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 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.