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

Structural basis of the regulation by CDK11 kinase of early spliceosome activation and evidence for its proofreading by DHX15 helicase.

Nature communications·2026

Same author

SynCAR platform for capturing neuronal synaptic proteopathic seeds.

iScience·2026

Same author

Targeting intracellular cholesterol imbalance rescues sarcomere-ER contact site signaling and ER remodeling in dilated cardiomyopathy.

Signal transduction and targeted therapy·2026

Same author

Pathogenesis of diffuse large B cell lymphoma proteogenotypes.

Cancer cell·2026

Same author

Stable β2-Microglobulin-HLA Class I Association Reshapes the Antigenic Landscape and TCR Recognition of Cancer-Associated Epitopes.

European journal of immunology·2026

Same author

A versatile nanobody platform for live and super-resolution imaging of synaptic vesicle dynamics and plasticity in rodent and human neurons.

Journal of nanobiotechnology·2026

Search research articles

Related Experiment Video

Updated: Dec 25, 2025

Simultaneous Affinity Enrichment of Two Post-Translational Modifications for Quantification and Site Localization

Simultaneous Affinity Enrichment of Two Post-Translational Modifications for Quantification and Site Localization

Published on: February 27, 2020

An experimentally generated peptide database increases the sensitivity of XL-MS with complex samples.

Iwan Parfentev¹, Sandra Schilbach², Patrick Cramer²

¹Research group Bioanalytical Mass Spectrometry, Max-Planck-Institute for Biophysical Chemistry, Goettingen, Germany.

Journal of Proteomics

|March 24, 2020

Summary

A new cross-linking mass spectrometry (XL-MS) strategy reduces search time and increases identifications by focusing on experimentally validated cross-linked peptides. This peptide-focused approach overcomes the quadratic search space challenge in XL-MS analysis.

Keywords:

20 S proteasome Bacillus Cross-linking mass spectrometry Peptide database Polymerase II Transcription factor IIH

More Related Videos

High-Resolution Complexome Profiling by Cryoslicing BN-MS Analysis

High-Resolution Complexome Profiling by Cryoslicing BN-MS Analysis

Published on: October 15, 2019

A Hydrogen-Deuterium Exchange Mass Spectrometry HDX-MS Platform for Investigating Peptide Biosynthetic Enzymes

A Hydrogen-Deuterium Exchange Mass Spectrometry HDX-MS Platform for Investigating Peptide Biosynthetic Enzymes

Published on: May 4, 2020

Related Experiment Videos

Last Updated: Dec 25, 2025

Simultaneous Affinity Enrichment of Two Post-Translational Modifications for Quantification and Site Localization

Simultaneous Affinity Enrichment of Two Post-Translational Modifications for Quantification and Site Localization

Published on: February 27, 2020

High-Resolution Complexome Profiling by Cryoslicing BN-MS Analysis

High-Resolution Complexome Profiling by Cryoslicing BN-MS Analysis

Published on: October 15, 2019

A Hydrogen-Deuterium Exchange Mass Spectrometry HDX-MS Platform for Investigating Peptide Biosynthetic Enzymes

A Hydrogen-Deuterium Exchange Mass Spectrometry HDX-MS Platform for Investigating Peptide Biosynthetic Enzymes

Published on: May 4, 2020

Area of Science:

Biochemistry
Proteomics
Mass Spectrometry

Background:

Cross-linking mass spectrometry (XL-MS) is expanding to complex biological samples.
A key challenge in XL-MS is the quadratic increase in search space (n² problem) with non-cleavable cross-linkers.
This limits the efficiency and sensitivity of identifying cross-linked peptides.

Purpose of the Study:

To develop and validate an alternative XL-MS search strategy to overcome the n² problem.
To reduce search time and increase the number of confident cross-link identifications.
To enable XL-MS analysis of more complex proteomes.

Main Methods:

A parallel XL-MS experiment using a thiol-cleavable cross-linker identified peptides involved in cross-linking.
A focused peptide database was generated from these identified cross-linked peptides.
This peptide-focused database was used for searching experiments with non-cleavable cross-linkers.

Main Results:

The peptide-focused approach successfully identified cross-linked peptides in protein complexes, correlating well with conventional searches.
Application to in vivo cross-linked bacterial cells (Bacillus subtilis and Bacillus cereus) showed a 5- to 10-fold reduction in search time.
Significantly more identifications were achieved for B. cereus using this method compared to searching the entire proteome.

Conclusions:

Pre-filtering for experimentally validated cross-link peptide candidates dramatically decreases the search space.
This strategy enhances XL-MS sensitivity by reducing false positives and increasing identification rates.
The peptide-focused approach enables faster and more sensitive XL-MS analysis, even for complex mammalian proteomes.