Metadata

Classes that capture meta data about a MS or HPLC-MS experiment. More...

Classes
class	Acquisition
	Information about one raw data spectrum that was combined with several other raw data spectra. More...
class	AcquisitionInfo
	Description of the combination of raw data to a single spectrum. More...
class	ChromatogramSettings
	Representation of chromatogram settings, e.g. SRM/MRM chromatograms. More...
class	ContactPerson
	Contact person information. More...
struct	CVTerm::Unit
class	CVTerm
	Representation of controlled vocabulary term. More...
class	CVTermList
	Representation of controlled vocabulary term list. More...
class	DataProcessing
	Description of the applied preprocessing steps. More...
class	Digestion
	Meta information about digestion of a sample. More...
class	DocumentIdentifier
	Manage source document information. More...
class	DocumentIDTagger
	Tags OpenMS file containers with a DocumentID. More...
class	ExperimentalSettings
	Description of the experimental settings. More...
class	Gradient
	Representation of a HPLC gradient. More...
class	HPLC
	Representation of a HPLC experiment. More...
class	Identification
	Represents a object which can store the information of an analysisXML instance. More...
class	IdentificationHit
	Represents a object which can store the information of an analysisXML instance. More...
class	Instrument
	Description of a MS instrument. More...
class	InstrumentSettings
	Description of the settings a MS Instrument was run with. More...
class	IonDetector
	Description of a ion detector (part of a MS Instrument) More...
class	IonSource
	Description of an ion source (part of a MS Instrument) More...
class	MassAnalyzer
	Description of a mass analyzer (part of a MS Instrument) More...
class	MetaInfo
	A Type-Name-Value tuple class. More...
class	MetaInfoDescription
	Description of the meta data arrays of MSSpectrum. More...
class	MetaInfoInterface
	Interface for classes that can store arbitrary meta information (Type-Name-Value tuples). More...
class	MetaInfoRegistry
	Registry which assigns unique integer indices to strings. More...
class	Modification
	Meta information about chemical modification of a sample. More...
class	PeptideEvidence
	Representation of a peptide evidence. More...
class	PeptideHit::ScoreMore
	Greater predicate for scores of hits. More...
class	PeptideHit::ScoreLess
	Lesser predicate for scores of hits. More...
class	PeptideHit
	Representation of a peptide hit. More...
class	PeptideIdentification
	Represents the peptide hits for a spectrum. More...
class	Precursor
	Precursor meta information. More...
class	Product
	Product meta information. More...
class	ProteinHit::ScoreMore
	Greater predicate for scores of hits. More...
class	ProteinHit::ScoreLess
	Lesser predicate for scores of hits. More...
class	ProteinHit
	Representation of a protein hit. More...
struct	ProteinIdentification::ProteinGroup
	Bundles multiple (e.g. indistinguishable) proteins in a group. More...
struct	ProteinIdentification::SearchParameters
	Search parameters of the DB search. More...
class	ProteinIdentification
	Representation of a protein identification run. More...
class	Sample
	Meta information about the sample. More...
class	SampleTreatment
	Base class for sample treatments (Digestion, Modification, Tagging, ...) More...
struct	ScanWindow
	Scan window description. More...
class	Software
	Description of the software used for processing. More...
class	SourceFile
	Description of a file location, used to store the origin of (meta) data. More...
class	SpectrumIdentification
	Represents a object which can store the information of an analysisXML instance. More...
class	SpectrumSettings
	Representation of 1D spectrum settings. More...
class	Tagging
	Meta information about tagging of a sample e.g. ICAT labeling. More...

Enumerations
enum	ChromatogramType {   MASS_CHROMATOGRAM = 0, TOTAL_ION_CURRENT_CHROMATOGRAM, SELECTED_ION_CURRENT_CHROMATOGRAM, BASEPEAK_CHROMATOGRAM,   SELECTED_ION_MONITORING_CHROMATOGRAM, SELECTED_REACTION_MONITORING_CHROMATOGRAM, ELECTROMAGNETIC_RADIATION_CHROMATOGRAM, ABSORPTION_CHROMATOGRAM,   EMISSION_CHROMATOGRAM, SIZE_OF_CHROMATOGRAM_TYPE }
enum	ProcessingAction {   DATA_PROCESSING, CHARGE_DECONVOLUTION, DEISOTOPING, SMOOTHING,   CHARGE_CALCULATION, PRECURSOR_RECALCULATION, BASELINE_REDUCTION, PEAK_PICKING,   ALIGNMENT, CALIBRATION, NORMALIZATION, FILTERING,   QUANTITATION, FEATURE_GROUPING, IDENTIFICATION_MAPPING, FORMAT_CONVERSION,   CONVERSION_MZDATA, CONVERSION_MZML, CONVERSION_MZXML, CONVERSION_DTA,   SIZE_OF_PROCESSINGACTION }
enum	IonOpticsType {   UNKNOWN, MAGNETIC_DEFLECTION, DELAYED_EXTRACTION, COLLISION_QUADRUPOLE,   SELECTED_ION_FLOW_TUBE, TIME_LAG_FOCUSING, REFLECTRON, EINZEL_LENS,   FIRST_STABILITY_REGION, FRINGING_FIELD, KINETIC_ENERGY_ANALYZER, STATIC_FIELD,   SIZE_OF_IONOPTICSTYPE }
	ion optics type More...
enum	ScanMode {   UNKNOWN, MASSSPECTRUM, MS1SPECTRUM, MSNSPECTRUM,   SIM, SRM, CRM, CNG,   CNL, PRECURSOR, EMC, TDF,   EMR, EMISSION, ABSORBTION, SIZE_OF_SCANMODE }
	scan mode More...
enum	Type {   TYPENULL, ELECTRONMULTIPLIER, PHOTOMULTIPLIER, FOCALPLANEARRAY,   FARADAYCUP, CONVERSIONDYNODEELECTRONMULTIPLIER, CONVERSIONDYNODEPHOTOMULTIPLIER, MULTICOLLECTOR,   CHANNELELECTRONMULTIPLIER, CHANNELTRON, DALYDETECTOR, MICROCHANNELPLATEDETECTOR,   ARRAYDETECTOR, CONVERSIONDYNODE, DYNODE, FOCALPLANECOLLECTOR,   IONTOPHOTONDETECTOR, POINTCOLLECTOR, POSTACCELERATIONDETECTOR, PHOTODIODEARRAYDETECTOR,   INDUCTIVEDETECTOR, ELECTRONMULTIPLIERTUBE, SIZE_OF_TYPE }
	Detector type. More...
enum	AcquisitionMode {   ACQMODENULL, PULSECOUNTING, ADC, TDC,   TRANSIENTRECORDER, SIZE_OF_ACQUISITIONMODE }
	Acquisition mode. More...
enum	InletType {   INLETNULL, DIRECT, BATCH, CHROMATOGRAPHY,   PARTICLEBEAM, MEMBRANESEPARATOR, OPENSPLIT, JETSEPARATOR,   SEPTUM, RESERVOIR, MOVINGBELT, MOVINGWIRE,   FLOWINJECTIONANALYSIS, ELECTROSPRAYINLET, THERMOSPRAYINLET, INFUSION,   CONTINUOUSFLOWFASTATOMBOMBARDMENT, INDUCTIVELYCOUPLEDPLASMA, MEMBRANE, NANOSPRAY,   SIZE_OF_INLETTYPE }
	inlet type More...
enum	IonizationMethod {   IONMETHODNULL, ESI, EI, CI,   FAB, TSP, LD, FD,   FI, PD, SI, TI,   API, ISI, CID, CAD,   HN, APCI, APPI, ICP,   NESI, MESI, SELDI, SEND,   FIB, MALDI, MPI, DI,   FA, FII, GD_MS, NICI,   NRMS, PI, PYMS, REMPI,   AI, ASI, AD, AUI,   CEI, CHEMI, DISSI, LSI,   PEI, SOI, SPI, SUI,   VI, AP_MALDI, SILI, SALDI,   SIZE_OF_IONIZATIONMETHOD }
	ionization method More...
enum	Polarity { POLNULL, POSITIVE, NEGATIVE, SIZE_OF_POLARITY }
	Polarity of the ion source. More...
enum	AnalyzerType {   ANALYZERNULL, QUADRUPOLE, PAULIONTRAP, RADIALEJECTIONLINEARIONTRAP,   AXIALEJECTIONLINEARIONTRAP, TOF, SECTOR, FOURIERTRANSFORM,   IONSTORAGE, ESA, IT, SWIFT,   CYCLOTRON, ORBITRAP, LIT, SIZE_OF_ANALYZERTYPE }
	analyzer type More...
enum	ResolutionMethod {   RESMETHNULL, FWHM, TENPERCENTVALLEY, BASELINE,   SIZE_OF_RESOLUTIONMETHOD }
	resolution method More...
enum	ResolutionType { RESTYPENULL, CONSTANT, PROPORTIONAL, SIZE_OF_RESOLUTIONTYPE }
	Resolution type. More...
enum	ScanDirection { SCANDIRNULL, UP, DOWN, SIZE_OF_SCANDIRECTION }
	direction of scanning More...
enum	ScanLaw {   SCANLAWNULL, EXPONENTIAL, LINEAR, QUADRATIC,   SIZE_OF_SCANLAW }
	Scan law. More...
enum	ReflectronState {   REFLSTATENULL, ON, OFF, NONE,   SIZE_OF_REFLECTRONSTATE }
	Reflectron state. More...
enum	SpecificityType {   AA, AA_AT_CTERM, AA_AT_NTERM, CTERM,   NTERM, SIZE_OF_SPECIFICITYTYPE }
	specificity of the reagent. More...
enum	ActivationMethod {   CID, PSD, PD, SID,   BIRD, ECD, IMD, SORI,   HCID, LCID, PHD, ETD,   PQD, SIZE_OF_ACTIVATIONMETHOD }
	Method of activation. More...
enum	PeakMassType { MONOISOTOPIC, AVERAGE, SIZE_OF_PEAKMASSTYPE }
	Peak mass type. More...
enum	DigestionEnzyme {   TRYPSIN, PEPSIN_A, PROTEASE_K, CHYMOTRYPSIN,   NO_ENZYME, UNKNOWN_ENZYME, SIZE_OF_DIGESTIONENZYME }
enum	SampleState {   SAMPLENULL, SOLID, LIQUID, GAS,   SOLUTION, EMULSION, SUSPENSION, SIZE_OF_SAMPLESTATE }
	state of aggregation of the sample More...
enum	ChecksumType { UNKNOWN_CHECKSUM, SHA1, MD5, SIZE_OF_CHECKSUMTYPE }
	Type of the checksum. More...
enum	SpectrumType { UNKNOWN, PEAKS, RAWDATA, SIZE_OF_SPECTRUMTYPE }
	Spectrum peak type. More...
enum	IsotopeVariant { LIGHT, HEAVY, SIZE_OF_ISOTOPEVARIANT }
	Isotope variants (light and heavy) More...

Detailed Description

Classes that capture meta data about a MS or HPLC-MS experiment.

The top-level classes are OpenMS::ExperimentalSettings and OpenMS::SpectrumSettings .

Enumeration Type Documentation

enum AcquisitionMode

Acquisition mode.

Enumerator
ACQMODENULL	Unknown.
PULSECOUNTING	Pulse counting.
ADC	Analog-digital converter.
TDC	Time-digital converter.
TRANSIENTRECORDER	Transient recorder.
SIZE_OF_ACQUISITIONMODE

enum ActivationMethod

Method of activation.

Enumerator
CID	Collision-induced dissociation.
PSD	Post-source decay.
PD	Plasma desorption.
SID	Surface-induced dissociation.
BIRD	Blackbody infrared radiative dissociation.
ECD	Electron capture dissociation.
IMD	Infrared multiphoton dissociation.
SORI	Sustained off-resonance irradiation.
HCID	High-energy collision-induced dissociation.
LCID	Low-energy collision-induced dissociation.
PHD	Photodissociation.
ETD	Electron transfer dissociation.
PQD	Pulsed q dissociation.
SIZE_OF_ACTIVATIONMETHOD

enum AnalyzerType

analyzer type

Enumerator
ANALYZERNULL	Unknown.
QUADRUPOLE	Quadrupole.
PAULIONTRAP	Quadrupole ion trap / Paul ion trap.
RADIALEJECTIONLINEARIONTRAP	Radial ejection linear ion trap.
AXIALEJECTIONLINEARIONTRAP	Axial ejection linear ion trap.
TOF	Time-of-flight.
SECTOR	Magnetic sector.
FOURIERTRANSFORM	Fourier transform ion cyclotron resonance mass spectrometer.
IONSTORAGE	Ion storage.
ESA	Electrostatic energy analyzer.
IT	Ion trap.
SWIFT	Stored waveform inverse fourier transform.
CYCLOTRON	Cyclotron.
ORBITRAP	Orbitrap.
LIT	Linear ion trap.
SIZE_OF_ANALYZERTYPE

enum ChecksumType

Type of the checksum.

Enumerator
UNKNOWN_CHECKSUM	Unknown checksum type.
SHA1	Secure Hash Algorithm-1.
MD5	Message-Digest algorithm 5.
SIZE_OF_CHECKSUMTYPE

enum ChromatogramType

List of chromatogram names, e.g., SELECTED_REACTION_MONITORING_CHROMATOGRAM. Actual names can be accessed using the ChromatogramNames[] array

Enumerator
MASS_CHROMATOGRAM
TOTAL_ION_CURRENT_CHROMATOGRAM
SELECTED_ION_CURRENT_CHROMATOGRAM
BASEPEAK_CHROMATOGRAM
SELECTED_ION_MONITORING_CHROMATOGRAM
SELECTED_REACTION_MONITORING_CHROMATOGRAM
ELECTROMAGNETIC_RADIATION_CHROMATOGRAM
ABSORPTION_CHROMATOGRAM
EMISSION_CHROMATOGRAM
SIZE_OF_CHROMATOGRAM_TYPE

enum DigestionEnzyme

Enumerator
TRYPSIN
PEPSIN_A
PROTEASE_K
CHYMOTRYPSIN
NO_ENZYME
UNKNOWN_ENZYME
SIZE_OF_DIGESTIONENZYME

enum InletType

inlet type

Enumerator
INLETNULL	Unknown.
DIRECT	Direct.
BATCH	Batch (e.g. in MALDI)
CHROMATOGRAPHY	Chromatography (liquid)
PARTICLEBEAM	Particle beam.
MEMBRANESEPARATOR	Membrane separator.
OPENSPLIT	Open split.
JETSEPARATOR	Jet separator.
SEPTUM	Septum.
RESERVOIR	Reservoir.
MOVINGBELT	Moving belt.
MOVINGWIRE	Moving wire.
FLOWINJECTIONANALYSIS	Flow injection analysis.
ELECTROSPRAYINLET	Electro spray.
THERMOSPRAYINLET	Thermo spray.
INFUSION	Infusion.
CONTINUOUSFLOWFASTATOMBOMBARDMENT	Continuous flow fast atom bombardment.
INDUCTIVELYCOUPLEDPLASMA	Inductively coupled plasma.
MEMBRANE	Membrane inlet.
NANOSPRAY	Nanospray inlet.
SIZE_OF_INLETTYPE

enum IonizationMethod

ionization method

Enumerator
IONMETHODNULL	Unknown.
ESI	electrospray ionisation
EI	electron ionization
CI	chemical ionisation
FAB	fast atom bombardment
TSP	thermospray
LD	laser desorption
FD	field desorption
FI	flame ionization
PD	plasma desorption
SI	secondary ion MS
TI	thermal ionization
API	atmospheric pressure ionisation
ISI
CID	collision induced decomposition
CAD	collision activated decomposition
HN
APCI	atmospheric pressure chemical ionization
APPI	atmospheric pressure photo ionization
ICP	inductively coupled plasma
NESI	Nano electrospray ionization.
MESI	Micro electrospray ionization.
SELDI	Surface enhanced laser desorption ionization.
SEND	Surface enhanced neat desorption.
FIB	Fast ion bombardment.
MALDI	Matrix-assisted laser desorption ionization.
MPI	Multiphoton ionization.
DI	desorption ionization
FA	flowing afterglow
FII	field ionization
GD_MS	glow discharge ionization
NICI	negative ion chemical ionization
NRMS	neutralization reionization mass spectrometry
PI	photoionization
PYMS	pyrolysis mass spectrometry
REMPI	resonance enhanced multiphoton ionization
AI	adiabatic ionization
ASI	associative ionization
AD	autodetachment
AUI	autoionization
CEI	charge exchange ionization
CHEMI	chemi-ionization
DISSI	dissociative ionization
LSI	liquid secondary ionization
PEI	penning ionization
SOI	soft ionization
SPI	spark ionization
SUI	surface ionization
VI	vertical ionization
AP_MALDI	atmospheric pressure matrix-assisted laser desorption ionization
SILI	desorption/ionization on silicon
SALDI	surface-assisted laser desorption ionization
SIZE_OF_IONIZATIONMETHOD

enum IonOpticsType

ion optics type

Enumerator
UNKNOWN	unknown
MAGNETIC_DEFLECTION	magnetic deflection
DELAYED_EXTRACTION	delayed extraction
COLLISION_QUADRUPOLE	collision quadrupole
SELECTED_ION_FLOW_TUBE	selected ion flow tube
TIME_LAG_FOCUSING	time lag focusing
REFLECTRON	reflectron
EINZEL_LENS	einzel lens
FIRST_STABILITY_REGION	first stability region
FRINGING_FIELD	fringing field
KINETIC_ENERGY_ANALYZER	kinetic energy analyzer
STATIC_FIELD	static field
SIZE_OF_IONOPTICSTYPE

enum IsotopeVariant

Isotope variants (light and heavy)

Enumerator
LIGHT
HEAVY
SIZE_OF_ISOTOPEVARIANT

enum PeakMassType

Peak mass type.

Enumerator
MONOISOTOPIC
AVERAGE
SIZE_OF_PEAKMASSTYPE

enum Polarity

Polarity of the ion source.

Enumerator
POLNULL	Unknown.
POSITIVE	Positive polarity.
NEGATIVE	Negative polarity.
SIZE_OF_POLARITY

enum ProcessingAction

Enumerator
DATA_PROCESSING	General data processing (if no other term applies)
CHARGE_DECONVOLUTION	Charge deconvolution.
DEISOTOPING	Deisotoping.
SMOOTHING	Smoothing of the signal to reduce noise.
CHARGE_CALCULATION	Determination of the peak charge.
PRECURSOR_RECALCULATION	Recalculation of precursor m/z.
BASELINE_REDUCTION	Baseline reduction.
PEAK_PICKING	Peak picking (conversion from raw to peak data)
ALIGNMENT	Retention time alignment of different maps.
CALIBRATION	Calibration of m/z positions.
NORMALIZATION	Normalization of intensity values.
FILTERING	Data filtering or extraction.
QUANTITATION	Quantitation.
FEATURE_GROUPING	Feature grouping
IDENTIFICATION_MAPPING	Identification mapping
FORMAT_CONVERSION	General file format conversion (if no other term applies)
CONVERSION_MZDATA	Conversion to mzData format.
CONVERSION_MZML	Conversion to mzML format.
CONVERSION_MZXML	Conversion to mzXML format.
CONVERSION_DTA	Conversion to DTA format.
SIZE_OF_PROCESSINGACTION

enum ReflectronState

Reflectron state.

Enumerator
REFLSTATENULL	Unknown.
ON	On.
OFF	Off.
NONE	None.
SIZE_OF_REFLECTRONSTATE

enum ResolutionMethod

resolution method

Which of the available standard measures is used to define whether two peaks are separate

Enumerator
RESMETHNULL	Unknown.
FWHM	Full width at half max.
TENPERCENTVALLEY	Ten percent valley.
BASELINE	Baseline.
SIZE_OF_RESOLUTIONMETHOD

enum ResolutionType

Resolution type.

Enumerator
RESTYPENULL	Unknown.
CONSTANT	Constant.
PROPORTIONAL	Proportional.
SIZE_OF_RESOLUTIONTYPE

enum SampleState

state of aggregation of the sample

Enumerator
SAMPLENULL
SOLID
LIQUID
GAS
SOLUTION
EMULSION
SUSPENSION
SIZE_OF_SAMPLESTATE

enum ScanDirection

direction of scanning

Enumerator
SCANDIRNULL	Unknown.
UP	Up.
DOWN	Down.
SIZE_OF_SCANDIRECTION

enum ScanLaw

Scan law.

Enumerator
SCANLAWNULL	Unknown.
EXPONENTIAL	Unknown.
LINEAR	Linear.
QUADRATIC	Quadratic.
SIZE_OF_SCANLAW

enum ScanMode

scan mode

Enumerator
UNKNOWN	Unknown scan method.
MASSSPECTRUM	general spectrum type
MS1SPECTRUM	full scan mass spectrum, is a "mass spectrum" Synonyms: 'full spectrum', 'Q1 spectrum', 'Q3 spectrum', 'Single-Stage Mass Spectrometry'
MSNSPECTRUM	MS2+ mass spectrum, is a "mass spectrum".
SIM	Selected ion monitoring scan Synonyms: 'Multiple ion monitoring scan', 'SIM scan', 'MIM scan'.
SRM	Selected reaction monitoring scan Synonyms: 'Multiple reaction monitoring scan', 'SRM scan', 'MRM scan'.
CRM	Consecutive reaction monitoring scan Synonyms: 'CRM scan'.
CNG	Constant neutral gain scan Synonyms: 'CNG scan'.
CNL	Constant neutral loss scan Synonyms: 'CNG scan'.
PRECURSOR	Precursor ion scan.
EMC	Enhanced multiply charged scan.
TDF	Time-delayed fragmentation scan.
EMR	Electromagnetic radiation scan Synonyms: 'EMR spectrum'.
EMISSION	Emission scan.
ABSORBTION	Absorbtion scan.
SIZE_OF_SCANMODE

enum SpecificityType

specificity of the reagent.

Enumerator
AA	specified amino acids are modified
AA_AT_CTERM	specified amino acids are modified, if they are at the C-terminus
AA_AT_NTERM	specified amino acids are modified, if they are at the N-terminus
CTERM	the C-terminus is modified
NTERM	the N-terminus is modified
SIZE_OF_SPECIFICITYTYPE

enum SpectrumType

Spectrum peak type.

Enumerator
UNKNOWN	Unknown spectrum type.
PEAKS	Peak data (also called centroided data or stick data)
RAWDATA	Raw data (also called profile data)
SIZE_OF_SPECTRUMTYPE

enum Type

Detector type.

Enumerator
TYPENULL	Unknown.
ELECTRONMULTIPLIER	Electron multiplier.
PHOTOMULTIPLIER	Photo multiplier.
FOCALPLANEARRAY	Focal plane array.
FARADAYCUP	Faraday cup.
CONVERSIONDYNODEELECTRONMULTIPLIER	Conversion dynode electron multiplier.
CONVERSIONDYNODEPHOTOMULTIPLIER	Conversion dynode photo multiplier.
MULTICOLLECTOR	Multi-collector.
CHANNELELECTRONMULTIPLIER	Channel electron multiplier.
CHANNELTRON	channeltron
DALYDETECTOR	daly detector
MICROCHANNELPLATEDETECTOR	microchannel plate detector
ARRAYDETECTOR	array detector
CONVERSIONDYNODE	conversion dynode
DYNODE	dynode
FOCALPLANECOLLECTOR	focal plane collector
IONTOPHOTONDETECTOR	ion-to-photon detector
POINTCOLLECTOR	point collector
POSTACCELERATIONDETECTOR	postacceleration detector
PHOTODIODEARRAYDETECTOR	photodiode array detector
INDUCTIVEDETECTOR	inductive detector
ELECTRONMULTIPLIERTUBE	electron multiplier tube
SIZE_OF_TYPE