MSSpectrum#

class pyopenms.MSSpectrum#

Bases: object

Cython implementation of _MSSpectrum

Original C++ documentation is available here: – Inherits from [‘SpectrumSettings’, ‘RangeManagerMzInt’]

The representation of a 1D spectrum. Raw data access is proved by get_peaks and set_peaks, which yields numpy arrays Iterations yields access to underlying peak objects but is slower Extra data arrays can be accessed through getFloatDataArrays / getIntegerDataArrays / getStringDataArrays See help(SpectrumSettings) for information about meta-information

Usage:

ms_level = spectrum.getMSLevel()
rt = spectrum.getRT()
mz, intensities = spectrum.get_peaks()

Usage:

from pyopenms import *

spectrum = MSSpectrum()
spectrum.setDriftTime(25) # 25 ms
spectrum.setRT(205.2) # 205.2 s
spectrum.setMSLevel(3) # MS3
p = Precursor()
p.setIsolationWindowLowerOffset(1.5)
p.setIsolationWindowUpperOffset(1.5)
p.setMZ(600) # isolation at 600 +/- 1.5 Th
p.setActivationEnergy(40) # 40 eV
p.setCharge(4) # 4+ ion
spectrum.setPrecursors( [p] )

# Add raw data to spectrum
spectrum.set_peaks( ([401.5], [900]) )

# Additional data arrays / peak annotations
fda = FloatDataArray()
fda.setName("Signal to Noise Array")
fda.push_back(15)
sda = StringDataArray()
sda.setName("Peak annotation")
sda.push_back("y15++")
spectrum.setFloatDataArrays( [fda] )
spectrum.setStringDataArrays( [sda] )

# Add spectrum to MSExperiment
exp = MSExperiment()
exp.addSpectrum(spectrum)

# Add second spectrum and store as mzML file
spectrum2 = MSSpectrum()
spectrum2.set_peaks( ([1, 2], [1, 2]) )
exp.addSpectrum(spectrum2)

MzMLFile().store("testfile.mzML", exp)

__init__()#

Overload:

__init__(self) → None

Overload:

__init__(self, in_0: MSSpectrum) → None

Methods

`__init__`	Overload:
`calculateTIC`(self)	Returns the total ion current (=sum) of peak intensities in the spectrum
`clear`(self, clear_meta_data)	Clears all data (and meta data if clear_meta_data is true)
`clearMetaInfo`(self)	Removes all meta values
`clearRanges`(self)	Resets all range dimensions as empty
`containsIMData`(self)
`findHighestInWindow`(self, mz, ...)	Returns the index of the highest peak in the provided abs.
`findNearest`	Overload:
`getAcquisitionInfo`(self)	Returns a const reference to the acquisition info
`getComment`(self)	Returns the free-text comment
`getDataProcessing`(self)
`getDriftTime`(self)	Returns the drift time (-1 if not set)
`getDriftTimeUnit`(self)
`getDriftTimeUnitAsString`(self)
`getFloatDataArrays`(self)	Returns the additional float data arrays to store e.g.
`getIMData`
`getInstrumentSettings`(self)	Returns a const reference to the instrument settings of the current spectrum
`getIntegerDataArrays`(self)	Returns the additional int data arrays to store e.g.
`getKeys`(self, keys)	Fills the given vector with a list of all keys for which a value is set
`getMSLevel`(self)	Returns the MS level
`getMaxIntensity`(self)	Returns the maximum intensity
`getMaxMZ`(self)	Returns the maximum m/z
`getMetaValue`(self, in_0)	Returns the value corresponding to a string, or
`getMinIntensity`(self)	Returns the minimum intensity
`getMinMZ`(self)	Returns the minimum m/z
`getName`(self)
`getNativeID`(self)	Returns the native identifier for the spectrum, used by the acquisition software
`getPeptideIdentifications`(self)	Returns a const reference to the PeptideIdentification vector
`getPrecursors`(self)	Returns a const reference to the precursors
`getProducts`(self)	Returns a const reference to the products
`getRT`(self)	Returns the absolute retention time (in seconds)
`getSourceFile`(self)	Returns a const reference to the source file
`getStringDataArrays`(self)	Returns the additional string data arrays to store e.g.
`getType`(self)	Returns the spectrum type (centroided (PEAKS) or profile data (RAW))
`get_peaks`	Cython signature: numpy_vector, numpy_vector get_peaks()
`intensityInRange`
`isMetaEmpty`(self)	Returns if the MetaInfo is empty
`isSorted`(self)	Returns true if the spectrum is sorte by m/z
`metaRegistry`(self)	Returns a reference to the MetaInfoRegistry
`metaValueExists`(self, in_0)	Returns whether an entry with the given name exists
`push_back`(self, in_0)	Append a peak
`removeMetaValue`(self, in_0)	Removes the DataValue corresponding to name if it exists
`reserve`(self, n)
`resize`(self, n)	Resize the peak array
`select`(self, indices)	Subset the spectrum by indices.
`setAcquisitionInfo`(self, in_0)	Sets the acquisition info
`setComment`(self, in_0)	Sets the free-text comment
`setDataProcessing`(self, in_0)
`setDriftTime`(self, in_0)	Sets the drift time (-1 if not set)
`setDriftTimeUnit`(self, dt)
`setFloatDataArrays`(self, fda)	Sets the additional float data arrays to store e.g.
`setInstrumentSettings`(self, in_0)	Sets the instrument settings of the current spectrum
`setIntegerDataArrays`(self, ida)	Sets the additional int data arrays to store e.g.
`setMSLevel`(self, in_0)	Sets the MS level
`setMetaValue`(self, in_0, in_1)	Sets the DataValue corresponding to a name
`setName`(self, in_0)
`setNativeID`(self, in_0)	Sets the native identifier for the spectrum, used by the acquisition software
`setPeptideIdentifications`(self, in_0)	Sets the PeptideIdentification vector
`setPrecursors`(self, in_0)	Sets the precursors
`setProducts`(self, in_0)	Sets the products
`setRT`(self, in_0)	Sets the absolute retention time (in seconds)
`setSourceFile`(self, in_0)	Sets the source file
`setStringDataArrays`(self, sda)	Sets the additional string data arrays to store e.g.
`setType`(self, in_0)	Sets the spectrum type
`set_peaks`	Cython signature: set_peaks((numpy_vector, numpy_vector))
`size`(self)	Returns the number of peaks in the spectrum
`sortByIntensity`(self, reverse)
`sortByPosition`(self)
`unify`(self, in_0)
`updateRanges`(self)

calculateTIC(self) → float#: Returns the total ion current (=sum) of peak intensities in the spectrum

clear(self, clear_meta_data: bool) → None#: Clears all data (and meta data if clear_meta_data is true)

clearMetaInfo(self) → None#: Removes all meta values

clearRanges(self) → None#: Resets all range dimensions as empty

containsIMData(self) → bool#

findHighestInWindow(self, mz: float, tolerance_left: float, tolerance_right: float) → int#: Returns the index of the highest peak in the provided abs. m/z tolerance window to the left and right (-1 if none match)

findNearest()#

Overload:

findNearest(self, mz: float) → int

Returns the index of the closest peak in m/z

Overload:

findNearest(self, mz: float, tolerance: float) → int

Returns the index of the closest peak in the provided +/- m/z tolerance window (-1 if none match)

Overload:

findNearest(self, mz: float, tolerance_left: float, tolerance_right: float) → int

Returns the index of the closest peak in the provided abs. m/z tolerance window to the left and right (-1 if none match)

getAcquisitionInfo(self) → AcquisitionInfo#: Returns a const reference to the acquisition info

getComment(self) → bytes | str | String#: Returns the free-text comment

getDataProcessing(self) → List[DataProcessing]#

getDriftTime(self) → float#: Returns the drift time (-1 if not set)

getDriftTimeUnit(self) → int#

getDriftTimeUnitAsString(self) → bytes | str | String#

getFloatDataArrays(self) → List[FloatDataArray]#: Returns the additional float data arrays to store e.g. meta data

getIMData()#

getInstrumentSettings(self) → InstrumentSettings#: Returns a const reference to the instrument settings of the current spectrum

getIntegerDataArrays(self) → List[IntegerDataArray]#: Returns the additional int data arrays to store e.g. meta data

getKeys(self, keys: List[bytes]) → None#: Fills the given vector with a list of all keys for which a value is set

getMSLevel(self) → int#: Returns the MS level

getMaxIntensity(self) → float#: Returns the maximum intensity

getMaxMZ(self) → float#: Returns the maximum m/z

getMetaValue(self, in_0: bytes | str | String) → int | float | bytes | str | List[int] | List[float] | List[bytes]#: Returns the value corresponding to a string, or

getMinIntensity(self) → float#: Returns the minimum intensity

getMinMZ(self) → float#: Returns the minimum m/z

getName(self) → bytes | str | String#

getNativeID(self) → bytes | str | String#: Returns the native identifier for the spectrum, used by the acquisition software

getPeptideIdentifications(self) → List[PeptideIdentification]#: Returns a const reference to the PeptideIdentification vector

getPrecursors(self) → List[Precursor]#: Returns a const reference to the precursors

getProducts(self) → List[Product]#: Returns a const reference to the products

getRT(self) → float#: Returns the absolute retention time (in seconds)

getSourceFile(self) → SourceFile#: Returns a const reference to the source file

getStringDataArrays(self) → List[StringDataArray]#: Returns the additional string data arrays to store e.g. meta data

getType(self) → int#: Returns the spectrum type (centroided (PEAKS) or profile data (RAW))

get_peaks()#

Cython signature: numpy_vector, numpy_vector get_peaks()

Will return a tuple of two numpy arrays (m/z, intensity) corresponding to the peaks in the MSSpectrum. Provides fast access to peaks.

intensityInRange()#

isMetaEmpty(self) → bool#: Returns if the MetaInfo is empty

isSorted(self) → bool#: Returns true if the spectrum is sorte by m/z

metaRegistry(self) → MetaInfoRegistry#: Returns a reference to the MetaInfoRegistry

metaValueExists(self, in_0: bytes | str | String) → bool#: Returns whether an entry with the given name exists

push_back(self, in_0: Peak1D) → None#: Append a peak

removeMetaValue(self, in_0: bytes | str | String) → None#: Removes the DataValue corresponding to name if it exists

reserve(self, n: int) → None#

resize(self, n: int) → None#: Resize the peak array

select(self, indices: List[int]) → MSSpectrum#: Subset the spectrum by indices. Also applies to associated data arrays if present.

setAcquisitionInfo(self, in_0: AcquisitionInfo) → None#: Sets the acquisition info

setComment(self, in_0: bytes | str | String) → None#: Sets the free-text comment

setDataProcessing(self, in_0: List[DataProcessing]) → None#

setDriftTime(self, in_0: float) → None#: Sets the drift time (-1 if not set)

setDriftTimeUnit(self, dt: int) → None#

setFloatDataArrays(self, fda: List[FloatDataArray]) → None#: Sets the additional float data arrays to store e.g. meta data

setInstrumentSettings(self, in_0: InstrumentSettings) → None#: Sets the instrument settings of the current spectrum

setIntegerDataArrays(self, ida: List[IntegerDataArray]) → None#: Sets the additional int data arrays to store e.g. meta data

setMSLevel(self, in_0: int) → None#: Sets the MS level

setMetaValue(self, in_0: bytes | str | String, in_1: int | float | bytes | str | List[int] | List[float] | List[bytes]) → None#: Sets the DataValue corresponding to a name

setName(self, in_0: bytes | str | String) → None#

setNativeID(self, in_0: bytes | str | String) → None#: Sets the native identifier for the spectrum, used by the acquisition software

setPeptideIdentifications(self, in_0: List[PeptideIdentification]) → None#: Sets the PeptideIdentification vector

setPrecursors(self, in_0: List[Precursor]) → None#: Sets the precursors

setProducts(self, in_0: List[Product]) → None#: Sets the products

setRT(self, in_0: float) → None#: Sets the absolute retention time (in seconds)

setSourceFile(self, in_0: SourceFile) → None#: Sets the source file

setStringDataArrays(self, sda: List[StringDataArray]) → None#: Sets the additional string data arrays to store e.g. meta data

setType(self, in_0: int) → None#: Sets the spectrum type

set_peaks()#

Cython signature: set_peaks((numpy_vector, numpy_vector))

Takes a tuple or list of two arrays (m/z, intensity) and populates the MSSpectrum. The arrays can be numpy arrays (faster).

size(self) → int#: Returns the number of peaks in the spectrum

sortByIntensity(self, reverse: bool) → None#

sortByPosition(self) → None#

unify(self, in_0: SpectrumSettings) → None#

updateRanges(self) → None#