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OpenMS
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QC metric to determine the number of MS2 scans per MS1 scan over RT. More...
#include <OpenMS/QC/Ms2SpectrumStats.h>
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 | requirements () 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... | |
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)
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default |
Constructor.
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virtualdefault |
Destructor.
| 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.
| 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 |
| MissingInformation | If exp is empty |
| InvalidParameter | PeptideID is missing meta value 'spectrum_reference' |
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staticprivate |
calculate highest intensity (base peak intensity)
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private |
return all unidentified MS2-Scans as unassignedPeptideIDs, these contain only Information about RT and "ScanEventNumber"
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overridevirtual |
define the required input file: featureXML after FDR (=POSTFDRFEAT), MzML-file (MSExperiment) with all MS2-Spectra (=RAWMZML)
Implements QCBase.
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private |
set ms2_included_ bool to true, if PeptideID exist and set "ScanEventNumber" for every PeptideID
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private |
compute "ScanEventNumber" for every spectrum: MS1=0, MS2=1-n, write into ms2_included_
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private |
ms2_included_ contains for every spectrum the information "ScanEventNumber" and presence MS2-scan in PeptideIDs
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private |
name of the metric
1.9.1 
