Identification

Protein and peptide identification classes. More...

Collaboration diagram for Identification:

Classes
class	AccurateMassSearchEngine
	An algorithm to search for exact mass matches from a spectrum against a database (e.g. HMDB). More...
class	ConsensusIDAlgorithm
	Abstract base class for all ConsensusID algorithms (that calculate a consensus from multiple ID runs). More...
class	ConsensusIDAlgorithmAverage
	Calculates a consensus from multiple ID runs by averaging the search scores. More...
class	ConsensusIDAlgorithmBest
	Calculates a consensus from multiple ID runs by taking the best search score. More...
class	ConsensusIDAlgorithmIdentity
	Abstract base class for ConsensusID algorithms that compare only identical sequences. More...
class	ConsensusIDAlgorithmPEPIons
	Calculates a consensus from multiple ID runs based on PEPs and shared ions. More...
class	ConsensusIDAlgorithmPEPMatrix
	Calculates a consensus from multiple ID runs based on PEPs and sequence similarities. More...
class	ConsensusIDAlgorithmRanks
	Calculates a consensus from multiple ID runs based on the ranks of the search hits. More...
class	ConsensusIDAlgorithmSimilarity
	Abstract base class for ConsensusID algorithms that take peptide similarity into account. More...
class	ConsensusIDAlgorithmWorst
	Calculates a consensus from multiple ID runs by taking the worst search score (conservative approach). More...
class	FalseDiscoveryRate
	Calculates false discovery rates (FDR) from identifications. More...
class	IDBoostGraph
	Creates and maintains a boost graph based on the OpenMS ID datastructures. More...
class	IDDecoyProbability
	IDDecoyProbability calculates probabilities using decoy approach. More...
class	IDRipper
	Ripping protein/peptide identification according their file origin. More...
class	PeptideProteinResolution
	Resolves shared peptides based on protein scores. More...
class	PrecursorPurity
	Precursor purity or noise estimation. More...

Functions
static void	store (const MSExperiment &spectra, std::ofstream &os, const FeatureMapping::FeatureToMs2Indices &feature_mapping, const bool &feature_only, const int &isotope_pattern_iterations, const bool no_masstrace_info_isotope_pattern, std::vector< SiriusMSFile::CompoundInfo > &v_cmpinfo, const size_t &file_index)
	Internal structure used in SiriusExport that is used for the conversion of a MzMlFile to an internal format. More...

Detailed Description

Protein and peptide identification classes.

Function Documentation

store()

static void store ( const MSExperiment &  spectra, std::ofstream &  os, const FeatureMapping::FeatureToMs2Indices &  feature_mapping, const bool &  feature_only, const int &  isotope_pattern_iterations, const bool  no_masstrace_info_isotope_pattern, std::vector< SiriusMSFile::CompoundInfo > &  v_cmpinfo, const size_t &  file_index  )

static

Internal structure used in SiriusExport that is used for the conversion of a MzMlFile to an internal format.

Write content of one mzML/featureXML(optional) file pair to SIRIUS .ms file ofstream. Comments (see CompoundInfo) are written to SIRIUS .ms file and additionally stored in CompoundInfo struct. If adduct information for a spectrum is missing, no adduct information is added. In this case, SIRIUS assumes default adducts for the respective spectrum.

Parameters

spectra	Peakmap from input mzML.
os	Write output for .ms file to ofstream.
feature_mapping	Adducts and features (index).
feature_only	Only use features.
isotope_pattern_iterations	At which depth to stop isotope_pattern extraction (if possible).
no_masstrace_info_isotope_pattern	bool if isotope pattern should be extracted (if not in feature)
v_cmpinfo	Vector of CompoundInfo.
file_index	file index (to differentiate entries derived from different mzML files and resolve ambiguities)