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

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

iDeepLC: Chemical Structure Information Yields Improved Retention Time Prediction of Peptides with Unseen Modifications.

Analytical chemistry·2026

Same author

Genomic Exaptation and Regulatory Landscape Shifts as Key Mechanisms Enabling Flatworm Terrestrialization.

Genome biology and evolution·2026

Same author

Proteome-Wide Multipoint Internal Calibration Curves for Evaluating Peptide-Level Linearity in Relative Quantitative Proteomics.

Journal of proteome research·2025

Same author

Koina: Democratizing machine learning for proteomics research.

Nature communications·2025

Same author

Increased LEF1 protein levels and isoform switching drive cell proliferation in chronic lymphocytic leukemia.

Blood·2025

Same author

Context-dependent phosphorylation of CSDE1 drives interactions with ribosomes.

RNA (New York, N.Y.)·2025

Same journal

Deep Plasma Proteomics-Based Diagnostic Panel for Early Detection of Amnestic Mild Cognitive Impairment.

Journal of proteome research·2026

Same journal

Proteomic and Phosphoproteomic Characterization of Disease-Associated Alterations in Nerve Terminals and Protein Inclusions of Alzheimer's Disease Patients.

Journal of proteome research·2026

Same journal

Proteomic Profiling of Endothelial Cells Under Laminar Shear Stress Confirms the Importance of KLF4 in the Regulation of Membrane Protein Expression Compared to Oscillatory Flow.

Journal of proteome research·2026

Same journal

Identification of Age-Associated Circulating Proteins and Lipids in 3800 Comorbidity-Enriched Older Adults from Japan-Based Cohorts Using Olink Assays and MRM Mass Spectrometry.

Journal of proteome research·2026

Same journal

Molecular Solution to the Paradox of Ancient Brain Preservation.

Journal of proteome research·2026

Same journal

From Method-Defined Signals to Reference Measurement Procedures: Two Decades of Mass Spectrometry-Based ProGRP Quantification.

Journal of proteome research·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Mar 8, 2026

Selected Reaction Monitoring Mass Spectrometry for Absolute Protein Quantification

Selected Reaction Monitoring Mass Spectrometry for Absolute Protein Quantification

Published on: August 17, 2015

Peptide Selection for Targeted Protein Quantitation.

Cristina Chiva^1,2, Eduard Sabidó^1,2

¹Proteomics Unit, Centre de Regulació Genòmica (CRG), Barcelona Institute of Science and Technology (BIST) , Dr. Aiguader 88, 08003 Barcelona, Spain.

Journal of Proteome Research

|January 20, 2017

Summary

This summary is machine-generated.

Selecting peptides for targeted proteomics is crucial for accurate protein quantitation. Current rules based on amino acid composition may not guarantee reproducible peptide generation or representative protein abundance.

More Related Videos

Quantification of Proteins Using Peptide Immunoaffinity Enrichment Coupled with Mass Spectrometry

Quantification of Proteins Using Peptide Immunoaffinity Enrichment Coupled with Mass Spectrometry

Published on: July 31, 2011

Detection of Protein Ubiquitination Sites by Peptide Enrichment and Mass Spectrometry

Detection of Protein Ubiquitination Sites by Peptide Enrichment and Mass Spectrometry

Published on: March 23, 2020

Related Experiment Videos

Last Updated: Mar 8, 2026

Selected Reaction Monitoring Mass Spectrometry for Absolute Protein Quantification

Selected Reaction Monitoring Mass Spectrometry for Absolute Protein Quantification

Published on: August 17, 2015

Quantification of Proteins Using Peptide Immunoaffinity Enrichment Coupled with Mass Spectrometry

Quantification of Proteins Using Peptide Immunoaffinity Enrichment Coupled with Mass Spectrometry

Published on: July 31, 2011

Detection of Protein Ubiquitination Sites by Peptide Enrichment and Mass Spectrometry

Detection of Protein Ubiquitination Sites by Peptide Enrichment and Mass Spectrometry

Published on: March 23, 2020

Area of Science:

Proteomics
Biochemistry
Analytical Chemistry

Background:

Targeted proteomics quantifies proteins using a limited set of peptides as proxies.
Discovery proteomics utilizes all identified peptides for abundance estimation.
Peptide selection is critical in targeted proteomics due to limited peptide usage per protein.

Purpose of the Study:

To evaluate the effectiveness of current peptide selection rules in targeted proteomics.
To highlight the limitations of amino acid composition-based rules for peptide selection.
To emphasize the need for improved strategies for selecting peptides that accurately reflect protein abundance.

Main Methods:

Review of existing peptide selection guidelines for targeted proteomics.
Analysis of factors influencing peptide reproducibility and representativeness.
Comparison of rule-based peptide selection with actual experimental outcomes.

Main Results:

Existing peptide selection rules, often based on amino acid composition, are insufficient.
Compliance with these rules does not ensure reproducible peptide generation.
Selected peptides may not accurately represent protein abundance variations across conditions.

Conclusions:

Current peptide selection strategies for targeted proteomics require re-evaluation.
Improved methods are needed to ensure selected peptides are both reproducible and representative of protein behavior.
Robust peptide selection is essential for reliable protein quantitation in targeted proteomics studies.