Here is a list of all related documentation pages:

OpenMS Developer Quickstart Guide
pyOpenMS (Python bindings)
MapAlignerBase	Base class for different MapAligner TOPP tools
FLASHDeconvWizard	An assistant for FLASHDeconv execution
INIFileEditor	Can be used to visually edit INI files of TOPP tools
SwathWizard	An assistant for Swath analysis
TOPPAS	An assistant for GUI-driven TOPP workflow design
TOPPView
FeatureLinkerBase	Base class for different FeatureLinker tools
TOPP_FLASHDeconv	FLASHDeconv performs ultrafast deconvolution of top down proteomics MS datasets. FLASHDeconv takes mzML file as input and outputs deconvolved feature list (.tsv) and deconvolved spectra files (.tsv, .mzML, .msalign, .ms1ft). FLASHDeconv uses FLASHDeconvAlgorithm for spectral level deconvolution and MassFeatureTracer to detect mass features. Also for MSn spectra, the precursor masses (not peak m/zs) should be determined and assigned in most cases. This assignment can be done by tracking MSn-1 spectra deconvolution information. Thus FLASHDeconv class keeps MSn-1 spectra deconvolution information for a certain period for precursor mass assignment in DeconvolvedSpectrum class. In case of FLASHIda runs, this precursor mass assignment is done by FLASHIda. Thus FLASHDeconv class simply parses the log file from FLASHIda runs and pass the parsed information to DeconvolvedSpectrum class
CVInspector	A tool for visualization and validation of PSI mapping and CV files
MzMLToMatlab	Make spectrum variable txt for MATLAB from mzml file
OpenMSDatabasesInfo	Information about OpenMS' internal databases
Todo List
Improvements List
Experimental List
Deprecated List
Bug List