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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...

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Related Experiment Video

Updated: May 20, 2026

Combining Chemical Cross-linking and Mass Spectrometry of Intact Protein Complexes to Study the Architecture of Multi-subunit Protein Assemblies

Combining Chemical Cross-linking and Mass Spectrometry of Intact Protein Complexes to Study the Architecture of Multi-subunit Protein Assemblies

Published on: November 28, 2017

Identification of cross-linked peptides from complex samples.

Bing Yang¹, Yan-Jie Wu, Ming Zhu

¹College of Biological Sciences, China Agricultural University, Beijing, China.

|July 10, 2012

Summary

pLink software analyzes cross-linked proteins from mass spectrometry data, reliably identifying cross-links. This robust tool aids protein structure and interaction studies using various cross-linkers.

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Multimer-PAGE: A Method for Capturing and Resolving Protein Complexes in Biological Samples

Multimer-PAGE: A Method for Capturing and Resolving Protein Complexes in Biological Samples

Published on: May 5, 2017

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Last Updated: May 20, 2026

Combining Chemical Cross-linking and Mass Spectrometry of Intact Protein Complexes to Study the Architecture of Multi-subunit Protein Assemblies

Combining Chemical Cross-linking and Mass Spectrometry of Intact Protein Complexes to Study the Architecture of Multi-subunit Protein Assemblies

Published on: November 28, 2017

Multimer-PAGE: A Method for Capturing and Resolving Protein Complexes in Biological Samples

Multimer-PAGE: A Method for Capturing and Resolving Protein Complexes in Biological Samples

Published on: May 5, 2017

Area of Science:

Proteomics
Structural Biology
Bioinformatics

Background:

Mass spectrometry-based proteomics enables the study of protein interactions and structures.
Analyzing cross-linked peptides requires specialized software for accurate identification and false discovery rate estimation.

Purpose of the Study:

To introduce pLink, a novel software tool for the analysis of cross-linked protein mass spectrometry data.
To provide a robust and versatile platform for identifying cross-linked peptides and studying protein structures and interactions.

Main Methods:

Development of pLink software for processing cross-linked peptide data.
Validation using proteins with known structures.
Testing on complex biological samples including protein complexes, immunoprecipitates, and whole-cell lysates.

Main Results:

pLink accurately estimates the false discovery rate for cross-link identification.
The software is compatible with various homo- and hetero-bifunctional cross-linkers.
Successful application of pLink to diverse biological samples, demonstrating its robustness.

Conclusions:

pLink is a reliable software tool for analyzing cross-linked mass spectrometry data.
The software facilitates protein-structure determination and protein-protein interaction studies.
pLink offers a versatile solution for complex proteomics research.