IsotopeLabelingMDVs#

class pyopenms.IsotopeLabelingMDVs(*args, **kwargs)#

Bases: DefaultParamHandler

IsotopeLabelingMDVs is a class to support and analyze isotopic labeling experiments (i.e. MDVs : Mass Distribution Vectors, also known as Mass Isotopomer Distribution (MID))

__init__(self) → None#
__init__(self, arg: pyopenms._pyopenms_misc.IsotopeLabelingMDVs, /) → None

Attributes

`calculateIsotopicPurity`	This function performs an isotopic correction to account for unlabeled abundances coming from the derivatization agent (e.g., tBDMS) using correction matrix method and is calculated as follows: :param normalized_featuremap: FeatureMap with normalized values for each component and unlabeled chemical formula for each component group :param correction_matrix: Square matrix holding correction factors derived either experimentally or theoretically which describe how spectral peaks of naturally abundant 13C contribute to spectral peaks that overlap (or convolve) the spectral peaks of the corrected MDV of the derivatization agent :param correction_matrix_agent: Name of the derivatization agent, the internally stored correction matrix if the name of the agent is supplied, only "TBDMS" is supported for now :return corrected_featuremap: FeatureMap with corrected values for each component
`calculateMDV`	This function calculates the accuracy of the MDV as compared to the theoretical MDV (only for 12C quality control experiments) using average deviation to the mean param normalized_featuremap: FeatureMap with normalized values for each component and the chemical formula of the component group.
`calculateMDVAccuracies`	Calculate MDV accuracies
`calculateMDVAccuracy`	This function calculates the isotopic purity of the MDV using the following formula: isotopic purity of tracer (atom % 13C) = n / [n + (M + n-1)/(M + n)], where n in M+n is represented as the index of the result The formula is extracted from "High-resolution 13C metabolic flux analysis", Long et al, doi:10.1038/s41596-019-0204-0 :param normalized_feature: Feature with normalized values for each component and the number of heavy labeled e.g., carbons.
`calculateMDVs`
`getDefaults`	Returns the default parameters
`getName`	Returns the name
`getParameters`	Returns the parameters
`getSubsections`
`isotopicCorrection`
`isotopicCorrections`	This function performs an isotopic correction to account for unlabeled abundances coming from the derivatization agent (e.g., tBDMS) using correction matrix method and is calculated as follows: :param normalized_feature: Feature with normalized values for each component and unlabeled chemical formula for each component group :param correction_matrix: Square matrix holding correction factors derived either experimentally or theoretically which describe how spectral peaks of naturally abundant 13C contribute to spectral peaks that overlap (or convolve) the spectral peaks of the corrected MDV of the derivatization agent :param correction_matrix_agent: Name of the derivatization agent, the internally stored correction matrix if the name of the agent is supplied, only "TBDMS" is supported for now :return: corrected_feature: Feature with corrected values for each component
`setName`	Sets the name
`setParameters`	Sets the parameters

calculateIsotopicPurity#: This function performs an isotopic correction to account for unlabeled abundances coming from the derivatization agent (e.g., tBDMS) using correction matrix method and is calculated as follows: :param normalized_featuremap: FeatureMap with normalized values for each component and unlabeled chemical formula for each component group :param correction_matrix: Square matrix holding correction factors derived either experimentally or theoretically which describe how spectral peaks of naturally abundant 13C contribute to spectral peaks that overlap (or convolve) the spectral peaks of the corrected MDV of the derivatization agent :param correction_matrix_agent: Name of the derivatization agent, the internally stored correction matrix if the name of the agent is supplied, only “TBDMS” is supported for now :return corrected_featuremap: FeatureMap with corrected values for each component

calculateMDV#: This function calculates the accuracy of the MDV as compared to the theoretical MDV (only for 12C quality control experiments) using average deviation to the mean param normalized_featuremap: FeatureMap with normalized values for each component and the chemical formula of the component group. Out is a FeatureMap with the component group accuracy and accuracy for the error for each component param fragment_isotopomer_measured: Measured scan values param fragment_isotopomer_theoretical_formula: A map of ProteinName/peptideRef to Empirical formula from which the theoretical values will be generated

calculateMDVAccuracies#: Calculate MDV accuracies

calculateMDVAccuracy#: This function calculates the isotopic purity of the MDV using the following formula: isotopic purity of tracer (atom % 13C) = n / [n + (M + n-1)/(M + n)], where n in M+n is represented as the index of the result The formula is extracted from “High-resolution 13C metabolic flux analysis”, Long et al, doi:10.1038/s41596-019-0204-0 :param normalized_feature: Feature with normalized values for each component and the number of heavy labeled e.g., carbons. Out is a Feature with the calculated isotopic purity for the component group :param experiment_data: Vector of experiment data in percent :param isotopic_purity_name: Name of the isotopic purity tracer to be saved as a meta value

calculateMDVs#

getDefaults#: Returns the default parameters

getName#: Returns the name

getParameters#: Returns the parameters

getSubsections#

isotopicCorrection#

isotopicCorrections#: This function performs an isotopic correction to account for unlabeled abundances coming from the derivatization agent (e.g., tBDMS) using correction matrix method and is calculated as follows: :param normalized_feature: Feature with normalized values for each component and unlabeled chemical formula for each component group :param correction_matrix: Square matrix holding correction factors derived either experimentally or theoretically which describe how spectral peaks of naturally abundant 13C contribute to spectral peaks that overlap (or convolve) the spectral peaks of the corrected MDV of the derivatization agent :param correction_matrix_agent: Name of the derivatization agent, the internally stored correction matrix if the name of the agent is supplied, only “TBDMS” is supported for now :return: corrected_feature: Feature with corrected values for each component

setName#: Sets the name

setParameters#: Sets the parameters