Proteome Discoverer software supports multiple dissociation techniques, quantitation technologies, and database search algorithms for comprehensive protein identification, characterization, and quantitation.       

Comprehensive       

• Provides a choice of search algorithms (SEQUEST, Z-Core, Mascot, etc.) and can combine output from multiple algorithms to maximize and cross-validate results       
• Supports multiple dissociation techniques (CID, HCD, and ETD) for more complete coverage and confident identification of PTMs       
• Supports isobaric mass tagging (TMT, iTRAQ) and heavy-peptide techniques, enabling relative or absolute quantitation       
• Leverages high-mass-accuracy MALDI data in a Mascot-based peptide mass fingerprinting workflow       
• Validates protein IDs with false discovery rate (FDR) determination       

Productive and Expandable       

• Automates data analysis       
• Simplifies analysis of MSn data using wizards and customizable workflows       
• Provides effective location of low-level sample components using creative data interrogation strategies such as generating inclusion and exclusion lists and importing those lists directly into instrument methods     
• Illustrates biological context by automatically annotating identified proteins with GO classifications, PTMs sites, and literature references from public databases
• Facilitates data comparison, exchange, and verification with support for data standards developed by the HUPO Proteomics Standards Initiative (PSI)     
• Provides a seamless transition from Thermo Scientific™ BioWorks™ platform using the SRF file import wizard     
• Expands through the integration of custom software tools