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; and visualize peptide-protein associations and relationships. Now with generic input for non-AB SCIEX instruments via .mgf format, the software is compatible with all proteomics MS/MS systems.
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 search time, or complexity of multi-stage analysis that plague alternate approaches
‘One click pipeline’ – a single click triggers complete processing that includes signal processing to make peak lists and integrate signals for quantitation, peptide identification which includes recalibration of the data, protein inference of the identified peptides, and analysis of relative quantitation for label-based workflows
Distinguish protein isoforms, protein subsets and suppress false positives using the embedded industry-leading Pro Group™ Algorithm for protein grouping analysis
Easier search setup — Sample information is entered into the software’s unique user interface in the terms used by the scientist in the lab, and the software intelligently determines the search parameters. Top quality identification results are delivered without need for informatics experitise
Quantitiative workflows – Optimized support for iTRAQ™, ICAT®, and SILAC™ reagent workflows, including 4plex, 8plex and the new mTRAQ reagents for biomarker discovery and verification
Automatic and rigorous False Discovery Rate (FDR) Analysis using decoy database searching provides the highest level of defense of the quality of your results
Automatic and Rigorous False Discovery Rate (FDR) AnalysisThe scope of the ‘one click pipeline’ now also includes an independent analysis of your identification results using decoy database searching. The detailed Excel report generated as part of the analysis gives you a rigorous defense of the quality of your results that is second to none. The report includes analysis using both conventional FDR analysis and also our recently published novel extensions to give you even more information.
Improved Quantitation for iTRAQ Reagent-Based WorkflowsThe centerpiece of new quantitation processing for the 3.0 release is a new background correction algorithm. This optional processing corrects for an effect sometimes observed differential expression studies in complex mixtures where the reported ratios are less extreme than expected. The new algorithm inproves the accuracy of ratios while maintaining the ability to detect true differential proteins with good discrimination. A new category of automatic curation now excludes discordant types of peptides such as semitryptics and low stoichiometry modifications, improving the estimation of protein-level ratios. New integration algorithms improve the quality of quantitation for wiff data.
Extended Support for Instruments from Other VendorsData from any instrument may now be searched with all versions of ProteinPilot 3.0 by submitting Mascot Generic Format (MGF) peak lists as was previously only available in the Universal version of ProteinPilot 2.0.1. Instrument settings are included for several non-AB SCIEX instruments, and the open parameter control function would allow you to add support for other instruments not already included. The MGF function is for identification only; no quantitation support is provided.
Improved Identification QualityThe modification catalog has been extended to include all ‘post-translational’-classified modifications in UniMod as of Jan. 8, 2009. The feature probabilities for modifications and digestion agents have been refined significantly for the first time since the 1.0 release. Most instrument definitions have optimized. All of this gives you faster and better results.