Thermo Scientific™ Proteome Discoverer™ 3.0 with CHIMERYS™ Full (DDA & DIA)

The Thermo Scientific™ Proteome Discoverer™ Software with CHIMERYS™ Full is a comprehensive, extensible, and intelligent proteomics data analysis platform designed to transform complex mass spectrometry datasets into meaningful biological insights. Supporting Data-Dependent Acquisition (DDA), Data-Independent Acquisition (DIA), and Wide Window Acquisition (WWA) workflows, it delivers robust protein identification, accurate quantification, and deep proteome coverage across a wide range of applications.

At the core of its advanced capabilities are CHIMERYS™ intelligent search algorithms and INFERYS™ rescoring, which significantly enhance the interpretation of complex and chimeric MS/MS spectra. These technologies enable researchers to identify more peptides, uncover low-abundance proteins, and confidently detect post-translational modifications (PTMs), even in highly complex biological samples.

Key Features

Comprehensive Proteomics Workflow Platform

• Supports DDA, DIA, and WWA acquisition methods
• Enables peptide and protein identification, quantification, and validation
• Handles complex biological datasets with high confidence

CHIMERYS™ Intelligent Search & INFERYS™ Rescoring

• AI-driven spectral deconvolution and peptide identification
• Improved detection of chimeric spectra and co-isolated precursors
• Increased protein coverage, identification rates, and PTM discovery

Customizable Node-Based Workflow System

• Flexible drag-and-drop workflow editor
• Build linear or branched analysis pipelines
• Preconfigured workflows for TMT, LFQ, PTM analysis, and cross-linking studies
• Integrates multiple search engines including:
  • SEQUEST™ HT
  • MSPepSearch
  • Mascot
  • MSAmanda
  • Comet
  • Byonic™
  • ProSightPD

Advanced Quantitative Proteomics Tools

• Supports multiple quantitation strategies:
  • Tandem Mass Tag (TMT / TMTpro) (MS2 & MS3)
  • Label-Free Quantification (LFQ)
  • SILAC workflows
• Accurate relative protein expression analysis
• Advanced peak detection and quantification algorithms

Broad Analytical Capabilities

• PTM identification and localization (phosphorylation, glycosylation, etc.)
• Top-down proteomics and proteoform analysis
• Glycopeptide analysis
• Cross-linking mass spectrometry (XL-MS)
• Supports multiple fragmentation techniques:
  • CID, HCD, ETD, UVPD, PTR

Integrated Data Interpretation & Visualization

• Built-in statistical validation and FDR control
• Advanced data visualization and reporting tools
• Biological interpretation and pathway analysis support
• Compliance with HUPO Proteomics Standards Initiative (PSI)

Applications

• Bottom-up and top-down proteomics
• Quantitative proteomics (TMT, LFQ, SILAC)
• Post-translational modification (PTM) analysis
• Biomarker discovery and validation
• Single-cell proteomics
• Biopharmaceutical protein characterization
• Structural proteomics (XL-MS)
• Systems biology and pathway analysis

Technical Highlights

Unique Advantages

The Proteome Discoverer™ with CHIMERYS™ Full stands out as a next-generation proteomics software platform by combining AI-powered spectral interpretation, multi-engine search capabilities, and fully customizable workflows in a single environment.

Its ability to process DDA, DIA, and WWA datasets simultaneously, combined with advanced quantification strategies and PTM analysis, makes it a highly versatile tool for modern proteomics laboratories. The integration of CHIMERYS™ and INFERYS™ significantly enhances data depth and confidence, enabling researchers to extract maximum biological insight from complex datasets.

The Thermo Scientific™ Proteome Discoverer™ Software with CHIMERYS™ Full is a powerful, flexible, and intelligent solution for advanced proteomics data analysis. By combining AI-enhanced identification, comprehensive quantification tools, and customizable workflows, it empowers researchers to achieve deeper proteome coverage, higher confidence results, and faster scientific discovery.