ProteinPilot™ Software

ProteinPilot™ Software

Applied Biosystems

ProteinPilot Software from Applied Biosystems Easy-to-use ProteinPilot™ 2.0.1 Software from Applied Biosystems streamlines protein identification and quantitation, enabling you to: • more

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ProteinPilot Software from Applied Biosystems

Easy-to-use ProteinPilot™ 2.0.1 Software from Applied Biosystems streamlines protein identification and quantitation, enabling you to:

• Search for hundreds of peptide modifications and non-tryptic cleavages simultaneously;
• Easily distinguish protein isoforms, protein subsets, and suppress false positives; 
• Visualize peptide-protein associations and relationships.

The Applied Biosystems ProteinPilot software is compatible with all Applied Biosystems/MDS SCIEX proteomics MS/MS systems, this software is ideal for protein identification and relative protein expression analysis for discovery research.

Features of ProteinPilot include:

• Search for hundreds of biological and other modifications, genetic variants and unexpected cleavages simultaneously with the Paragon™ Algorithm, without the typical explosion of false positives that plagues traditional algorithms. 
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 biologists’ terms, and the software intelligently determines the search parameters. 
Optimized support for iTRAQ™, ICAT®, and SILAC™ reagent workflows, including the iTRAQ Reagent – 8plex, for biomarker discovery and protein expression analysis. 
Accurately distinguish and quantify differentially regulated proteins with closely related sequences with statistical rigor.

ProteinPilot is Designed to Provide the Most Information from Applied Biosystems/MDS SCIEX Proteomics MS/MS Platforms
Applied Biosystems ProteinPilot 2.0.1 software is optimized to provide the highest level of protein coverage, and confidence in results for identification, characterization, and quantitation on the 4800 Plus MALDI TOF/TOF™ Analyzer, the 4700 Proteomics Analyzer, the QSTAR® Elite Hybrid LC/MS/MS System, and the 4000 and 3200 Q TRAP® LC/MS/MS Systems.

Distinguish Protein Isoforms and Protein Subsets with ProteinPilot
To distinguish protein isoforms, protein subsets, and suppress false positives, the Pro Group™ Algorithm statistically analyzes the confidence of peptide identifications, accurately assesses how peptides are shared with other proteins, and accounts for the redundancy of search databases.

Optional Mascot Integration
ProteinPilot 2.0.1 software can provide the power of two search engines. Either as an additional purchased component or by connecting your existing installation, you can submit searches to Matrix Science’s MASCOT™ 2.2 Database Search Engine. The widely accepted Mascot algorithm is incorporated directly into ProteinPilot Software and displays results in the familiar MASCOT html format.

Determine Biological Significance with ProteinPilot
When searching a database containing information from the PANTHER protein classification system, molecular function and biological process protein classification information is displayed directly in the results for identified proteins with a direct link to the PANTHER site also available for deeper investigation.


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