#include <OpenMS/KERNEL/FeatureMap.h>
#include <OpenMS/KERNEL/Feature.h>
#include <OpenMS/FORMAT/MzMLFile.h>
#include <OpenMS/CONCEPT/Constants.h>
#include <OpenMS/APPLICATIONS/TOPPBase.h>
#include <OpenMS/CHEMISTRY/ModificationsDB.h>
#include <OpenMS/DATASTRUCTURES/Param.h>
#include <OpenMS/FORMAT/FeatureXMLFile.h>
#include <OpenMS/FORMAT/FASTAFile.h>
#include <OpenMS/CHEMISTRY/Element.h>
#include <OpenMS/CHEMISTRY/ElementDB.h>
#include <OpenMS/MATH/STATISTICS/StatisticFunctions.h>
#include <OpenMS/TRANSFORMATIONS/RAW2PEAK/PeakPickerHiRes.h>
#include <OpenMS/MATH/MISC/NonNegativeLeastSquaresSolver.h>
#include <OpenMS/FORMAT/SVOutStream.h>
#include <OpenMS/FORMAT/TextFile.h>
#include <OpenMS/FILTERING/TRANSFORMERS/Normalizer.h>
#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/GaussModel.h>
#include <OpenMS/COMPARISON/SPECTRA/SpectrumAlignment.h>
#include <OpenMS/FILTERING/TRANSFORMERS/ThresholdMower.h>
#include <OpenMS/MATH/MISC/CubicSpline2d.h>
#include <OpenMS/CHEMISTRY/MASSDECOMPOSITION/MassDecomposition.h>
#include <OpenMS/CHEMISTRY/MASSDECOMPOSITION/MassDecompositionAlgorithm.h>
#include <OpenMS/CHEMISTRY/ISOTOPEDISTRIBUTION/CoarseIsotopePatternGenerator.h>
#include <OpenMS/SYSTEM/File.h>
#include <boost/math/distributions/normal.hpp>
#include <QtCore/QStringList>
#include <QtCore/QFile>
#include <QtCore/QDir>
#include <QtCore/QFileInfo>
#include <QtCore/QProcess>
#include <algorithm>
#include <iostream>
#include <iomanip>
#include <fstream>
#include <map>
#include <cmath>

Classes
struct	RateScorePair

struct	SIPIncorporation
	datastructure for reporting an incorporation event More...

struct	SIPPeptide
	datastructure for reporting a peptide with one or more incorporation rates comparator for vectors of SIPPeptides based on their size. Used to sort by group size. More...

struct	SizeLess

struct	SequenceLess

struct	RIALess

class	MetaProSIPInterpolation

class	MetaProSIPClustering

class	MetaProSIPReporting

class	MetaProSIPDecomposition

class	MetaProSIPXICExtraction

class	RIntegration

Typedefs
typedef map< double, double >	MapRateToScoreType

typedef pair< double, vector< double > >	IsotopePattern

typedef vector< IsotopePattern >	IsotopePatterns

Class Documentation

◆ RateScorePair

struct RateScorePair

Class Members
double	rate
double	score

◆ SIPIncorporation

struct SIPIncorporation

datastructure for reporting an incorporation event

Class Members
double	abundance	abundance of isotopologue
double	correlation	correlation coefficient
double	rate	rate

◆ SIPPeptide

struct SIPPeptide

datastructure for reporting a peptide with one or more incorporation rates comparator for vectors of SIPPeptides based on their size. Used to sort by group size.

Class Members
vector< String >	accessions	protein accessions of the peptide
PeakSpectrum	accumulated
Int	charge	charge of the peptide feature
MapRateToScoreType	correlation_map
vector< RateScorePair >	correlation_maxima
MapRateToScoreType	decomposition_map
double	explained_TIC_fraction	fraction of the MS2 TIC that is explained by the maximum correlating decomposition weights
double	feature_mz	mz of feature apex [s]
double	feature_rt	measurement time of feature apex [s]
String	feature_type	used to distinguish features from FeatureFinder, or synthetised from ids or averagine ids in reporting
double	global_LR	labeling ratio for the whole spectrum used to detect global drifts. 13C/(12C+13C) intensities. (15N analogous)
vector< SIPIncorporation >	incorporations
double	mass_diff
double	mass_theo	uncharged theoretical mass
double	mz_theo	theoretical mz
Size	non_zero_decomposition_coefficients	decomposition coefficients significantly larger than 0
IsotopePatterns	patterns
PeakSpectrum	reconstruction	signal reconstruction (debugging)
vector< double >	reconstruction_monoistopic	signal reconstruction of natural peptide (at mono-isotopic peak)
double	RR	R squared of NNLS fit.
double	score	search engine score or q-value if fdr filtering is applied
AASequence	sequence	sequence of the peptide
bool	unique	if the peptide is unique and therefor identifies the protein umambigously

Typedef Documentation

◆ IsotopePattern

typedef pair<double, vector<double> > IsotopePattern

◆ IsotopePatterns

typedef vector<IsotopePattern> IsotopePatterns

◆ MapRateToScoreType

typedef map<double, double> MapRateToScoreType

Classes

Typedefs