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.

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'