SIPPeptide Struct Reference

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...

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

Detailed Description

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.

Member Data Documentation

accessions

vector<String> accessions

protein accessions of the peptide

Referenced by MetaProSIPReporting::createCSVReport(), MetaProSIPReporting::createPeptideCentricCSVReport(), and TOPPMetaProSIP::main_().

accumulated

PeakSpectrum accumulated

Referenced by MetaProSIPReporting::createPeptideCentricCSVReport(), and TOPPMetaProSIP::main_().

charge

Int charge

charge of the peptide feature

Referenced by MetaProSIPDecomposition::calculateDecompositionWeightsIsotopicPatterns(), MetaProSIPReporting::createPeptideCentricCSVReport(), TOPPMetaProSIP::extractIncorporationsAtCorrelationMaxima(), TOPPMetaProSIP::extractIncorporationsAtHeighestDecompositionWeights(), and TOPPMetaProSIP::main_().

correlation_map

MapRateToScoreType correlation_map

Referenced by TOPPMetaProSIP::extractIncorporationsAtCorrelationMaxima(), TOPPMetaProSIP::extractIncorporationsAtHeighestDecompositionWeights(), and TOPPMetaProSIP::main_().

correlation_maxima

vector<RateScorePair> correlation_maxima

Referenced by TOPPMetaProSIP::extractIncorporationsAtCorrelationMaxima(), and TOPPMetaProSIP::main_().

decomposition_map

MapRateToScoreType decomposition_map

Referenced by TOPPMetaProSIP::extractIncorporationsAtCorrelationMaxima(), TOPPMetaProSIP::extractIncorporationsAtHeighestDecompositionWeights(), and TOPPMetaProSIP::main_().

explained_TIC_fraction

double explained_TIC_fraction

fraction of the MS2 TIC that is explained by the maximum correlating decomposition weights

Referenced by MetaProSIPReporting::createPeptideCentricCSVReport(), TOPPMetaProSIP::extractIncorporationsAtCorrelationMaxima(), and TOPPMetaProSIP::extractIncorporationsAtHeighestDecompositionWeights().

feature_mz

double feature_mz

mz of feature apex [s]

Referenced by MetaProSIPReporting::createPeptideCentricCSVReport(), and TOPPMetaProSIP::main_().

feature_rt

double feature_rt

measurement time of feature apex [s]

Referenced by MetaProSIPReporting::createPeptideCentricCSVReport(), and TOPPMetaProSIP::main_().

feature_type

String feature_type

used to distinguish features from FeatureFinder, or synthetised from ids or averagine ids in reporting

Referenced by MetaProSIPReporting::createPeptideCentricCSVReport(), and TOPPMetaProSIP::main_().

global_LR

double global_LR

labeling ratio for the whole spectrum used to detect global drifts. 13C/(12C+13C) intensities. (15N analogous)

Referenced by MetaProSIPReporting::createPeptideCentricCSVReport(), and TOPPMetaProSIP::main_().

incorporations

vector<SIPIncorporation> incorporations

Referenced by MetaProSIPReporting::createPeptideCentricCSVReport(), TOPPMetaProSIP::extractIncorporationsAtCorrelationMaxima(), TOPPMetaProSIP::extractIncorporationsAtHeighestDecompositionWeights(), and TOPPMetaProSIP::main_().

mass_diff

double mass_diff

Referenced by MetaProSIPDecomposition::calculateDecompositionWeightsIsotopicPatterns(), TOPPMetaProSIP::extractIncorporationsAtCorrelationMaxima(), TOPPMetaProSIP::extractIncorporationsAtHeighestDecompositionWeights(), and TOPPMetaProSIP::main_().

mass_theo

double mass_theo

uncharged theoretical mass

Referenced by TOPPMetaProSIP::main_().

mz_theo

double mz_theo

theoretical mz

Referenced by MetaProSIPDecomposition::calculateDecompositionWeightsIsotopicPatterns(), MetaProSIPReporting::createPeptideCentricCSVReport(), TOPPMetaProSIP::extractIncorporationsAtCorrelationMaxima(), TOPPMetaProSIP::extractIncorporationsAtHeighestDecompositionWeights(), and TOPPMetaProSIP::main_().

non_zero_decomposition_coefficients

Size non_zero_decomposition_coefficients

decomposition coefficients significantly larger than 0

Referenced by MetaProSIPReporting::createPeptideCentricCSVReport(), TOPPMetaProSIP::extractIncorporationsAtCorrelationMaxima(), and TOPPMetaProSIP::extractIncorporationsAtHeighestDecompositionWeights().

patterns

IsotopePatterns patterns

Referenced by TOPPMetaProSIP::main_().

reconstruction

PeakSpectrum reconstruction

signal reconstruction (debugging)

Referenced by MetaProSIPDecomposition::calculateDecompositionWeightsIsotopicPatterns().

reconstruction_monoistopic

vector<double> reconstruction_monoistopic

signal reconstruction of natural peptide (at mono-isotopic peak)

Referenced by MetaProSIPDecomposition::calculateDecompositionWeightsIsotopicPatterns(), and TOPPMetaProSIP::main_().

RR

double RR

R squared of NNLS fit.

Referenced by MetaProSIPDecomposition::calculateDecompositionWeightsIsotopicPatterns(), and TOPPMetaProSIP::main_().

score

double score

search engine score or q-value if fdr filtering is applied

Referenced by MetaProSIPReporting::createPeptideCentricCSVReport(), and TOPPMetaProSIP::main_().

sequence

AASequence sequence

sequence of the peptide

Referenced by MetaProSIPReporting::createCSVReport(), MetaProSIPReporting::createPeptideCentricCSVReport(), and TOPPMetaProSIP::main_().

unique

bool unique

if the peptide is unique and therefor identifies the protein umambigously

Referenced by MetaProSIPReporting::createCSVReport(), MetaProSIPReporting::createPeptideCentricCSVReport(), and TOPPMetaProSIP::main_().