#include <OpenMS/FORMAT/DATAACCESS/SiriusFragmentAnnotation.h>

Classes
class	SiriusTargetDecoySpectra
	SiriusTargetDecoySpectra holds the target and/or decoy information for one entry (subdirectory from SIRIUS) More...

Static Public Member Functions
static std::vector< SiriusTargetDecoySpectra >	extractAndResolveSiriusAnnotations (const std::vector< String > &sirius_workspace_subdirs, const double &score_threshold, bool use_exact_mass)
	extractAndResolveSiriusAnnotations Extract and resolves SIRIUS target and/or decoy annotation for mapping native_id to MSSpectrum. More...

static void	extractSiriusFragmentAnnotationMapping (const String &path_to_sirius_workspace, MSSpectrum &msspectrum_to_fill, bool use_exact_mass=false)
	extractSiriusFragmentAnnotationMapping Extract concatenated native ids and concatenated m_ids (unique identifier) from (./spectrum.ms) and fragment annotation (./spectra/1_sumformula.tsv) from SIRIUS output (per compound). More...

static void	extractSiriusDecoyAnnotationMapping (const String &path_to_sirius_workspace, MSSpectrum &msspectrum_to_fill)
	extractSiriusDecoyAnnotationMapping Extract concatenated native ids and concatenated m_ids (./spectrum.ms) and fragment annotation (./decoy/1_sumformula.tsv) from SIRIUS/PASSATUTTO output (per compound). More...

Static Protected Member Functions
static OpenMS::String	extractConcatNativeIDsFromSiriusMS_ (const OpenMS::String &path_to_sirius_workspace)
	extractConcatNativeIDsFromSiriusMS Extract concatenated native id from SIRIUS output (./spectrum.ms) and concatenates them. More...

static OpenMS::String	extractConcatMIDsFromSiriusMS_ (const String &path_to_sirius_workspace)
	extractConcatMIDsFromSiriusMS Extract m_ids from SIRIUS output (./spectrum.ms) and concatenates them. M_id is the native id + an index, which is incremented based on the number of possible identifications (accurate mass search). More...

static void	extractAnnotationFromSiriusFile_ (const String &path_to_sirius_workspace, MSSpectrum &msspectrum_to_fill, bool use_exact_mass=false)
	extractAnnotationFromSiriusFile Extract fragment annotation from SIRIUS (./spectra/1_sumformula.tsv). More...

static std::map< Size, String >	extractCompoundRankingAndFilename_ (const String &path_to_sirius_workspace)
	extractCompoundRankingAndFilename Extract compound ranking and filename (./formula_candidates.tsv). More...

static std::map< Size, double >	extractCompoundRankingAndScore_ (const String &path_to_sirius_workspace)
	extractCompoundRankingAndFilename Extract compound ranking and score (./formula_candidates.tsv). More...

static void	extractAnnotationFromDecoyFile_ (const String &path_to_sirius_workspace, MSSpectrum &msspectrum_to_fill)
	extractAnnotationFromDecoyFile Extract decoy annotation from SIRIUS/PASSATUTTO (./decoys/1_sumformula.tsv). More...

Member Function Documentation

◆ extractAndResolveSiriusAnnotations()

static std::vector<SiriusTargetDecoySpectra> extractAndResolveSiriusAnnotations	(	const std::vector< String > &	sirius_workspace_subdirs,
		const double &	score_threshold,
		bool	use_exact_mass
	)

static

extractAndResolveSiriusAnnotations Extract and resolves SIRIUS target and/or decoy annotation for mapping native_id to MSSpectrum.

Returns: map native_id to annotated MSSpectrum (target or decoy)

If there are multiple identifications for a feature with the same MS2 spectras (concatenated native ids) the identification with the higher SIRIUS score is chosen (currently based on the explained peak intensities).

Parameters

sirius_workspace_subdirs	Vector of paths to SIRIUS subdirectories.
use_exact_mass	Option to use exact mass instead of peak mz in MSSpectrum.

◆ extractAnnotationFromDecoyFile_()

static void extractAnnotationFromDecoyFile_	(	const String &	path_to_sirius_workspace,
		MSSpectrum &	msspectrum_to_fill
	)

staticprotected

extractAnnotationFromDecoyFile Extract decoy annotation from SIRIUS/PASSATUTTO (./decoys/1_sumformula.tsv).

Returns: annotated decoy MSSpectrum (mz, rel. int, fragment explanation, ionization).

MetaValues: peak_mz annotated_sumformula annotated_adduct

Parameters

path_to_sirius_workspace	Path to SIRIUS workspace.
use_exact_mass	Option to use exact mass instead of peak mz in MSSpectrum.

◆ extractAnnotationFromSiriusFile_()

static void extractAnnotationFromSiriusFile_	(	const String &	path_to_sirius_workspace,
		MSSpectrum &	msspectrum_to_fill,
		bool	use_exact_mass = `false`
	)

staticprotected

extractAnnotationFromSiriusFile Extract fragment annotation from SIRIUS (./spectra/1_sumformula.tsv).

Returns: annotated (consensus) MSSpectrum (mz, int, exact mass, fragment explanation).

MetaValues: peak_mz indicates which mass input was used in Peak1D (mz or exact_mass). annotated_sumformula annotated_adduct

Parameters

path_to_sirius_workspace	Path to SIRIUS workspace.
use_exact_mass	Option to use exact mass instead of peak mz in MSSpectrum.

◆ extractCompoundRankingAndFilename_()

static std::map< Size, String > extractCompoundRankingAndFilename_ ( const String & path_to_sirius_workspace )

staticprotected

extractCompoundRankingAndFilename Extract compound ranking and filename (./formula_candidates.tsv).

Returns: a map with specified rank and filename (formula_adduct.tsv) (based on the annotation)

Parameters

path_to_sirius_workspace Path to SIRIUS workspace.

◆ extractCompoundRankingAndScore_()

static std::map< Size, double > extractCompoundRankingAndScore_ ( const String & path_to_sirius_workspace )

staticprotected

extractCompoundRankingAndFilename Extract compound ranking and score (./formula_candidates.tsv).

Returns: a map with specified rank and score (explainedIntensity) (based on the annotation)

Parameters

path_to_sirius_workspace Path to SIRIUS workspace.

◆ extractConcatMIDsFromSiriusMS_()

static OpenMS::String extractConcatMIDsFromSiriusMS_ ( const String & path_to_sirius_workspace )

staticprotected

extractConcatMIDsFromSiriusMS Extract m_ids from SIRIUS output (./spectrum.ms) and concatenates them. M_id is the native id + an index, which is incremented based on the number of possible identifications (accurate mass search).

Returns: String m_id of current SIRIUS compound

Parameters

path_to_sirius_workspace Path to SIRIUS workspace.

◆ extractConcatNativeIDsFromSiriusMS_()

static OpenMS::String extractConcatNativeIDsFromSiriusMS_ ( const OpenMS::String & path_to_sirius_workspace )

staticprotected

extractConcatNativeIDsFromSiriusMS Extract concatenated native id from SIRIUS output (./spectrum.ms) and concatenates them.

Returns: String native id of current SIRIUS compound

Parameters

path_to_sirius_workspace Path to SIRIUS workspace.

◆ extractSiriusDecoyAnnotationMapping()

static void extractSiriusDecoyAnnotationMapping	(	const String &	path_to_sirius_workspace,
		MSSpectrum &	msspectrum_to_fill
	)

static

extractSiriusDecoyAnnotationMapping Extract concatenated native ids and concatenated m_ids (./spectrum.ms) and fragment annotation (./decoy/1_sumformula.tsv) from SIRIUS/PASSATUTTO output (per compound).

Returns: annotated decoy MSSpectrum with associated native id

MetaValues: peak_mz annotated_sumformula annotated_adduct

The data is stored in a MSSpectrum, which contains a Peak1D (mz, int), a FloatDataArray (exact mass),a StringDataArray (explanation), and a StringDataArray (ionization).

MSSpectrum
Peak1D		FloatDataArray	StringDataArray
mz	intensity	exact_mass	explanation
56.050855	20794.85	56.049476	C3H5N

Parameters

path_to_sirius_workspace	Path to SIRIUS workspace.
use_exact_mass	Option to use exact mass instead of peak mz in MSSpectrum.

◆ extractSiriusFragmentAnnotationMapping()

static void extractSiriusFragmentAnnotationMapping	(	const String &	path_to_sirius_workspace,
		MSSpectrum &	msspectrum_to_fill,
		bool	use_exact_mass = `false`
	)

static

extractSiriusFragmentAnnotationMapping Extract concatenated native ids and concatenated m_ids (unique identifier) from (./spectrum.ms) and fragment annotation (./spectra/1_sumformula.tsv) from SIRIUS output (per compound).

Returns: annotated (consensus) MSSpectrum with associated native id

MetaValues: peak_mz indicates which mass input was used in Peak1D (mass or exact_mass). annotated_sumformula annotated_adduct

The data is stored in a MSSpectrum, which contains a Peak1D (mz, int), a FloatDataArray (exact mass), and a StringDataArray (explanation).

MSSpectrum
Peak1D		FloatDataArray	StringDataArray
mz	intensity	exact_mass	explanation
56.050855	20794.85	56.049476	C3H5N

Parameters

path_to_sirius_workspace	Path to SIRIUS workspace.
use_exact_mass	Option to use exact mass instead of peak mz in MSSpectrum.

Classes

Static Public Member Functions

Static Protected Member Functions

Member Function Documentation

◆ extractAndResolveSiriusAnnotations()

◆ extractAnnotationFromDecoyFile_()

◆ extractAnnotationFromSiriusFile_()

◆ extractCompoundRankingAndFilename_()

◆ extractCompoundRankingAndScore_()

◆ extractConcatMIDsFromSiriusMS_()

◆ extractConcatNativeIDsFromSiriusMS_()

◆ extractSiriusDecoyAnnotationMapping()

◆ extractSiriusFragmentAnnotationMapping()