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Updated: May 19, 2026

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

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A software toolkit and interface for performing stable isotope labeling and top3 quantification using Progenesis

Da Qi1, Philip Brownridge, Dong Xia

  • 1Institute of Integrative Biology, University of Liverpool, Merseyside, UK. D.Qi@liv.ac.uk

Omics : a Journal of Integrative Biology
|August 15, 2012
PubMed
Summary

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This study introduces a Java interface and post-processing software to expand Progenesis LC-MS capabilities for stable isotope labeling and quantitation. This integration enhances mass spectrometry data analysis across diverse experimental workflows.

Area of Science:

  • Proteomics
  • Computational Biology
  • Mass Spectrometry

Background:

  • Multiple software packages are often required for mass spectrometry (MS) data analysis due to limited support for diverse experimental methods and instrument types.
  • Progenesis LC-MS software facilitates label-free quantitation but lacks native support for stable isotope labeling methods.

Purpose of the Study:

  • To develop a flexible software solution that integrates Progenesis LC-MS output with stable isotope labeling and other quantitation methods.
  • To enhance the utility of Progenesis LC-MS for a broader range of proteomics research applications.
  • To promote data standardization through export to the mzQuantML format.

Main Methods:

  • Development of a Java programming interface to process Progenesis LC-MS output files.

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Last Updated: May 19, 2026

Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification
10:37

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

Published on: November 15, 2017

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11:53

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Published on: July 1, 2014

  • Creation of post-processing software (Progenesis Post-Processor) for stable isotope labeling and pseudo-absolute quantitation.
  • Implementation of export functionality to the mzQuantML data standard.

    • Main Results:

    • The developed Java interface enables the use of Progenesis quantified MS features across various experimental methods.
    • The Progenesis Post-Processor successfully integrates stable isotope labeling data analysis.
    • Export to mzQuantML facilitates data standardization and interoperability.

    Conclusions:

    • The new software extends Progenesis LC-MS capabilities, offering a unified platform for diverse quantitation strategies.
    • This solution improves the adaptability of Progenesis for complex proteomics studies.
    • The integration and standardization efforts support reproducible and collaborative research in proteomics.