ProteinPilot™ Software

Mass Spectrometry Software-ProteinPilot™ Software
Mass Spectrometry Software-ProteinPilot™ Software
Mass Spectrometry Software-ProteinPilot™ Software
Mass Spectrometry Software-ProteinPilot™ Software
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Easy-to-use ProteinPilot Software streamlines protein identification and quantitation, enabling you to identify hundreds of peptide modifications and non-tryptic cleavages simultaneously.  Easily distinguish protein isoforms, protein subsets, and suppress false positives, as well as visualize peptide-protein associations and relationships. With generic input for non-AB SCIEX instruments via .mgf format, the software is compatible with all proteomics MS/MS systems.

Trial software downloads
To download a trial version and obtain license keys, visit our ProteinPilot™ Trial Software Download Registration Site.


    Status: Available  Item status information


    Key Features of ProteinPilot™ Software

    • Automatic extensive peptide identification – Search for hundreds of biological and other modifications, genetic variants, and unexpected cleavages simultaneously with the Paragon™ Algorithm, without an explosion of false positives, cost in expanded search time, or the complexity of multi-stage analyses that plague alternate approaches.
    • "One-click pipeline" – a single click triggers complete data processing (including signal processing) to make peak lists and integrate signals for quantitation, peptide identification (including data re-calibration), protein inference of identified peptides, and analysis of relative quantitation for label-based workflows.
    • Protein isoform and protein subset differentiation, as well as false positives supression using the embedded, industry-leading Pro Group™ Algorithm for protein-grouping analysis.
    • Easier search setup – The unique user-interface allows sample information to be entered based on terms used by laboratory scientists, and the software intelligently determines the search parameters. Top-quality identification results are delivered without the need for informatics expertise.
    • Quantitiative workflows – Optimized support for iTRAQ®, ICAT®, and SILAC™ Reagent workflows, including 4-plex, 8-plex, and the new mTRAQ® Reagents for biomarker discovery and verification
    • Automatic and rigorous false discovery rate (FDR) analysis using decoy database searching provides highest-level defense of your results quality.


    Support for new instruments

    This software supports the new AB SCIEX TripleTOF® 5600 System.


    Command line control and open results

    To support users and third-party software vendors that want to integrate ProteinPilot™ Software, it is possible to script searches via command line and decrypt the .group file results into clear XML for full access to all the data it contains.



    For research use only. Not for use in diagnostic procedures.