OpenMS  2.4.0

Application to generate seed lists for feature detection.

potential predecessor tools $ \longrightarrow $ SeedListGenerator $ \longrightarrow $ potential successor tools
IDFilter FeatureFinderCentroided
(or another feature grouping algorithm)

Weisser et al.: An automated pipeline for high-throughput label-free quantitative proteomics (J. Proteome Res., 2013, PMID: 23391308).

In feature detection algorithms, an early step is generally to identify points of interest in the LC-MS map (so-called seeds) that may later be extended to features. If supported by the feature detection algorithm (currently only the "centroided" algorithm), user-supplied seed lists allow greater control over this process.

The SeedListGenerator can automatically create seed lists from a variety of sources. The lists are exported in featureXML format - suitable as input to FeatureFinder -, but can be converted to or from text formats using the TextExporter (with "-minimal" option to convert to CSV) and FileConverter (to convert from CSV) tools.

Seed lists can be generated from the file types below. The seeds are created at the indicated positions (RT/MZ):

If input is consensusXML, one output file per constituent map is required (same order as in the consensusXML). Otherwise, exactly one output file.

What are possible use cases for custom seed lists?

Currently mzIdentML (mzid) is not directly supported as an input/output format of this tool. Convert mzid files to/from idXML using IDFileConverter if necessary.

The command line parameters of this tool are:

SeedListGenerator -- Generates seed lists for feature detection.
Version: 2.4.0 Oct 29 2018, 15:52:19, Revision: 9690d06
To cite OpenMS:
  Rost HL, Sachsenberg T, Aiche S, Bielow C et al.. OpenMS: a flexible open-source software platform for mass spectrometry data analysis. Nat Meth. 2016; 13, 9: 741-748. doi:10.1038/nmeth.3959.

  SeedListGenerator <options>

Options (mandatory options marked with '*'):
  -in <file>*         Input file (see below for details) (valid formats: 'mzML', 'idXML', 'featureXML', 'cons
  -out <file(s)>*     Output file(s) (valid formats: 'featureXML')
  -use_peptide_mass   [idXML input only] Use the monoisotopic mass of the best peptide hit for the m/z positi
                      on (default: use precursor m/z)
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:

required parameter
advanced parameter
+SeedListGeneratorGenerates seed lists for feature detection.
version2.4.0 Version of the tool that generated this parameters file.
++1Instance '1' section for 'SeedListGenerator'
in Input file (see below for details)input file*.mzML,*.idXML,*.featureXML,*.consensusXML
out[] Output file(s)output file*.featureXML
use_peptide_massfalse [idXML input only] Use the monoisotopic mass of the best peptide hit for the m/z position (default: use precursor m/z)true,false
log Name of log file (created only when specified)
debug0 Sets the debug level
threads1 Sets the number of threads allowed to be used by the TOPP tool
no_progressfalse Disables progress logging to command linetrue,false
forcefalse Overwrite tool specific checks.true,false
testfalse Enables the test mode (needed for internal use only)true,false