategies for comprehensive proteome analysis.

More Related Videos

Shotgun Proteomics Sample Processing Automated by an Open-Source Lab Robot

Shotgun Proteomics Sample Processing Automated by an Open-Source Lab Robot

Published on: October 28, 2021

Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification

Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification

Published on: November 15, 2017

Related Experiment Videos

Last Updated: Jul 14, 2026

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

Shotgun Proteomics Sample Processing Automated by an Open-Source Lab Robot

Shotgun Proteomics Sample Processing Automated by an Open-Source Lab Robot

Published on: October 28, 2021

Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification

Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification

Published on: November 15, 2017

Area of Science:

Proteomics
Biochemistry
Analytical Chemistry

Background:

Liquid chromatography coupled to tandem mass spectrometry is the primary method for analyzing complex peptide mixtures in proteomics.
This technique relies on the assumption of a limited, predictable peptide output per protein.

Purpose of the Study:

To investigate the assumption of limited peptide generation per protein using a targeted sequencing strategy.
To assess the complexity of peptide mixtures in proteomic samples.

Main Methods:

Targeted peptide sequencing strategy.
Utilized inclusion lists to guide peptide fragmentation attempts.
Analyzed complex peptide mixtures generated by protein proteolysis.

Main Results:

The number of observed peptides per protein is at least ten times greater than previously estimated.
Revealed unexpected complexity in proteomics samples.

Conclusions:

The assumption of limited peptide generation is incorrect, highlighting significant technical challenges in current proteomics.
The findings explain puzzling results in the field and underscore the need for novel, comprehensive proteome analysis strategies.