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SeedListGenerator

Application to generate seed lists for feature detection.

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

Reference:
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?

Note
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:

INI file documentation of this tool:


OpenMS / TOPP release 2.0.0 Documentation generated on Wed Jan 27 2016 17:11:53 using doxygen 1.8.10