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...

class	ProteinResolver
	Helper class for peptide and protein quantification based on feature data annotated with IDs. More...

class	SiriusMzTabWriter::SiriusAdapterHit
	Internal structure used in SiriusAdapter that is used for the conversion of the sirius output to an mzTab. More...

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

Detailed Description

Protein and peptide identification classes.

Class Documentation

◆ OpenMS::SiriusMzTabWriter::SiriusAdapterHit

class OpenMS::SiriusMzTabWriter::SiriusAdapterHit

Internal structure used in SiriusAdapter that is used for the conversion of the sirius output to an mzTab.

SiriusAdapterHit: formula (String) - Sumformula adduct (String) - Assigned adduct precursor_formula (String) - Sumformula of the precursor (can be the same as formula) rank (int) - Rank of the possible sumformula for a compound (spectrum) calculated by Sirius rank_score (double) - Ranking score iso_score (double) - Isotope pattern score tree_score (double) - Fragmentation pattern score sirius_score (double) - Overall score of the possible sumformula for a compound (spectrum) calculated by Sirius explainedpeaks (int) - Number of explained peaks explainedintensity (double) - Relative amount of explained intensity

SiriusAdapterIdentification: scan_index (int) - Index of the spectrum used scan_number (int) - NativeId of the spectrum used feature_id (String) - FeatureId (if spectrum was assigned to a feature) hits (vector<SiriusAdapterHit>)

SiriusAdapterRun: identifications (vector<SiriusAdapterIdentification>)

Store a specific

Parameters

number of lines from sirius output

Returns: mzTab

Collaboration diagram for SiriusMzTabWriter::SiriusAdapterHit:

[legend]

Class Members
String	adduct
double	explainedintensity
int	explainedpeaks
String	formula
double	iso_score
double	mass_error_precursor_ppm
double	median_absolute_mass_error_fragment_peaks_ppm
double	median_mass_error_fragment_peaks_ppm
String	precursor_formula
int	rank
double	sirius_score
double	tree_score

Function Documentation

◆ store()

static void store	(	const MSExperiment &	spectra,
		const OpenMS::String &	msfile,
		const FeatureMapping::FeatureToMs2Indices &	feature_mapping,
		const bool &	feature_only,
		const int &	isotope_pattern_iterations,
		const bool	no_mt_info,
		std::vector< SiriusMSFile::CompoundInfo > &	v_cmpinfo
	)

static

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

Store .ms file. Comments (see CompoundInfo) are written to SIRIUS .ms file and additionally stores 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.