SiriusMSFile Class Reference

Writes a SIRIUS .ms file from an MSExperiment, optionally enriched with feature/adduct/formula annotations. More...

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

Classes
class	AccessionInfo
	Source-file accession metadata of the input mzML, captured for the mzTab-M MS_RUN section. More...
class	CompoundInfo
	Per-compound metadata accumulated while writing the .ms file. More...

Static Public Member 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)
	Write one mzML/featureXML pair to a SIRIUS .ms output stream.
static void	saveFeatureCompoundInfoAsTSV (const std::vector< SiriusMSFile::CompoundInfo > &v_cmpinfo, const std::string &filename)
	Serialise the CompoundInfo records collected during store as a TSV file.

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< std::string > &v_description, const std::vector< std::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, const size_t &file_index)
	Internal structure to write the .ms file (called in store function)
static Int	getHighestIntensityPeakInMZRange_ (double test_mz, const MSSpectrum &spectrum, double tolerance, bool ppm)
	Return the index of the most-intense peak of spectrum whose m/z lies within a tolerance window around test_mz.
static std::vector< Peak1D >	extractPrecursorIsotopePattern_ (const double &precursor_mz, const MSSpectrum &precursor_spectrum, int &iterations, const int &charge)
	Walk an isotope ladder from the precursor m/z, picking the most-intense peak at each C12-C13 step.

Detailed Description

Writes a SIRIUS .ms file from an MSExperiment, optionally enriched with feature/adduct/formula annotations.

Used by SiriusExport to translate centroided MS2 data (and, optionally, feature annotations from FeatureFindingMetabo, MetaboliteAdductDecharger, and/or AccurateMassSearch) into the .ms compound format consumed by SIRIUS.

The writer chooses one of three layouts based on the input FeatureMapping::FeatureToMs2Indices —

• feature-driven (assignedMS2 non-empty): one compound block per feature, carrying its associated MS2 spectra plus adduct / formula / description metadata if those are present on the feature.
• unassigned-MS2 (only when unassignedMS2 is non-empty and feature_only is false): an additional compound block per unassigned MS2 spectrum with UNKNOWN description / sumformula / adducts.
• no-feature-information (both maps empty): every MS2 spectrum in spectra is emitted as its own UNKNOWN compound. This is the mzML-only fallback. The first two layouts can both fire in the same call (feature-driven followed by unassigned-MS2). For each compound emitted, a matching CompoundInfo entry is appended to v_cmpinfo for downstream mzTab-M export.

Constraints enforced during store —

• Spectra must be centroided. If the first spectrum is SpectrumSettings::PROFILE, OpenMS::Exception::IllegalArgument is thrown.
• The input mzML must carry SourceFile annotation; an empty MSExperiment::getSourceFiles also throws OpenMS::Exception::IllegalArgument.
• SIRIUS supports only singly charged precursors: features (and spectra) with |charge| > 1 are dropped and counted; a per-call summary is written via OPENMS_LOG_WARN at the end of store.

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Class Documentation

OpenMS::SiriusMSFile::AccessionInfo

class OpenMS::SiriusMSFile::AccessionInfo

Source-file accession metadata of the input mzML, captured for the mzTab-M MS_RUN section.

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

Per-compound metadata accumulated while writing the .ms file.

One entry is appended for every compound block emitted by store. The same data is later serialised via saveFeatureCompoundInfoAsTSV and used by downstream tools to map SIRIUS results back to their originating spectra / features and to populate the mzTab-M SmallMolecule / SmallMoleculeFeature sections.

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)
int	file_index	source file index >
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

Walk an isotope ladder from the precursor m/z, picking the most-intense peak at each C12-C13 step.

Used by store when no per-feature mass-trace information is available. The monoisotopic peak is located inside a fixed 10 ppm window around precursor_mz; subsequent traces are located at precursor_mz + k * C13C12_MASSDIFF_U / |charge| inside a 1 ppm window, stopping when iterations reaches zero or when no peak is found at the current step.

Parameters

[in]	precursor_mz	Precursor m/z to start the ladder from.
[in]	precursor_spectrum	Spectrum to search.
[in,out]	iterations	Maximum number of isotope-trace steps; decremented per successful step.
[in]	charge	Precursor charge (used to scale the C12-C13 distance; 0 disables scaling).

Returns

Sequence of picked isotope peaks, starting with the monoisotopic peak (empty if not even that is found).

getHighestIntensityPeakInMZRange_()

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

staticprotected

Return the index of the most-intense peak of spectrum whose m/z lies within a tolerance window around test_mz.

Parameters

[in]	test_mz	Target m/z; the search window is built around this value.
[in]	spectrum	Spectrum to scan.
[in]	tolerance	Half-width of the tolerance window (in Da or ppm, depending on ppm).
[in]	ppm	If true, tolerance is interpreted as ppm; otherwise as Da.

Returns

Index of the most-intense peak inside the window, or -1 if the window contains no peak.

saveFeatureCompoundInfoAsTSV()

static void saveFeatureCompoundInfoAsTSV ( const std::vector< SiriusMSFile::CompoundInfo > &  v_cmpinfo, const std::string &  filename  )

static

Serialise the CompoundInfo records collected during store as a TSV file.

The file is written with a fixed 16-column header line in the order: cmp, file_index, pmass, pint_mono, rt, fmz, fid, formula, charge, ionization, des, specref_format, source_file, source_format, native_ids_id, m_ids_id. The columns native_ids and m_ids (the raw vector versions) are not written — only their already-concatenated _id forms.

Parameters

[in]	v_cmpinfo	Compound records to write (typically the vector populated by store).
[in]	filename	Destination path of the TSV file.

Exceptions

std::runtime_error

if filename cannot be opened for writing.

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

Write one mzML/featureXML pair to a SIRIUS .ms output stream.

Selects the .ms layout (feature-driven, unassigned-MS2, or no-feature-information) according to the contents of feature_mapping; see the class documentation for the branching rules. For every compound block emitted, a CompoundInfo record is appended to v_cmpinfo for downstream mzTab-M export. When adduct information is missing for a spectrum no adduct line is written — SIRIUS will then assume defaults.

The accession-CV term for the sourcefile is resolved by loading the PSI-MS OBO (CV/psi-ms.obo via File::find) and locating the term whose name matches the SourceFile type. The output stream os is written to but not closed; ownership remains with the caller.

Parameters

[in]	spectra	Peakmap from the input mzML. The first spectrum must be centroided.
[in]	os	Open output stream the .ms text is written to.
[in]	feature_mapping	Result of FeatureMapping::assignMS2IndexToFeature; selects the output layout.
[in]	feature_only	If true, MS2 spectra that are not associated with any feature are dropped instead of being emitted as additional UNKNOWN compounds.
[in]	isotope_pattern_iterations	Upper bound on the number of isotope-trace peaks searched per precursor when no feature mass-traces are available.
[in]	no_masstrace_info_isotope_pattern	If true, fall back to spectrum-based isotope-pattern extraction when feature mass-traces are absent.
[in,out]	v_cmpinfo	Receives one CompoundInfo per emitted compound (appended; existing entries preserved).
[in]	file_index	Numeric identifier mixed into compound IDs to disambiguate entries from different mzML files.

Exceptions

OpenMS::Exception::IllegalArgument	if spectra contains profile data (centroiding is required).
OpenMS::Exception::IllegalArgument	if spectra carries no SourceFile annotation.

Note

SIRIUS supports only singly charged precursors: features (and spectra) with |charge| > 1 are skipped. A summary of the skipped/assumed counts is emitted via OPENMS_LOG_WARN at the end of the call (even when all counts are zero).

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< std::string > &  v_description, const std::vector< std::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, const size_t &  file_index  )

staticprotected

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

Parameters

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