SiriusMSFile Class Reference

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

Classes
class	AccessionInfo
	< class to store information about accessions More...
class	CompoundInfo

Static Public Member 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...

Static Protected Member Functions
static void	writeMsFile_ (std::ofstream &os, const MSExperiment &spectra, const std::vector< size_t > &ms2_spectra_index, const SiriusMSFile::AccessionInfo &ainfo, const StringList &adducts, const std::vector< String > &v_description, const std::vector< String > &v_sumformula, const std::vector< std::pair< double, double >> &f_isotopes, int &feature_charge, uint64_t &feature_id, const double &feature_rt, const double &feature_mz, bool &writecompound, const bool &no_masstrace_info_isotope_pattern, const int &isotope_pattern_iterations, int &count_skipped_spectra, int &count_assume_mono, int &count_no_ms1, std::vector< SiriusMSFile::CompoundInfo > &v_cmpinfo)
	Internal structure to write the .ms file (called in store function) More...
static Int	getHighestIntensityPeakInMZRange_ (double test_mz, const MSSpectrum &spectrum, double tolerance, bool ppm)
	Find highest intensity peak near target mz to test if within a margin of error. More...
static std::vector< Peak1D >	extractPrecursorIsotopePattern_ (const double &precursor_mz, const MSSpectrum &precursor_spectrum, int &iterations, const int &charge)
	Extract precursor isotope pattern if no feature information is available based on C12C13 distance. More...

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Class Documentation

OpenMS::SiriusMSFile::AccessionInfo

class OpenMS::SiriusMSFile::AccessionInfo

< class to store information about accessions

class to store the compound information needed for the mapping of compound and fragment annotated spectrum

Collaboration diagram for SiriusMSFile::AccessionInfo:

Class Members
String	native_id_accession	nativeID accession for mztab-m
String	native_id_type	nativeID type for mztab-m
String	sf_accession	sourcefile accessions for mztab-m
String	sf_filename	sourcefile name for mztab-m
String	sf_path	sourcefile path for mztab-m
String	sf_type	sourcefile type for mztab-m

OpenMS::SiriusMSFile::CompoundInfo

class OpenMS::SiriusMSFile::CompoundInfo

Collaboration diagram for SiriusMSFile::CompoundInfo:

Class Members
int	charge	precursor/feature charge
String	cmp	query_id used compound in .ms file
String	des	description/name of the compound
String	fid	annotated feature_id (if available)
double	fmz	annotated mass of a feature (if available)
String	formula	sumformula of the compound
String	ionization	adduct information
vector< String >	m_ids	native ids and identifier for multiple possible identification via AMS ("|" separator)
String	m_ids_id	concatenated list of native ids and identifier for multiple possible identification via AMS ("|" separator) used for mapping of compounds and the annotated spectrum.
vector< String >	native_ids	native ids of the associated spectra
String	native_ids_id	concatenated list of the associated spectra
double	pint_mono	parent/precursor intensity of the compound
double	pmass	parent/precursor mass of the compound
double	rt	retention time of the compound
vector< String >	scan_indices	index of the associated spectra
String	source_file	sourcefile for mztab-m
String	source_format	format of the sourcefile for mztab-m
String	specref_format	spectra ref format for mztab-m
vector< String >	specrefs	spectra reference for mztab-m

Member Function Documentation

extractPrecursorIsotopePattern_()

static std::vector<Peak1D> extractPrecursorIsotopePattern_ ( const double &  precursor_mz, const MSSpectrum &  precursor_spectrum, int &  iterations, const int &  charge  )

staticprotected

Extract precursor isotope pattern if no feature information is available based on C12C13 distance.

Parameters

precursor_mz	Precursor mass-to-charge
precursor_spectrum	Precursor spectrum
iterations	Number of isotopes, which are tried to be extracted
charge	Charge of the precursor

getHighestIntensityPeakInMZRange_()

static Int getHighestIntensityPeakInMZRange_ ( double  test_mz, const MSSpectrum &  spectrum, double  tolerance, bool  ppm  )

staticprotected

Find highest intensity peak near target mz to test if within a margin of error.

Parameters

test_mz	Mass-to-charge to test
spectrum	Spectrum to test
tolerance	Tolerance window (e.g. 10)
ppm	Unit of tolerance window either ppm or Da

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.

Returns

writes .ms file

stores CompoundInfo

Parameters

spectra	Peakmap from input mzml.
msfile	Writes .ms file from sirius.
feature_mapping	Adducts and features (index).
feature_only	Only use features.
isotope_pattern_iterations	At which depth to stop isotope_pattern extraction (if possible).
v_cmpinfo	Vector of CompoundInfo.

writeMsFile_()

static void writeMsFile_ ( std::ofstream &  os, const MSExperiment &  spectra, const std::vector< size_t > &  ms2_spectra_index, const SiriusMSFile::AccessionInfo &  ainfo, const StringList &  adducts, const std::vector< String > &  v_description, const std::vector< String > &  v_sumformula, const std::vector< std::pair< double, double >> &  f_isotopes, int &  feature_charge, uint64_t &  feature_id, const double &  feature_rt, const double &  feature_mz, bool &  writecompound, const bool &  no_masstrace_info_isotope_pattern, const int &  isotope_pattern_iterations, int &  count_skipped_spectra, int &  count_assume_mono, int &  count_no_ms1, std::vector< SiriusMSFile::CompoundInfo > &  v_cmpinfo  )

staticprotected

Internal structure to write the .ms file (called in store function)

Parameters

os	stream
spectra	spectra
ms2_spectra_index	vector of index ms2 spectra (in feature)
ainfo	accession information
adducts	vector of adducts
v_description	vector of descriptions
v_sumformula	vector of sumformulas
f_isotopes	isotope pattern of the feature
feature_charge	feature charge
feature_id	feature id
feature_rt	features retention time
feature_mz	feature mass to charge
writecompound	bool if new compound should be written in .ms file
no_masstrace_info_isotope_pattern	bool if isotope pattern should be extracted (if not in feature)
isotope_pattern_iterations	number of iterations (trying to find a C13 pattern)
count_skipped_spectra	count number of skipped spectra
count_assume_mono	count number of features where mono charge was assumed
count_no_ms1	count number of compounds without a valid ms1 spectrum
v_cmpinfo	vector of CompoundInfo