Biosaur

Biosaur enhances peptide feature detection in liquid chromatography-mass spectrometry (LC-MS) data by incorporating ion mobility support to improve identification accuracy and characterization of peptide features.

Key Features:

• Implementation: Implemented in Python 3.8 for computational processing of LC-MS data.
• Ion mobility support: Incorporates the ion mobility dimension to leverage structural separation information in feature detection.
• Peptide feature detection: Detects peptide features within full-range mass spectra to support proteomics analyses.
• Extension of Dinosaur: Extends the functionality of Dinosaur by utilizing additional ion mobility information to improve detection accuracy and efficiency.
• Instrument compatibility: Designed to process data acquired on ion mobility-enabled mass spectrometers such as timsTOF and FAIMS-Orbitrap systems.
• Ion mode handling: Processes datasets containing both positive and negative ion modes.
• Cosine correlation table: Generates a cosine correlation table for peptide features to aid feature comparison and characterization.
• Fragment/peptide discrimination: Provides analyses to help distinguish in-source fragments from semi-tryptic peptides.

Scientific Applications:

• Fragment vs semi-tryptic discrimination: Use the cosine correlation table to distinguish in-source fragments from semi-tryptic peptides.
• Proteomics initial processing: Perform initial data processing of peptide mass spectra for downstream proteomics workflows.
• Ion mobility-enhanced MS analysis: Analyze datasets from ion mobility-enabled instruments such as timsTOF and FAIMS-Orbitrap to exploit the mobility dimension.
• Multi-mode ion analyses: Support analyses of experiments run in both positive and negative ion modes.

Methodology:

Implemented in Python 3.8; incorporates the ion mobility dimension into LC-MS feature detection; generates cosine correlation tables for peptide features; extends Dinosaur's detection approach by using ion mobility information to improve feature detection accuracy and efficiency.