Here are the classes, structs, unions and interfaces with brief descriptions:

[detail level 12345]

Npappso	Tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multicharge peaks to monocharge
Nmasschroq
CAlignmentMethod
CJsonInput
CPrecursorParser
CMbrPeptideMeasurements
CMsRun
CMsRunGroup
CMsRunPeptideList
CCborOutputStream
CPeptide
CAlignedPeakPositionElement	Internal structure to compute consensus retention times
CMsRunXicCoordCharge	Internal structure to store msrun + charge + intensity + xic coordinate
CPeptideBase
CPeptideLabel
CPeptideMeasurements
CPeptideMeasurementsBase
CMeasurement
CPeptideObservation
CObservation
CPrecursor	A Precursor object represents the parent/precursor of the MS level 2 scan with number _scan_num in the mzxml file
CProtein
CQuantificationMethod
CUtils
Ncbor
Nmzcbor
CBinaryDataArray
CConvertToMzml
CMzcborCopyReplaceBase	Base class to transform mzCBOR stream in a new mzCBOR output stream
CMzcborPrecursorFinder	Base class to transform mzCBOR stream in a new mzCBOR output stream
CQcborSpectrum
CQcborSpectrumPrecursor
CSpectrumTube
CCvParam
CCvParamMap
CMzcborBuildIndexReader
CMzcborIndexReader
CMzcborReaderBase	Base class to initialize mzCBOR file parsing
CMzcborSpectrumCollectionReader
CMzmlConvert
CIsolationWindow
CSelectedIon
CPrecursor
CScan
CSpectrum
Npsm
CCborScanMapBase
CPsmFeatures
CPsmFeaturesScan
CPsmIonSeries	Computes spectrum isotope match for each PSM and stores ion series in "props"
CPsmIonSeriesScan
CPsmNewEval
CPsmSpecGlob
CPsmSpecGlobScan
CPsmSpecPeptidOms
CPsmSpecPeptidOmsScan
CMzIdentMlReader
CCvParam
CModification
CMzidDBSequence
CMzidSearchDatabase
CMzidSpectraData
CMzidPeptideEvidence
CUserParam
CSpectrumIdentificationItem
CSpectrumIdentificationResult
CPsmCbor2Json
CPsmCborUtils	Utilities to help managing data in PSM CBOR data file
CPsmProteinRef
CPsmFileAppend
CSampleStorage
CPsmFile
CPsmFileReaderBase
CPsmProteinRef
CPsmFileScanProcess	Basic PSM file reader to process scan (parallelized scan processing)
CPsmFileScanProcessAndCopy	Basic PSM file reader to process scan (parallelized scan processing) and write a new resulting PSM file
CPsmProtein
CPsmProteinMap	Store PsmProtein in a map with accession as key
CSageFileReader
CSageReader
CSageModification
CFastaSeq
CSageTsvHandler
CLine
CPsm
CScan
CSample
CCborStreamReader	Simple override of the raw QCborStreamReader This adds convenient functions to put CBOR data into C++ structures
CCborStreamReaderInterface	Base class to start a CBOR reader
CCborStreamWriter	Overrides QCborStreamWriter base class to provide convenient functions
CJsonStreamWriter	Helper class to write json text using CBOR data structures
Nspecglob
CExperimentalSpectrumDataPoint
CExperimentalSpectrum
CAminoAcidModel
CTheoreticalPeakDataPoint
CPeptideModel
CPeptideSpectrumDataPoint
CPeptideSpectrum
CPostTreatment
CScoreValues
CSpectralAlignmentDataPoint
CSpectralAlignment
Nspecpeptidoms
CCorrectionTree
CLocation
CLocationSaver
CAminoAcidModel
CPeptideModel	Modelize peptide sequence to facilitate rendering in bracket or proforma
CScenarioCell
CScenario
CScoreValues
CKeyCell
CAlignment
CSemiGlobalAlignment
CSpOMSAa
CSpOMSProtein
CAaPosition
CSpOMSSpectrum
Nspecself
CSelfSpectrum
CSelfSpectrumDataPoint
Nspectree
CBucket
CBucketClustering
CItemCart	Container for spectree items
CSpecTree
CSpecTreeNode
CMapSimilarityCountElement
CMapSimilarityCount
CSpecXtractInterface	Yield similarities between pairs of ItemCart
CSpecXtractMap	Store all similarities in vectors an map : very costly for memory and CPU
CAa
CAaBase
CAaCode	Collection of integer code for each amino acid 0 => null 1 to 20 => amino acid sorted by there mass (lower to higher). Leucine is replaced by Isoleucine
CAaModification
CCodeToMass
CAaStringCodec	Code and decode amino acid string sequence to unique integer
CAaStringCodeMassMatching	Convert a list of mass to amino acid string codes
CaaCodeAndMassRange
CAtomNumberInterface
CIsotopeCount
CChemicalFormula
CExceptionInterrupted
CExceptionNotFound
CExceptionNotImplemented
CExceptionNotPossible
CExceptionNotRecognized	Excetion to use when an item type is not recognized
CExceptionOutOfRange
CFastaFileIndexerInterface
CFastaFileIndexer
CFastaHandlerInterface
CFastaSeqHandler
CFastaOutputStream
CFastaReader
CFastaWriterInterface
CGrpExperiment
CGrpGroup
CGrpGroupingMonitorInterface
CGrpGroupingMonitor
CGrpMapPeptideToGroup
CGrpMapPeptideToSubGroupSet
CGrpPeptide
CGrpPeptideSet
CGrpProtein
CGrpSubGroup
CGrpSubGroupSet
CMassSpectrum	Class to represent a mass spectrum
CMassSpectrumId
CPrecursorIonData
CQualifiedMassSpectrum	Class representing a fully specified mass spectrum
CBafAsciiFileReader
CMsFileAccessor
CMsFileReader
CMzcborMsFileReader
CMsDataFormatEnumStr	Static functions to convert mz file formats
CPwizMsFileReader
CTimsMsFileReader
CXyMsFileReader
CMsRunRetentionTimeSeamarkPoint
CMsRunRetentionTime
CPeptideMs2Point
CMassSpectrumLineData
CBafAsciiMsRunReader
CMsRunDataSetTree
CMsRunDataSetTreeNode
CMsRunDataSetTreeNodeVisitorInterface
CMsRunId	MS run identity MsRunId identifies an MS run with a unique ID (XmlId) and contains eventually informations on its location (local disk path or URL)
CMsRunReadConfig
CMsRunReader	Base class to read MSrun the only way to build a MsRunReader object is to use the MsRunReaderFactory
CMgfOutput
CMzxmlOutput
CTranslater
CMzcborMsRunReader
CPwizMsRunReader
CTimsFramesMsRunReader
CTimsMsRunReader
CTimsMsRunReaderBase
CTimsMsRunReaderDia
CTimsMsRunReaderMs2
CTimsMsRunReaderMs2Selected
CSpectrumCollectionHandlerInterface	Interface to collect spectrums from the MsRunReader class
CMsRunSimpleStatistics	Example of interface to count MS levels of all spectrum in an MSrun
CMsRunReaderScanNumberMultiMap	Multimap to find quickly spectrum index from scan number
CMsRunReaderRetentionTimeLine	Collect retention times along MS run
CMsRunReaderTicChromatogram	Calculate a TIC chromatogram
CMsRunQualifiedSpectrumLoader	Load all qualified spectrum into a vector
CIonMobilityGrid
CXicCoord	Coordinates of the XIC to extract and the resulting XIC after extraction
CXicCoordTims	Coordinates of the XIC to extract and the resulting XIC after extraction
CXyMsRunReader
CMzRange
CFilterOboPsiModMap
CFilterOboPsiModSink
CFilterOboPsiModTermAccession
CFilterOboPsiModTermDiffMono
CFilterOboPsiModTermLabel
CFilterOboPsiModTermName
COboPsiMod
COboPsiModHandlerInterface
COboPsiModTerm
COboPsiMs
COboUnimod
CPappsoException
CIon
CPeptide
CPeptideFragment
CPeptideFragmentIon
CPeptideFragmentIonListBase
CPeptideInterface
CPeptideNaturalIsotope
CPeptideNaturalIsotopeAverage
CPeptideNaturalIsotopeList
CPeptideProFormaParser
CSimplePeakIonMatch
CPeptideRawFragmentMasses
CPeptideStrParser
CPrecisionBase
CDaltonPrecision
CPpmPrecision
CResPrecision
CPrecisionFactory
CIntegrationScope
CIntegrationScopeBase
CIntegrationScopeSpec
CIntegrationScopeRect
CIntegrationScopeRhomb
CMassDataCombinerInterface
CMassSpectrumCombiner
CMassSpectrumMinusCombiner
CMassSpectrumPlusCombiner
CMzIntegrationParams	Parameters definining how m/z integrations must be performed
CSelectionPolygon
CSelectionPolygonSpec
CTraceCombiner
CTraceMinusCombiner
CTracePlusCombiner
CCosineSimilarity
CCubicSplineModel
CHighResPeakPicker
CParameters
CPeakRange
CLocalSignalToNoiseEstimator
CParameters
CGaussianEstimateParams
CTraceDetectionSinkInterface
CTraceDetectionInterface
CTraceDetectionMoulon
CTraceDetectionZivy
CTracePeak
CTracePeakList
CFilterCeilingAmplitudePercentage	Redefines the ceiling intensity of the Trace
CFilterChargeDeconvolution
CDataPointInfo
CFilterComplementIonEnhancer	Try to detect complementary ions and assign maximum intensity of both elements
CFilterMzExclusion
CFilterFloorAmplitudePercentage	Redefines the floor intensity of the Trace
CFilterInterface	Generic interface to apply a filter on a trace
CMassSpectrumFilterInterface	Generic interface to apply a filter on a MassSpectrum This is the same as FilterInterface, but some filter are only relevant if they are used on MassSpectrum using this interface means the filter can only be applied on MassSpectrum and not on Trace
CFilterLocalMaximum	Finds all local maxima, i.e. any point that has a greater y value than both of its neighboring points and only keep those points
CFilterLowIntensitySignalRemoval	Redefines the floor intensity of the Trace
CFilterMorphoWindowBase	Base class that apply a signal treatment based on a window
CFilterMorphoSum	Test purpose
CFilterMorphoMax	Transform the trace into its maximum over a window
CFilterMorphoMin	Transform the trace into its minimum over a window
CFilterMorphoMinMax	Transform the trace with the minimum of the maximum equivalent of the dilate filter for pictures
CFilterMorphoMaxMin	Transform the trace with the maximum of the minimum equivalent of the erode filter for pictures
CFilterMorphoAntiSpike	Anti spike filter set to zero alone values inside the window
CFilterMorphoMedian	Median filter apply median of y values inside the window
CFilterMorphoMean	Mean filter apply mean of y values inside the window : this results in a kind of smoothing
CFilterMorphoBackground	Compute background of a trace compute background noise on a trace
CFilterNameInterface	Interface that allows to build filter objects from strings
CFilterNormalizeIntensities	Sets the maximum intensity of the trace to the provided value
CFilterLowPass	Remove datapoints higher or equal to a given Y value (intensity)
CFilterHighPass	Remove datapoints below or equal to the given Y value (intensity)
CFilterHighPassPercentage	Remove datapoints below a given intensity percentage (ratio) of the maximum intensity
CFilterGreatestY	Keep N datapoints form the greatest intensities to the lowest
CFilterGreatestYperWindow	Keep N datapoints form the greatest intensities to the lowest within a mass range in dalton
CMassSpectrumFilterGreatestItensities
CFilterFloorY	Apply std::floor (round to lowest integer) to all Y values
CFilterRoundY	Apply std::round (round to nearest integer) to all Y values
CFilterRescaleY	Rescales Y values into a dynamic range if the dynamic range is set to 0, this filter is ignored
CFilterScaleFactorY	Rescales Y values given a tranformation factor
CFilterRemoveY	Removes a value to all Y values
CFilterQuantileBasedRemoveY	Removes a value found by quantile to all Y values
CFilterPeakDelta
CFilterRemoveC13
CFilterResampleKeepSmaller
CFilterResampleKeepGreater
CFilterResampleRemoveXRange
CFilterResampleKeepXRange
CFilterResampleKeepPointInPolygon
CMassSpectrumFilterResampleRemoveMzRange
CMassSpectrumFilterResampleKeepMzRange
CFilterSuite	Apply a suite of filters from a vector
CFilterSuiteString
CFilterTandemDeisotope	Deisotope the mass spectrum `this` mass spectrum is iterated over and according to a data point-based moving window progression does the following tests:
CFilterTriangle
CSavGolParams	Parameters for the Savitzky-Golay filter
CFilterSavitzkyGolay	Uses Savitsky-Golay filter on trace
CProjectParam
CProjectParameters
CXtandemError
CTandemWrapperRun
CWrapTandemInput
CWrapTandemResults
CXtandemPresetReader
CUiMonitorInterface
CUiMonitorText
CUiMonitorTextPercent
CUiMonitorVoid
CMzIdentMlWriter
CXmlStreamReaderInterface	Convenient xml reader helper
CEnzyme
CEnzymeProductInterface
CPeptideModificatorInterface
CPeptideSinkInterface
CPeptideSpSinkInterface
CPeptideBuilder	Builds a peptide shared pointer from peptide string and adds fixed modifications
CPeptideFixedModificationBuilder
CPeptideMethioninRemove	Potential remove Nter Methionin
CPeptideModificatorBase
CPeptideModificatorPipeline
CPeptideModificatorTee
CPeptideSemiEnzyme	Cut a regular peptide obtained with an enzyme at any position from Nter or Cter
CPeptideSizeFilter	Filter peptide string by size
CPeptideVariableModificationBuilder	Modify a peptide shared pointer with a variable modification on one AA
CPeptideVariableModificationReplacement
CProtein
CProteinIntegerCode
CProteinPresenceAbsenceMatrix
CDeepProtEnumStr
CIonIsotopeRatioScore
CPsmFeatures
CMorpheusScore
CPeakIonIsotopeMatch
CPeakIonMatch
CPeptideIsotopeSpectrumMatch
CPeptideSpectrumMatch
CXtandemHyperscore
CXtandemHyperscoreBis
CXtandemSpectrumProcess
CDataPoint
CLinearRegression
CMapTrace
CTrace	A simple container of DataPoint instances
CUtils
CTimsFrameMobilityTraces
CMzCalibrationInterface
CMzCalibrationModel1
CMzCalibrationModel1Cached
CMzCalibrationStore
CTimsBinDec
CFrameIdDescr
CTimsData
CTimsDataFastMap	Replacement for std::map
CTimsDataFastMapElement
CTimsDdaPrecursors
CSpectrumDescr
CTimsDiaSlices
CMsMsWindow
CMsMsWindowGroup
CMsMsWindowGroupList
CFrameSliceRange
CTimsFrame
CXicComputeStructure
CTimsFrameBase
CTofIndexIntensityPair
CTimsFrameRawDataChunck
CTimsFrameRecord
CTimsFrameType1
CTimsMs2CentroidFilter
CTimsDirectXicExtractor
CTimsXicExtractorInterface
CQualifiedXic
CXic
CXicPeptideFragmentIon
CXicPeptideFragmentIonNaturalIsotope
CXicPeptideInterface
CMsRunXicExtractorFactory	Factory to build different kinds of XIC extractors
CMsRunXicExtractorInterface
CMsRunSlice
CMsRunXicExtractor
CMsRunXicExtractorPoints
CMsRunXicExtractorReadPoints	Class to read retention time points of MsRun
CMsRunXicExtractorDisk
CMsRunXicExtractorDiskBuffer
CHttpButton
CMassSpectrumWidget
CQCPSpectrum
COboChooserWidget
COboListModel
COboPsiModHandler
COboListProxyModel
COboListWidget
COboTermForm
CBaseColorMapPlotWidget
CBasePlotContext
CBasePlotWidget
CBaseTracePlotWidget
CColorMapPlotConfig
CDriftSpecMassSpecColorMapPlotWidget
CDriftSpecTracePlotWidget
CMassSpecTracePlotContext
CMassSpecTracePlotWidget
CTicXicChromDriftSpecColorMapPlotWidget
CTicXicChromMassSpecColorMapPlotWidget
CTicXicChromTracePlotWidget
CPrecisionWidget
CSwitchWidget
CQCPXic
CXicWidget
CContainsAny
CFilterComplement	Try to detect complementary ions and assign maximum intensity of both elements
CFilterMs1WindowSelection	Try to detect complementary ions and assign maximum intensity of both elements
CGraphicDeviceWidget
CInHousePolynomialSolverResult
CProteinPeptideList