Enumerations

This section describes the main enumerations function parameters (which may be of interest to advanced users).

The enumerations module provides a set of enumerations (complete listings of all possible items in a collection) for common types referenced in profiling experiments.

class nPYc.enumerations.VariableType

Enumeration of data sampling modalities.

• Discreetly sampled data types are those where the adjacency of variables is unimportant
• In spectral, continuum, and synonymous data, the ordering of variables is important in the interpretation of the data

Discrete = 1

Continuum = 2

Spectral = 2

Profile = 2

class nPYc.enumerations.Ionisation

Enumeration of ionisation methods in Mass Spectrometry.

EI = 'Electron Impact'

ESI = 'Electrospray Ionisation'

DESI = 'Desorption Electrospray Ionisation'

MALDI = 'Matrix Assisted Laser Desorption Ionisation'

class nPYc.enumerations.SampleType

Enumeration of distinct sample types.

• Study Sample comprise the study in question
• Study Pool consists of a mixture of all study samples
• External Reference a sample of a comparable matrix to the Study Samples, but not a sample (or mixture) derived from samples acquired as part of the study. Acquired, for example, for assessing analytical quality between studies.
• Method Reference consists of a synthetic mixture of known chemical standards
• Procedural Blank a blank sample not expected to contain any signals from the sample matrix

StudySample = 'Study Sample'

StudyPool = 'Study Pool'

ExternalReference = 'External Reference'

MethodReference = 'Method Reference'

ProceduralBlank = 'Procedural Blank'

class nPYc.enumerations.DatasetLevel

An enumeration.

Unknown = 0

Empty = 1

ValuesOnly = 2

QCReady = 3

class nPYc.enumerations.AssayRole

Enumeration of assay roles.

• Assay form the core of an analysis
• Precision Reference repeatedly acquired, and used to calculate measures of analytical precision
• Linearity Reference used to assess the linearity of response in the dataset, often by repeated injection at varying concentrations or levels of dilution. If generated by dilution from a base-level, the percentage concentration of each Linearity Reference sample is indicated in the ‘Dilution’ field of the sampleMetadata table

Assay = 'Assay'

PrecisionReference = 'Precision Reference'

LinearityReference = 'Linearity Reference'

Blank = 'Blank'

class nPYc.enumerations.Polarity

Enumeration of ionisation polarity.

Positive = 1

Negative = 2

class nPYc.enumerations.QuantificationType

Enumeration of quantification types.

• IS for Internal Standards
• QuantOwnLabeledAnalogue for compounds quantified and validated with own labeled analogue
• QuantAltLabeledAnalogue for compounds quantified and validated with alternative labeled analogue
• QuantOther for compounds quantified using another method
• Monitored for compounds monitored for relative information
• BrukerivDrQuant for compounds quantified with Bruker ivDr methods
• BrukerivDrEstimate for compounds estimated with Bruker ivDr methods

IS = 'Internal Standard'

QuantOwnLabeledAnalogue = 'Quantified and validated with own labeled analogue'

QuantAltLabeledAnalogue = 'Quantified and validated with alternative labeled analogue'

QuantOther = 'Other quantification'

Monitored = 'Monitored for relative information'

BrukerivDrQuant = 'Quantified using Bruker Biospin ivDr methods'

BrukerivDrEstimate = 'Estimated from other parameters using Bruker Biospin ivDr methods'

class nPYc.enumerations.CalibrationMethod

Enumeration of distinct calibration methods.

• noCalibration for compounds not quantified (monitored for relative information)
• noIS for compounds without Internal Standard (and Internal Standards themselves)
• backcalculatedIS for compounds using an Internal Standard
• otherCalibration for compounds employing another calibration approach
• nmrCalibration for compounds quantified by NMR

noCalibration = 'No calibration'

noIS = 'No Internal Standard'

backcalculatedIS = 'Backcalculated with Internal Standard'

otherCalibration = 'Other calibration method'

nmrCalibration = 'NMR quantitation'

class nPYc.enumerations.AnalyticalPlatform

Enumeration of analytical platform types.

• NMR for Nuclear Magnetic Resonance Spectroscopy
• MS for Mass Spectrometry
• Other placeholder for any other type of instrumentation

NMR = 'NuclearMagneticResonanceSpectroscopy'

MS = 'MassSpectrometry'

Other = 'Other'