Quantitative mass spectrometry workflow. Currently supports proteomics experiments with complex experimental designs for DDA-LFQ, DDA-Isobaric and DIA-LFQ quantification.
Define where the pipeline should find input data and save output data.
Settings that relate to the mandatory protein database and the optional generation of decoy entries. Note: Decoys for DIA will be created internally.
In case you start from profile mode mzMLs or the internal preprocessing during conversion with the ThermoRawFileParser fails (e.g. due to new instrument types), preprocessing has to be performed with OpenMS. Use this section to configure.
Settings for calculating a localization probability with LucXor for modifications with multiple candidate amino acids in a peptide.
Choose between different rescoring/posterior probability calculation methods and set them up.
In the following you can find help for the Percolator specific options that are only used if [`--posterior_probabilities`](#posterior_probabilities) was set to 'percolator'. Note that there are currently some restrictions to the original options of Percolator: * no Percolator protein FDR possible (currently OpenMS' FDR is used on protein level) * no support for separate target and decoy databases (i.e. no min-max q-value calculation or target-decoy competition strategy) * no support for combined or experiment-wide peptide re-scoring. Currently search results per input file are submitted to Percolator independently.
Use this instead of Percolator if there are problems with Percolator (e.g. due to bad separation) or for performance
Extracts and normalizes labeling information
Assigns protein/peptide identifications to features or consensus features. Here, features generated from isobaric reporter intensities of fragment spectra.
To group proteins, calculate scores on the protein (group) level and to potentially modify associations from peptides to proteins.
General protein quantification settings for both LFQ and isobaric labelling.
Settings for DIA-NN - a universal software for data-independent acquisition (DIA) proteomics data processing.
Parameters used to describe centralised config profiles. These should not be edited.
Set the top limit for requested resources for any single job.
Less common options for the pipeline, typically set in a config file.