Abacus loads all data and creates the combined protein report.

AnnotateDatabase annotates the database on the first ds, and copy the bin data to the other folders.

BioQuant executes the bioquant quantification method.

CombinedPeptideList executes iProphet command creating the combined PepXML.

CombinedProteinList executes ProteinProphet command creating the combined ProtXML.

DBSearch executes the search engines if requested.

DeployParameterFile deploys the pipeline yaml config file.

Filter executes the Filter, Quantify and Report commands in tandem.

FreeQuant executes the LFQ method.

InitializeWorkspaces moves inside each data folder and initializes the Workspace with a database.

LabelQuant executes the isobaric-tag quantification method.

PeptideProphet executes PeptideProphet in Parallel mode.

ProteinProphet execute the TPP ProteinProphet.

PTMProphet execute the TPP PTMProphet.

Report executes the Report commands.

TMTIntegrator executes TMT-I on all PSM results.

DatabaseSearch keeps the options related to the search step.

Directives contains the instructions to run a pipeline.

Steps contains the high-level elements of the analysis to be executed.