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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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Quantification of Proteins Using Peptide Immunoaffinity Enrichment Coupled with Mass Spectrometry

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Published on: July 31, 2011

Validation and quantification of peptide antigens presented on MHCs using SureQuant.

Owen Leddy^1,2,3, Yufei Cui^1,3, Ryuhjin Ahn^1,3

¹Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.

Nature Protocols

|October 22, 2024

Summary

SureQuant MHC enables precise validation and quantification of peptide-MHC targets for cancer and infectious disease immunotherapies. This method confirms peptide identity, measures relative changes, and determines absolute abundance for therapeutic development.

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Last Updated: Jun 13, 2026

Quantification of Proteins Using Peptide Immunoaffinity Enrichment Coupled with Mass Spectrometry

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Published on: July 31, 2011

A High Throughput MHC II Binding Assay for Quantitative Analysis of Peptide Epitopes

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Published on: March 25, 2014

Immunopeptidomics: Isolation of Mouse and Human MHC Class I- and II-Associated Peptides for Mass Spectrometry Analysis

Immunopeptidomics: Isolation of Mouse and Human MHC Class I- and II-Associated Peptides for Mass Spectrometry Analysis

Published on: October 15, 2021

Area of Science:

Immunology
Mass Spectrometry
Proteomics

Background:

Peptide-major histocompatibility complexes (peptide-MHCs) are crucial targets for vaccines and immunotherapies in cancer and infectious diseases.
Accurate identification and quantification of target peptides are essential for designing effective therapeutic strategies.
Existing methods may require enhanced validation and quantification capabilities for MHC peptides.

Purpose of the Study:

To introduce and validate SureQuant MHC as a robust method for peptide-MHC analysis.
To demonstrate the utility of SureQuant MHC for confirming peptide identity, performing relative quantification, and enabling absolute quantification.
To provide immunologists with a reliable tool for validating antigenic targets and understanding MHC repertoire dynamics.

Main Methods:

Utilizing internal standard parallel reaction monitoring (SureQuant) with synthetic stable isotope labeled (SIL) peptide standards.
Employing pre-formed heavy isotope-labeled peptide-MHC complexes (hipMHCs) with SIL peptides for relative quantification.
Developing an internal standard curve using varying amounts of hipMHCs loaded with SIL peptides for absolute quantification.

Main Results:

Conclusive confirmation of putative MHC peptide identities through comparison with SIL peptide standards.
Accurate relative quantification of MHC peptides using hipMHCs as internal controls.
Precise absolute quantification of target peptides, crucial for assessing therapeutic modality suitability.

Conclusions:

SureQuant MHC offers a powerful solution for validating antigenic targets and quantifying peptide-MHCs.
The method supports diverse applications, from confirming peptide presence to determining abundance for therapeutic development.
This approach enhances the ability to design and optimize peptide-MHC-based vaccines and immunotherapies.