OpenMS  2.4.0
TargetedFileConverter

Converts different spectral libraries / transition files for targeted proteomics and metabolomics analysis.

Can convert multiple formats to and from TraML (standardized transition format). The following formats are supported:

Transition lists can be either comma- or tab-separated. Modifications should be provided in UniMod format1, but can also be provided in TPP format. The following columns are required:

For targeted proteomics files, the following additional columns should be provided:

OpenSWATH uses grouped transitions to detect candidate analyte signals. These groups are by default generated based on the input, but can also be manually specified:

Optionally, the following columns can be specified but they are not actively used by OpenSWATH:

For targeted metabolomics files, the following fields are also supported:

Fields indicated with * are strictly required while fields indicated with ** are only required in the specific context (proteomics or metabolomics).

Remarks:

The command line parameters of this tool are:

INI file documentation of this tool: