Feature detection for LC-MS1 data with ion mobility support (EXPERIMENTAL).

Note: This tool is experimental and under active development. The interface and behavior may change.

This TOPP tool is a C++ reimplementation of the Biosaur2 feature detection algorithm. It detects peptide features in centroided LC-MS1 data (with optional profile mode support) through:

Grouping peaks across scans into "hills" (continuous m/z traces)
Splitting hills at valley points to separate co-eluting species
Detecting isotope patterns based on expected mass differences and intensity correlations
Calculating comprehensive feature properties (m/z, RT, intensity, charge state)

Key Features:

FAIMS compensation voltage grouping for FAIMS-enabled instruments
Ion mobility-aware processing for PASEF/TIMS data (2D centroiding in m/z and ion mobility space)
TOF-specific intensity filtering for time-of-flight instruments
Automatic mass calibration to improve detection accuracy
Profile mode support via PeakPickerHiRes centroiding
Export to featureXML and Biosaur2-compatible TSV formats

The tool closely mirrors the Python reference implementation to ensure reproducible results and exposes all core parameters through the INI file for fine-tuning. Besides the mandatory featureXML output, optional TSV exports for both the peptide features and raw hills can be enabled for quality control and downstream analysis.

Reference: Abdrakhimov, et al. Biosaur: An open-source Python software for liquid chromatography-mass spectrometry peptide feature detection with ion mobility support. Rapid Communications in Mass Spectrometry, 2022. https://doi.org/10.1002/rcm.9045

The command line parameters of this tool are:

INI file documentation of this tool: