Ms2SpectrumStats Class Reference

QC metric to determine the number of MS2 scans per MS1 scan over RT. More...

#include <OpenMS/QC/Ms2SpectrumStats.h>

Inheritance diagram for Ms2SpectrumStats:

Collaboration diagram for Ms2SpectrumStats:

Classes
struct	ScanEvent

Public Member Functions
	Ms2SpectrumStats ()=default
	Constructor. More...
virtual	~Ms2SpectrumStats ()=default
	Destructor. More...
std::vector< PeptideIdentification >	compute (const MSExperiment &exp, FeatureMap &features, const QCBase::SpectraMap &map_to_spectrum)
	Calculate the ScanEventNumber, find all unidentified MS2-Spectra and add them to unassigned PeptideIdentifications, write meta values "ScanEventNumber" and "identified" in PeptideIdentification. More...
const String &	getName () const override
	returns the name of the metric More...
Status	requires () const override
	define the required input file: featureXML after FDR (=POSTFDRFEAT), MzML-file (MSExperiment) with all MS2-Spectra (=RAWMZML) More...
Public Member Functions inherited from QCBase
bool	isRunnable (const Status &s) const

Private Member Functions
void	setScanEventNumber_ (const MSExperiment &exp)
	compute "ScanEventNumber" for every spectrum: MS1=0, MS2=1-n, write into ms2_included_ More...
void	setPresenceAndScanEventNumber_ (PeptideIdentification &peptide_ID, const MSExperiment &exp, const QCBase::SpectraMap &map_to_spectrum)
	set ms2_included_ bool to true, if PeptideID exist and set "ScanEventNumber" for every PeptideID More...
std::vector< PeptideIdentification >	getUnassignedPeptideIdentifications_ (const MSExperiment &exp)
	return all unidentified MS2-Scans as unassignedPeptideIDs, these contain only Information about RT and "ScanEventNumber" More...

Static Private Member Functions
static MSSpectrum::PeakType::IntensityType	getBPI_ (const MSSpectrum &spec)
	calculate highest intensity (base peak intensity) More...

Private Attributes
const String	name_ = "Ms2SpectrumStats"
	name of the metric More...
std::vector< ScanEvent >	ms2_included_ {}
	ms2_included_ contains for every spectrum the information "ScanEventNumber" and presence MS2-scan in PeptideIDs More...

Additional Inherited Members
Public Types inherited from QCBase
enum class	Requires : UInt64 {   NOTHING , RAWMZML , POSTFDRFEAT , PREFDRFEAT ,   CONTAMINANTS , TRAFOALIGN , ID , SIZE_OF_REQUIRES }
	Enum to encode a file type as a bit. More...
enum class	ToleranceUnit { AUTO , PPM , DA , SIZE_OF_TOLERANCEUNIT }
using	Status = FlagSet< Requires >
Static Public Member Functions inherited from QCBase
static bool	isLabeledExperiment (const ConsensusMap &cm)
	check if the IsobaricAnalyzer TOPP tool was used to create this ConsensusMap More...
template<typename MAP >
static bool	hasPepID (const MAP &fmap)
	does the container have a PeptideIdentification in its members or as unassignedPepID ? More...
Static Public Attributes inherited from QCBase
static const std::string	names_of_requires []
	strings corresponding to enum Requires More...
static const std::string	names_of_toleranceUnit []
	strings corresponding to enum ToleranceUnit More...

Detailed Description

QC metric to determine the number of MS2 scans per MS1 scan over RT.

Ms2SpectrumStats collects data from MS2 scans and stores the result into PeptideIdentifications, which already exist in the FeatureMap, or are newly created as empty PeptideIdentifications (with no sequence).

The following meta-values are computed: "ScanEventNumber": consecutive number of each MS2 scan after the preceding MS1 scan "identified": All PeptideIdentifications of the FeatureMap are marked with '+' and all unidentified MS2-Spectra with '-'. "ion_injection_time": from MS2 spectrum "activation_method": from MS2 spectrum "total_ion_count": summed intensity from MS2 spectrum "base_peak_intensity": highest intensity from MS2 spectrum

"FWHM": RT peak width for all assigned PIs (if provided)

Constructor & Destructor Documentation

Ms2SpectrumStats()

Ms2SpectrumStats ( )

default

Constructor.

~Ms2SpectrumStats()

virtual ~Ms2SpectrumStats ( )

virtualdefault

Destructor.

Member Function Documentation

compute()

std::vector<PeptideIdentification> compute	(	const MSExperiment &	exp,
		FeatureMap &	features,
		const QCBase::SpectraMap &	map_to_spectrum
	)

Calculate the ScanEventNumber, find all unidentified MS2-Spectra and add them to unassigned PeptideIdentifications, write meta values "ScanEventNumber" and "identified" in PeptideIdentification.

Parameters

exp	Imported calibrated MzML file as MSExperiment
features	Imported featureXML file after FDR as FeatureMap
map_to_spectrum	Map to find index of spectrum given by meta value at PepID

Returns

unassigned peptide identifications newly generated from unidentified MS2-Spectra

Exceptions

MissingInformation	If exp is empty
InvalidParameter	PeptideID is missing meta value 'spectrum_reference'

getBPI_()

static MSSpectrum::PeakType::IntensityType getBPI_ ( const MSSpectrum &  spec )

staticprivate

calculate highest intensity (base peak intensity)

getName()

const String& getName ( ) const

overridevirtual

returns the name of the metric

Implements QCBase.

getUnassignedPeptideIdentifications_()

std::vector<PeptideIdentification> getUnassignedPeptideIdentifications_ ( const MSExperiment &  exp )

private

return all unidentified MS2-Scans as unassignedPeptideIDs, these contain only Information about RT and "ScanEventNumber"

requires()

Status requires ( ) const

overridevirtual

define the required input file: featureXML after FDR (=POSTFDRFEAT), MzML-file (MSExperiment) with all MS2-Spectra (=RAWMZML)

Implements QCBase.

setPresenceAndScanEventNumber_()

void setPresenceAndScanEventNumber_ ( PeptideIdentification &  peptide_ID, const MSExperiment &  exp, const QCBase::SpectraMap &  map_to_spectrum  )

private

set ms2_included_ bool to true, if PeptideID exist and set "ScanEventNumber" for every PeptideID

setScanEventNumber_()

void setScanEventNumber_ ( const MSExperiment &  exp )

private

compute "ScanEventNumber" for every spectrum: MS1=0, MS2=1-n, write into ms2_included_

Member Data Documentation

ms2_included_

std::vector<ScanEvent> ms2_included_ {}

private

ms2_included_ contains for every spectrum the information "ScanEventNumber" and presence MS2-scan in PeptideIDs

name_

const String name_ = "Ms2SpectrumStats"

private

name of the metric