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OpenMS
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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:
Key Features:
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:
FeatureFinderLFQ -- Feature detection for LC-MS1 data (EXPERIMENTAL)
Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_FeatureFinderLFQ.html
Version: 3.6.0-pre-nightly-2026-03-16 Mar 17 2026, 01:47:46, Revision: 1cafe71
To cite OpenMS:
+ Pfeuffer, J., Bielow, C., Wein, S. et al.. OpenMS 3 enables reproducible analysis of large-scale mass spec
trometry data. Nat Methods (2024). doi:10.1038/s41592-024-02197-7.
Usage:
FeatureFinderLFQ <options>
Options (mandatory options marked with '*'):
-in <file>* Input mzML file (centroided data) (valid formats: 'mzML')
-out <file>* Output featureXML file (valid formats: 'featureXML')
-out_tsv <file> Optional: output TSV file (Biosaur2 format) (valid formats: 'tsv')
-out_hills <file> Optional: write detected hills to TSV (valid formats: 'tsv')
-write_hills Force writing of hills file even if no output path was provided
-mini <value> Minimum intensity threshold (default: '1.0') (min: '0.0')
-minmz <value> Minimum m/z value (default: '350.0') (min: '0.0')
-maxmz <value> Maximum m/z value (default: '1500.0') (min: '0.0')
-htol <value> Mass accuracy in ppm for combining peaks into hills (default: '8.0') (min:
'0.0')
-itol <value> Mass accuracy in ppm for isotopic patterns (default: '8.0') (min: '0.0')
-hvf <value> Hill valley factor for splitting hills (default: '1.3') (min: '1.0')
-ivf <value> Isotope valley factor for splitting isotope patterns (default: '5.0') (min:
'1.0')
-minlh <number> Minimum number of scans for a hill (default: '2') (min: '1')
-pasefmini <value> Minimum combined intensity for PASEF/TIMS clusters after m/z–ion-mobility
centroiding. (default: '100.0') (min: '0.0')
-pasefminlh <number> Minimum number of raw points per PASEF/TIMS cluster during centroiding.
(default: '1') (min: '1')
-cmin <number> Minimum charge state (default: '1') (min: '1')
-cmax <number> Maximum charge state (default: '6') (min: '1')
-iuse <number> Number of isotopes for intensity calculation (0=mono only, -1=all, 1=mono+f
irst, etc.) (default: '0') (min: '-1')
-nm Negative mode (affects neutral mass calculation)
-tof Enable TOF-specific intensity filtering
-profile Enable profile mode processing (centroid spectra using PeakPickerHiRes)
-paseftol <value> Ion mobility accuracy for linking peaks into hills and grouping isotopes
(0 = disable IM-based gating). Default is for 1/K0 units (e.g., 0.03-0.08).
For CCS data, use larger values (e.g., 5-20 square angstroms). (default:
'0.05') (min: '0.0')
-use_hill_calib Enable automatic hill mass tolerance calibration
-ignore_iso_calib Disable automatic isotope mass error calibration
-hrttol <value> Maximum allowed RT difference (in seconds) between monoisotopic hill apex
and isotope hill apex when assembling isotope patterns (0 disables RT gatin
g). (default: '10.0') (min: '0.0')
-convex_hulls <choice> Representation of feature convex hulls in the output FeatureMap. 'bounding_
box' stores a single RT–m/z bounding box per feature (smaller featureXML,
no per-trace detail), whereas 'mass_traces' stores one convex hull per
contributing hill using all mass-trace points (larger featureXML, preserves
detailed trace shape). (default: 'bounding_box') (valid: 'mass_traces',
'bounding_box')
-faims_merge_features <choice> For FAIMS data with multiple compensation voltages: Merge features represen
ting the same analyte detected at different CV values into a single feature
. Only features with DIFFERENT FAIMS CV values are merged (same CV = differ
ent analytes). Has no effect on non-FAIMS data. (default: 'true') (valid:
'true', 'false')
Common TOPP options:
-ini <file> Use the given TOPP INI file
-threads <n> Sets the number of threads allowed to be used by the TOPP tool (default:
'1')
-write_ini <file> Writes the default configuration file
--help Shows options
--helphelp Shows all options (including advanced)
INI file documentation of this tool:
This section lists all parameters supported by the tool. Parameters are organized into hierarchical subsections that group related settings together. Subsections may contain further subsections or individual parameters.
Each parameter entry contains the following information:
Parameter tags provide additional information about how a parameter is used. Some tags indicate whether a parameter is required or intended for advanced configuration, while others may be used internally by OpenMS or workflow tools.
Parameters highlighted as required must be specified for the tool to run successfully. Parameters marked as advanced allow fine-tuning of algorithm behavior and are typically not needed for standard workflows.
1.9.8