Simplify and Accelerate Your Protein Identification
For research use only. Not for use in diagnostic procedures.
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-SCIEX instruments via .mgf format, the software is compatible with all proteomics MS/MS systems.
Trial software downloads Download a trial version and obtain license keys.
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 >
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
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.
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.
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.
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.
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.
Comprehensive ProteinPilot Report generated with each search, with over 20 informative dashboards of analysis
Support for new instruments This software supports the new SCIEX TripleTOF 6600 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.