MSn tree feature list builder¶
Feature detection → MSn → MSn tree feature list builder
This module is an alternative to the Chromatogram builder for creating chromatograms based on MS2 spectra or MSn trees.
- Groups all MS2 spectra are by an m/z tolerance.
- Adds MSn, multi-stage fragmentation, spectra to the MS2 groups, if they are present.
- Builds an extracted ion chromatogram (EIC) for each group around their first MS2 scans precursor m/z and the m/z tolerance.
- The EICs may be empty if the precursor m/z reported in the MS2 scan metadata does not match the MS1 data or if the m/z tolerance is too narrow.
- Even empty EICs will be reported in the resulting feature list with their respective precursor m/z and fragmentation scans.
Parameters¶
Raw data files¶
The selected data files to process.
EIC scans¶
A filter to select scans (usually MS1) for building extracted ion chromatograms.
m/z tolerance (scan-to-scan)¶
Defines the fluctuation of an individual m/z peak in between scans. For TOF instruments, 0.005 m/z or 20 ppm is a good starting point, while Orbitraps or FT-ICRs can achieve narrower signals depending on the set mass resolution.
Suffix¶
This suffix is added to the produced feature list.