ProteinPilot Software

Identify and Quantify Proteins Faster, With More Confidence

ProteinPilot™ Software is a paradigm shift in protein identification and relative protein expression analysis for protein research. Combining sophisticated algorithms with an intuitive interface, you can now confidently identify more proteins and search large numbers of post translational modifications, without increasing search time or false positives. ProteinPilot Software is compatible with all proteomics MS/MS systems via the.*mgf format. Get to Know ProteinPilot Software >

The ProteinPilot Software Difference


The incredibly intuitive and easy to use interface is designed with biology in mind.


Detect more peptides and PTMs than ever before with the Paragon™ Algorithm.


Identify the right list of proteins, not the longest list, with the Pro Group™ Algorithm

ProteinPilot Software has been a workhorse in our lab over the last 10 years in our study of the Immunopeptidome, it was the first and remains the best search tool for this challenging research. The unique capability of the Paragon algorithm to smartly manage search space such that we can perform no-enzyme database searching in combination with 100s of post-translational modifications let’s us deeply characterize the peptides isolated from MHC proteins and has been instrumental in defining the role of PTM peptides in autoimmunity and cancer.
Professor Tony Purcell,
Monash University, Australia

In-Depth Protein Identification Made Easy

Extensive Peptide Identification with Every Search

Search for hundreds of biological and other modifications, genetic variants and unexpected cleavages simultaneously with the Paragon™ Algorithm, and avoid an explosion of false positives.

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Industry Leading Pro Group

The embedded, industry-leading Pro Group Algorithm for protein-grouping analysis enables you to quickly and easily achieve protein isoform and protein subset differentiation, as well as false positives suppression.

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Easy on Top, Powerful Underneath

The unique user-interface is designed with biology in mind. It allows sample information to be entered based on terms used by laboratory scientists, and the software intelligently determines the search parameters using the novel Parameter Translation Layer Function.

Top-quality identification results are delivered without the need for informatics expertise. When you have new exciting biology, the Parameter Translation Layer can be edited by advanced users, to add new modifications or chemistries, to tune settings to optimize new workflows.

Valuable FDR Analysis

Automatic and rigorous false discovery rate (FDR) analysis uses decoy database searching to provide high quality, defensible protein identification results. A detailed report is generated with every search, with diagnostic dashboards to optimize sample prep and LC-MS acquisition conditions.

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Optimized Quantitative Workflows

Benefit from optimized integrated support for iTRAQ® Reagents (4-plex and 8-plex) and numerous MS1 quantitation strategies (e.g. ICAT®, SILAC, mTRAQ® Reagents) for protein expression analysis and biomarker discovery.

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