Proteome Discoverer

Proteome Discoverer processes tandem mass spectrometry data to identify and quantify peptides and proteins and to perform analyses such as crosslinking analysis, glycoproteomics, and top‑down proteomics for proteomics research.

Key Features:

• Versatile data processing: Performs peptide and protein identification, labeled and label‑free quantification, crosslinking analysis, glycoproteomics, and top‑down proteomics.
• MS/MS file processing: Converts tandem mass spectrometry (MS/MS) files into peptide and protein identifications.
• Spectra viewing and verification: Provides spectral visualization and manual verification of MS/MS spectra supporting identifications.
• Algorithms and quantification methods: Implements algorithms for mass spectrometry data processing and supports labeled and label‑free quantification workflows.
• Orbitrap compatibility: Handles data generated by Orbitrap mass spectrometers.

Scientific Applications:

• Protein identification: Converts tandem MS files into peptide and protein identifications for proteome characterization.
• Quantitative proteomics: Supports labeled and label‑free quantitative studies for comparative proteomics.
• Crosslinking analysis: Identifies and analyzes protein crosslinks to study interactions and structural topology.
• Glycoproteomics: Characterizes glycopeptides and glycoproteins.
• Top‑down proteomics: Enables analysis of intact proteins in top‑down workflows.
• Biomarker discovery and target identification: Used in applied studies for disease biomarker discovery and therapeutic target identification.
• Spectral validation: Facilitates manual inspection and verification of spectra underlying identifications.

Methodology:

Employs algorithms for peptide and protein identification, labeled and label‑free quantification, crosslinking analysis, glycoproteomics, top‑down proteomics, and spectral visualization from tandem mass spectrometry data.