MS Amanda

MS Amanda scores tandem mass spectrometry (MS/MS) spectra to identify peptide sequences from high-resolution, high-accuracy mass spectrometry data.

Key Features:

• High Mass Accuracy: Optimized for high-resolution, high-accuracy MS/MS spectra and explains more spectra at the same false discovery rate compared to Mascot and SEQUEST.
• Versatility Across Fragmentation Types: Supports Higher-energy Collisional Dissociation (HCD), Electron Transfer Dissociation (ETD), and Collision-Induced Dissociation (CID) fragmentation types.
• Continuous Improvement and Flexibility: MS Amanda 2.0 provides a reported 3–5× speedup over earlier versions and adds support for new ion types and standard data formats, with options to focus searches on the most common ion types to optimize performance.
• Innovative Approaches to Complex Challenges: Implements the CharmeRT workflow to detect and reanalyze chimeric/coeluting spectra and integrates with the Elutator validation system to increase unique peptide identifications in high-resolution datasets.

Scientific Applications:

• High-accuracy peptide identification: Identification of peptides from high-resolution, high-accuracy MS/MS datasets.
• Chimeric/coeluting peptide resolution: Detection and resolution of chimeric spectra and coeluting peptides via CharmeRT to increase identifications.
• Biomarker discovery and disease research: Supports discovery of protein biomarkers and proteomic studies of disease by improving confident peptide identifications.
• Protein function analysis: Facilitates protein function studies through more comprehensive peptide identification and validation.

Methodology:

Scores MS/MS spectra with an algorithm optimized for high-resolution, high-accuracy data; supports HCD, ETD, and CID fragmentation; applies the CharmeRT workflow to identify and reanalyze chimeric/coeluting spectra with validation via Elutator; MS Amanda 2.0 implements algorithmic and format support improvements and a reported 3–5× speedup while adding support for new ion types and standard data formats.