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FeatureFinderMetaboIdent

Detects features in MS1 data corresponding to small molecule identifications.

pot. predecessor tools → FeatureFinderMetaboIdent → pot. successor tools
PeakPickerHiRes (optional) TextExporter

This tool detects quantitative features in MS1 data for a list of targets, typically small molecule/metabolite identifications. It uses algorithms for targeted data analysis from the OpenSWATH pipeline.

Note
This tool is still experimental!
See also
FeatureFinderIdentification - targeted feature detection based on peptide identifications.

Input format

Spectra are expected in centroided or profile mode. Only MS1 level spectra are considered for feature detection.

The targets to quantify have to be specified in a tab-separated text file that is passed via the id parameter. This file has to start with the following header line, defining its columns:

CompoundName    SumFormula    Mass    Charge    RetentionTime    RetentionTimeRange    IsoDistribution

Every subsequent line defines a target. (Except lines starting with "#", which are considered as comments and skipped.) The following requirements apply:

  • CompoundName: unique name for the target compound
  • SumFormula: chemical sum formula (see OpenMS::EmpiricalFormula), optional
  • Mass: neutral mass; if zero calculated from Formula
  • Charge: charge state, or comma-separated list of multiple charges
  • RetentionTime: retention time (RT), or comma-separated list of multiple RTs
  • RetentionTimeRange: RT window around RetentionTime for chromatogram extraction, either one value or one per RT entry; if zero parameter extract:rt_window is used
  • IsoDistribution: comma-separated list of relative abundances of isotopologues (see OpenMS::IsotopeDistribution); if zero calculated from Formula

In the simplest case, only CompoundName, SumFormula, Charge and RetentionTime need to be given, all other values may be zero. Every combination of compound (mass), RT and charge defines one target for feature detection.

Output format

The main output (parameter out) is a featureXML file containing the detected features, with annotations in meta data entries. This file can be visualized in TOPPView - perhaps most usefully as a layer on top of the LC-MS data that gave rise to it. Compound annotations of features (Name entries from the id input) can be shown by clicking the "Show feature annotation" button in the tool bar and selecting "Label meta data". Positions of targets for which no feature was detected can be shown by clicking the "Show unassigned peptide identifications" button and selecting "Show label meta data".

To export the data from the featureXML file to a tabular text file (CSV), use TextExporter with the options no_ids and feature:add_metavalues 0 (to include all meta data annotations). In the result, the information from the CompoundName, SumFormula, Charge and RetentionTime columns from the input will be in the label, sum_formula, charge and expected_rt columns, respectively.

The command line parameters of this tool are:

INI file documentation of this tool: