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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.
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Related Experiment Video

Updated: Jun 6, 2026

Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification

Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification

Published on: November 15, 2017

Analysis of isobaric quantitative proteomic data using TMT-Integrator and FragPipe computational platform.

Hui-Yin Chang^1,2, Yamei Deng¹, Ruohong Li¹

¹Department of Pathology, University of Michigan, Ann Arbor, MI, USA.

Nature Communications

|March 2, 2026

Summary

This summary is machine-generated.

TMT-Integrator, a new bioinformatics tool, enhances quantitative proteomics by providing integrated reports from tandem mass tag (TMT) and isobaric tags for relative and absolute quantitation (iTRAQ) experiments. It offers more robust protein and phosphosite quantification compared to existing methods.

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Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification

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Navigating the Mass Spectrometry-Based Proteomic Data Using Free Computational Tools

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Published on: August 19, 2025

Area of Science:

Proteomics
Bioinformatics
Mass Spectrometry

Background:

Isobaric mass tags like TMT and iTRAQ are crucial for multiplex quantitative proteomics.
Accurate peptide and protein quantification is essential for biological discovery.

Purpose of the Study:

To introduce TMT-Integrator, a bioinformatics tool for processing TMT and iTRAQ quantitation results.
To provide integrative reports at multiple biological levels (gene, protein, peptide, PTM site).
To evaluate the performance of TMT-Integrator within the FragPipe computational platform.

Main Methods:

Development and integration of TMT-Integrator into the FragPipe computational platform.
Analysis of five diverse TMT datasets, including ccRCC, E. coli spike-in, and human cell lysates.
Performance benchmarking against MaxQuant and Proteome Discoverer using OmicsEV.

Main Results:

TMT-Integrator, via FragPipe, quantified more proteins in E. coli and ccRCC whole proteome datasets.
More phosphorylated sites were quantified in the ccRCC phosphoproteome dataset.
FragPipe coupled with TMT-Integrator demonstrated superior and more robust quantification performance.

Conclusions:

TMT-Integrator is a versatile tool for comprehensive analysis of TMT and iTRAQ quantitative proteomics data.
Integration with FragPipe offers a powerful and robust workflow for quantitative proteomics.
This tool advances the analysis of complex proteomic datasets, including phosphoproteomics.