An algorithm to search for exact mass matches from a spectrum against a database (e.g. HMDB). More...

#include <OpenMS/ANALYSIS/ID/AccurateMassSearchEngine.h>

Inheritance diagram for AccurateMassSearchEngine:

Collaboration diagram for AccurateMassSearchEngine:

Classes
struct	CompareEntryAndMass_

struct	MappingEntry_

Public Member Functions
	AccurateMassSearchEngine ()
	Default constructor. More...

	~AccurateMassSearchEngine () override
	Default destructor. More...

void	queryByMZ (const double &observed_mz, const Int &observed_charge, const String &ion_mode, std::vector< AccurateMassSearchResult > &results, const EmpiricalFormula &observed_adduct=EmpiricalFormula()) const
	search for a specific observed mass by enumerating all possible adducts and search M+X against database. If use_feature_adducts is activated, queryByMZ uses annotated, observed adducts as EmpiricalFormulas, restricting M+X candidates. More...

void	queryByFeature (const Feature &feature, const Size &feature_index, const String &ion_mode, std::vector< AccurateMassSearchResult > &results) const

void	queryByConsensusFeature (const ConsensusFeature &cfeat, const Size &cf_index, const Size &number_of_maps, const String &ion_mode, std::vector< AccurateMassSearchResult > &results) const

void	run (FeatureMap &, MzTab &) const

void	run (FeatureMap &, MzTabM &) const

void	run (ConsensusMap &, MzTab &) const

void	init ()
	parse database and adduct files More...

Public Member Functions inherited from DefaultParamHandler
	DefaultParamHandler (const String &name)
	Constructor with name that is displayed in error messages. More...

	DefaultParamHandler (const DefaultParamHandler &rhs)
	Copy constructor. More...

virtual	~DefaultParamHandler ()
	Destructor. More...

DefaultParamHandler &	operator= (const DefaultParamHandler &rhs)
	Assignment operator. More...

virtual bool	operator== (const DefaultParamHandler &rhs) const
	Equality operator. More...

void	setParameters (const Param &param)
	Sets the parameters. More...

const Param &	getParameters () const
	Non-mutable access to the parameters. More...

const Param &	getDefaults () const
	Non-mutable access to the default parameters. More...

const String &	getName () const
	Non-mutable access to the name. More...

void	setName (const String &name)
	Mutable access to the name. More...

const std::vector< String > &	getSubsections () const
	Non-mutable access to the registered subsections. More...

Public Member Functions inherited from ProgressLogger
	ProgressLogger ()
	Constructor. More...

virtual	~ProgressLogger ()
	Destructor. More...

	ProgressLogger (const ProgressLogger &other)
	Copy constructor. More...

ProgressLogger &	operator= (const ProgressLogger &other)
	Assignment Operator. More...

void	setLogType (LogType type) const
	Sets the progress log that should be used. The default type is NONE! More...

LogType	getLogType () const
	Returns the type of progress log being used. More...

void	startProgress (SignedSize begin, SignedSize end, const String &label) const
	Initializes the progress display. More...

void	setProgress (SignedSize value) const
	Sets the current progress. More...

void	endProgress (UInt64 bytes_processed=0) const

void	nextProgress () const
	increment progress by 1 (according to range begin-end) More...

Static Public Attributes
static constexpr char	search_engine_identifier [] = "AccurateMassSearchEngine"
	uses 'AccurateMassSearchEngine' as search engine id for protein and peptide ids which are generated by AMS More...

Protected Member Functions
void	updateMembers_ () override
	This method is used to update extra member variables at the end of the setParameters() method. More...

Protected Member Functions inherited from DefaultParamHandler
void	defaultsToParam_ ()
	Updates the parameters after the defaults have been set in the constructor. More...

Private Types
typedef std::vector< std::vector< AccurateMassSearchResult > >	QueryResultsTable

typedef std::vector< std::vector< String > >	MassIDMapping
	private member variables More...

typedef std::map< String, std::vector< String > >	HMDBPropsMapping

Private Member Functions
template<typename MAPTYPE >
String	resolveAutoMode_ (const MAPTYPE &map) const
	private member functions More...

void	parseMappingFile_ (const StringList &)

void	parseStructMappingFile_ (const StringList &)

void	parseAdductsFile_ (const String &filename, std::vector< AdductInfo > &result)

void	searchMass_ (double neutral_query_mass, double diff_mass, std::pair< Size, Size > &hit_indices) const

void	annotate_ (const std::vector< AccurateMassSearchResult > &, BaseFeature &) const
	Add search results to a Consensus/Feature. More...

std::vector< AccurateMassSearchResult >	extractQueryResults_ (const Feature &feature, const Size &feature_index, const String &ion_mode_internal, Size &dummy_count) const
	Extract query results from feature. More...

void	addMatchesToID_ (IdentificationData &id, const std::vector< AccurateMassSearchResult > &amr, const IdentificationData::InputFileRef &file_ref, const IdentificationData::ScoreTypeRef &mass_error_ppm_score_ref, const IdentificationData::ScoreTypeRef &mass_error_Da_score_ref, const IdentificationData::ProcessingStepRef &step_ref, BaseFeature &f) const
	Add resulting matches to IdentificationData. More...

double	computeCosineSim_ (const std::vector< double > &x, const std::vector< double > &y) const

double	computeIsotopePatternSimilarity_ (const Feature &feat, const EmpiricalFormula &form) const

void	exportMzTab_ (const QueryResultsTable &overall_results, const Size number_of_maps, MzTab &mztab_out, const std::vector< String > &file_locations) const

void	exportMzTabM_ (const FeatureMap &fmap, MzTabM &mztabm_out) const

Private Attributes
std::vector< MappingEntry_ >	mass_mappings_

HMDBPropsMapping	hmdb_properties_mapping_

bool	is_initialized_
	true if init_() was called without any subsequent param changes More...

bool	legacyID_ = true

double	mass_error_value_
	parameter stuff More...

String	mass_error_unit_

String	ion_mode_

bool	iso_similarity_

String	pos_adducts_fname_

String	neg_adducts_fname_

StringList	db_mapping_file_

StringList	db_struct_file_

std::vector< AdductInfo >	pos_adducts_

std::vector< AdductInfo >	neg_adducts_

String	database_name_

String	database_version_

String	database_location_

bool	keep_unidentified_masses_

Additional Inherited Members
Public Types inherited from ProgressLogger
enum	LogType { CMD , GUI , NONE }
	Possible log types. More...

Static Public Member Functions inherited from DefaultParamHandler
static void	writeParametersToMetaValues (const Param &write_this, MetaInfoInterface &write_here, const String &key_prefix="")
	Writes all parameters to meta values. More...

Static Protected Member Functions inherited from ProgressLogger
static String	logTypeToFactoryName_ (LogType type)
	Return the name of the factory product used for this log type. More...

Protected Attributes inherited from DefaultParamHandler
Param	param_
	Container for current parameters. More...

Param	defaults_
	Container for default parameters. This member should be filled in the constructor of derived classes! More...

std::vector< String >	subsections_
	Container for registered subsections. This member should be filled in the constructor of derived classes! More...

String	error_name_
	Name that is displayed in error messages during the parameter checking. More...

bool	check_defaults_
	If this member is set to false no checking if parameters in done;. More...

bool	warn_empty_defaults_
	If this member is set to false no warning is emitted when defaults are empty;. More...

Protected Attributes inherited from ProgressLogger
LogType	type_

time_t	last_invoke_

ProgressLoggerImpl *	current_logger_

Static Protected Attributes inherited from ProgressLogger
static int	recursion_depth_

Detailed Description

An algorithm to search for exact mass matches from a spectrum against a database (e.g. HMDB).

For each peak, neutral masses are reconstructed from observed (spectrum) m/z values by enumerating all possible adducts with matching charge. The resulting neutral masses (can be more than one, depending on list of possible adducts) are matched against masses from a database within a certain mass error (Da or ppm).

Supports any database which contains an identifier, chemical sum formula and (optional) mass. If masses in the database are not given (= set to 0), they are computed from sum formulas.

Both positive and negative ion mode is supported. Charge for (Consensus-)Features can be either positive or negative, but only the absolute value is used since many FeatureFinders will only report positive charges even in negative ion mode. Entities with charge=0 are treated as "unknown charge" and are tested with all potential adducts and subsequently matched against the database.

A file with a list of potential adducts can be given for each mode separately. Each line contains a chemical formula (plus quantor) and a charge (separated by semicolon), e.g. M+H;1+ The M can be preceded by a quantor (e.g.2M, 3M), implicitly assumed as 1. The chemical formula can contain multiple segments, separated by + or - operators, e.g. M+H-H2O;+1 (water loss in positive mode). Brackets are implicit per segment, i.e. M+H-H2O is parsed as M + (H) - (H2O). Each segment can also be preceded by a quantor, e.g. M+H-H2O would parse as M + (H) - 2x(H2O). If debug mode is enabled, the masses of each segment are printed for verification. In particular, typing H20 (twenty H) is different from H2O (water).

Ionization mode of the observed m/z values can be determined automatically if the input map (either FeatureMap or ConsensusMap) is annotated with a meta value, as done by FeatureFinderMetabo.

Class Documentation

◆ OpenMS::AccurateMassSearchEngine::MappingEntry_

struct OpenMS::AccurateMassSearchEngine::MappingEntry_

Collaboration diagram for AccurateMassSearchEngine::MappingEntry_:

[legend]

Class Members
String	formula
double	mass
vector< String >	massIDs

Member Typedef Documentation

◆ HMDBPropsMapping

typedef std::map<String, std::vector<String> > HMDBPropsMapping

private

◆ MassIDMapping

typedef std::vector<std::vector<String> > MassIDMapping

private

private member variables

◆ QueryResultsTable

typedef std::vector<std::vector<AccurateMassSearchResult> > QueryResultsTable

private

Constructor & Destructor Documentation

◆ AccurateMassSearchEngine()

AccurateMassSearchEngine ( )

Default constructor.

◆ ~AccurateMassSearchEngine()

~AccurateMassSearchEngine ( )

override

Default destructor.

Member Function Documentation

◆ addMatchesToID_()

void addMatchesToID_	(	IdentificationData &	id,
		const std::vector< AccurateMassSearchResult > &	amr,
		const IdentificationData::InputFileRef &	file_ref,
		const IdentificationData::ScoreTypeRef &	mass_error_ppm_score_ref,
		const IdentificationData::ScoreTypeRef &	mass_error_Da_score_ref,
		const IdentificationData::ProcessingStepRef &	step_ref,
		BaseFeature &	f
	)		const

private

Add resulting matches to IdentificationData.

◆ annotate_()

void annotate_	(	const std::vector< AccurateMassSearchResult > &	,
		BaseFeature &
	)		const

private

Add search results to a Consensus/Feature.

◆ computeCosineSim_()

double computeCosineSim_	(	const std::vector< double > &	x,
		const std::vector< double > &	y
	)		const

private

For two vectors of identical length, compute the cosine of the angle between them. Since we look at the angle, scaling of the vectors does not change the result (when ignoring numerical instability).

◆ computeIsotopePatternSimilarity_()

double computeIsotopePatternSimilarity_	(	const Feature &	feat,
		const EmpiricalFormula &	form
	)		const

private

◆ exportMzTab_()

void exportMzTab_	(	const QueryResultsTable &	overall_results,
		const Size	number_of_maps,
		MzTab &	mztab_out,
		const std::vector< String > &	file_locations
	)		const

private

◆ exportMzTabM_()

void exportMzTabM_	(	const FeatureMap &	fmap,
		MzTabM &	mztabm_out
	)		const

private

◆ extractQueryResults_()

std::vector<AccurateMassSearchResult> extractQueryResults_	(	const Feature &	feature,
		const Size &	feature_index,
		const String &	ion_mode_internal,
		Size &	dummy_count
	)		const

private

Extract query results from feature.

◆ init()

void init ( )

parse database and adduct files

◆ parseAdductsFile_()

void parseAdductsFile_	(	const String &	filename,
		std::vector< AdductInfo > &	result
	)

private

◆ parseMappingFile_()

void parseMappingFile_ ( const StringList & )

private

◆ parseStructMappingFile_()

void parseStructMappingFile_ ( const StringList & )

private

◆ queryByConsensusFeature()

void queryByConsensusFeature	(	const ConsensusFeature &	cfeat,
		const Size &	cf_index,
		const Size &	number_of_maps,
		const String &	ion_mode,
		std::vector< AccurateMassSearchResult > &	results
	)		const

◆ queryByFeature()

void queryByFeature	(	const Feature &	feature,
		const Size &	feature_index,
		const String &	ion_mode,
		std::vector< AccurateMassSearchResult > &	results
	)		const

◆ queryByMZ()

void queryByMZ	(	const double &	observed_mz,
		const Int &	observed_charge,
		const String &	ion_mode,
		std::vector< AccurateMassSearchResult > &	results,
		const EmpiricalFormula &	observed_adduct = `EmpiricalFormula()`
	)		const

search for a specific observed mass by enumerating all possible adducts and search M+X against database. If use_feature_adducts is activated, queryByMZ uses annotated, observed adducts as EmpiricalFormulas, restricting M+X candidates.

◆ resolveAutoMode_()

String resolveAutoMode_ ( const MAPTYPE & map ) const

inlineprivate

private member functions

if ion-mode is auto, this will set the internal mode according to input data

Exceptions

InvalidParameter if ion mode cannot be resolved

References File::basename(), and OPENMS_LOG_INFO.

◆ run() [1/3]

void run	(	ConsensusMap &	,
		MzTab &
	)		const

main method of AccurateMassSearchEngine input map is not const, since it will get annotated with results

Note: Call init() before calling run!

◆ run() [2/3]

void run	(	FeatureMap &	,
		MzTab &
	)		const

main method of AccurateMassSearchEngine input map is not const, since it will get annotated with results

◆ run() [3/3]

void run	(	FeatureMap &	,
		MzTabM &
	)		const

◆ searchMass_()

void searchMass_	(	double	neutral_query_mass,
		double	diff_mass,
		std::pair< Size, Size > &	hit_indices
	)		const

private

◆ updateMembers_()

void updateMembers_ ( )

overrideprotectedvirtual

This method is used to update extra member variables at the end of the setParameters() method.

Also call it at the end of the derived classes' copy constructor and assignment operator.

The default implementation is empty.

Reimplemented from DefaultParamHandler.

Member Data Documentation

◆ database_location_

String database_location_

private

◆ database_name_

String database_name_

private

◆ database_version_

String database_version_

private

◆ db_mapping_file_

StringList db_mapping_file_

private

◆ db_struct_file_

StringList db_struct_file_

private

◆ hmdb_properties_mapping_

HMDBPropsMapping hmdb_properties_mapping_

private

◆ ion_mode_

String ion_mode_

private

◆ is_initialized_

bool is_initialized_

private

true if init_() was called without any subsequent param changes

◆ iso_similarity_

bool iso_similarity_

private

◆ keep_unidentified_masses_

bool keep_unidentified_masses_

private

◆ legacyID_

bool legacyID_ = true

private

◆ mass_error_unit_

String mass_error_unit_

private

◆ mass_error_value_

double mass_error_value_

private

parameter stuff

◆ mass_mappings_

std::vector<MappingEntry_> mass_mappings_

private

◆ neg_adducts_

std::vector<AdductInfo> neg_adducts_

private

◆ neg_adducts_fname_

String neg_adducts_fname_

private

◆ pos_adducts_

std::vector<AdductInfo> pos_adducts_

private

◆ pos_adducts_fname_

String pos_adducts_fname_

private

◆ search_engine_identifier

constexpr char search_engine_identifier[] = "AccurateMassSearchEngine"

staticconstexpr

uses 'AccurateMassSearchEngine' as search engine id for protein and peptide ids which are generated by AMS

Classes

Public Member Functions

Static Public Attributes

Protected Member Functions

Private Types

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Class Documentation

◆ OpenMS::AccurateMassSearchEngine::MappingEntry_

Member Typedef Documentation

◆ HMDBPropsMapping

◆ MassIDMapping

◆ QueryResultsTable

Constructor & Destructor Documentation

◆ AccurateMassSearchEngine()

◆ ~AccurateMassSearchEngine()

Member Function Documentation

◆ addMatchesToID_()

◆ annotate_()

◆ computeCosineSim_()

◆ computeIsotopePatternSimilarity_()

◆ exportMzTab_()

◆ exportMzTabM_()

◆ extractQueryResults_()

◆ init()

◆ parseAdductsFile_()

◆ parseMappingFile_()

◆ parseStructMappingFile_()

◆ queryByConsensusFeature()

◆ queryByFeature()

◆ queryByMZ()

◆ resolveAutoMode_()

◆ run() [1/3]

◆ run() [2/3]

◆ run() [3/3]

◆ searchMass_()

◆ updateMembers_()

Member Data Documentation

◆ database_location_

◆ database_name_

◆ database_version_

◆ db_mapping_file_

◆ db_struct_file_

◆ hmdb_properties_mapping_

◆ ion_mode_

◆ is_initialized_

◆ iso_similarity_

◆ keep_unidentified_masses_

◆ legacyID_

◆ mass_error_unit_

◆ mass_error_value_

◆ mass_mappings_

◆ neg_adducts_

◆ neg_adducts_fname_

◆ pos_adducts_

◆ pos_adducts_fname_

◆ search_engine_identifier