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OpenSwathWorkflow

Complete workflow to run OpenSWATH

This implements the OpenSwath workflow as described in Roest and Rosenberger et al. (2013) and provides a complete, integrated analysis tool without the need to run multiple tools consecutively.

It executes the following steps in order:

See below or have a look at the INI file (via "OpenSwathWorkflow -write_ini myini.ini") for available parameters and more functionality.

Input: SWATH maps and transition list

SWATH maps can be provided as mzML files, either as single file directly from the machine (this assumes that the SWATH method has 1 MS1 and then n MS2 spectra which are ordered the same way for each cycle). E.g. a valid method would be MS1, MS2 [400-425], MS2 [425-450], MS1, MS2 [400-425], MS2 [425-450] while an invalid method would be MS1, MS2 [400-425], MS2 [425-450], MS1, MS2 [425-450], MS2 [400-425] where MS2 [xx-yy] indicates an MS2 scan with an isolation window starting at xx and ending at yy. OpenSwathWorkflow will try to read the SWATH windows from the data, if this is not possible please provide a tab-separated list with the correct windows using the -swath_windows_file parameter.

Alternatively, a set of split files (n+1 mzML files) can be provided, each containing one SWATH map (or MS1 map).

Since the file size can become rather large, it is recommended to not load the whole file into memory but rather cache it somewhere on the disk using a fast-access data format. This can be specified using the -readOptions cache parameter (this is recommended!).

Output: Feature list and chromatograms

The output of the OpenSwathWorkflow is a feature list, either as FeatureXML or as tsv (use -out_features or -out_tsv) while the latter is more memory friendly. If you analyze large dataset, it is recommended to only use -out_tsv and not -out_features. For downstream analysis (e.g. using mProphet) also the -out_tsv format is recommended.

In addition, the extracted chromatograms can be written out using the -out_chrom parameter.

The command line parameters of this tool are:

INI file documentation of this tool:


OpenMS / TOPP release 2.0.0 Documentation generated on Mon May 23 2016 19:47:16 using doxygen 1.8.11