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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...

Proteomics

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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...

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Updated: May 21, 2026

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

A highly scalable peptide-based assay system for proteomics.

Igor A Kozlov¹, Elliot R Thomsen, Sarah E Munchel

¹Prognosys Biosciences Inc., La Jolla, California, United States of America. ikozlov@prognosysbio.com

|June 16, 2012

Summary

This summary is machine-generated.

We developed a cost-effective technology to create and screen large, custom peptide libraries using peptide-cDNA fusions. This method efficiently identifies protease and kinase substrates, advancing biological research and drug discovery.

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Area of Science:

Biochemistry
Molecular Biology
Proteomics

Background:

Generating and screening large peptide libraries is crucial for understanding protein function and identifying drug targets.
Existing methods for peptide synthesis and screening can be costly and lack scalability.

Purpose of the Study:

To develop a scalable and cost-effective technology for generating and screening high-complexity peptide sets.
To demonstrate the utility of this technology in identifying protease and kinase substrates.

Main Methods:

Peptide-cDNA fusions were synthesized using in vitro transcription/translation from microarray-generated DNA template pools.
Activity-based assays were employed, including protease cleavage site identification and kinase phosphorylation site mapping.
Digital sequencing of cognate cDNAs was used to identify cleaved or phosphorylated peptides.

Main Results:

Successfully screened the HCV proteome for NS3/4A protease cleavage sites, identifying known sites with high specificity.
Screened a peptide pool against Abl kinase, confirming specific phosphorylation events consistent with known substrate preferences.
Demonstrated the scalability and adaptability of the peptide-cDNA fusion approach for various protein-based assays.

Conclusions:

The developed technology offers a scalable, cost-effective, and efficient method for designing, manufacturing, and assaying large custom peptide sets.
This approach significantly enhances the discovery of protease and kinase substrates, with broad applications in biological research and drug discovery.