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Proteolabels is new software for quantitative proteomics – supporting studies involving stable isotope labels, such as SILAC and dimethyl labelling in duplex or triplex.

Proteolabels has been designed a plugin for Progenesis QI for proteomics (Waters Corp.), with a focus on performance, usability and empowering scientists to explore their data.

Benefits of Proteolabels

  • Co-detection: The workflow builds upon the Progenesis QI for proteomics co-detection feature, in which features are aligned across LC-MS runs. This improves sensitivity and reproducibility.
  • Auto-detect: Proteolabels makes a first pass through the data to suggest optimal parameters, simplifying the analysis.
  • Peptide scoring: Proteolabels contains novel metrics for scoring the quality of pairs/triples detected, enabling users to measure the reliability of peptide-level quantification, remove peptide that are suspect, and giving higher quality protein-level quantification.
  • Intelligent protein inference: Intelligent weighted averaging of different peptide-level signals is performed, to give more accurate protein-level quantification results.
  • QC metrics: Proteolabels contains a large number of QC metrics and data plotting options, enabling users to interact and explore their data, and, where needed, make decisions as to how arrive at the best protein set.
  • Support for wide range of platforms: Through the integration with Progenesis QI for proteomics, Proteolabels supports data from a wide range of vendors and search engines, including from approaches employing data independent acquisition and ion mobility.

If you would like a free demo or to purchase Proteolabels, please contact your local Waters sales office, details available at, or contact

Download a Proteolabels brochure or view a recent webinar showcasing Proteolabels in action

Peptide Scoring

QC Metrics