Glossary¶

Aliquot
Aliquots are one or more sub-fractions of a sample that may be considered functionally equivalent. Setting aside handling considerations, aliquots may be combined or split with no impact on sample composition or the expected result of an assay.
Analytical Batch
Set of study and reference samples acquired in a single continuous analytical run, without planned interruption i.e. instrument maintenance.
Assay
Analytical procedure, encompassing sample preparation, data-acquisition, and feature extraction, for the characterisation of the chemical composition of samples. The datasets generated by an assay may provide measures as relative or absolute quantifications, for either absolute chemical names, or annotated and unknown features.
Assay Role
The rational for acquisition of a specific sample (see AssayRole).
Batch Effects
Analytical and preparative influences that may cause a systematic difference in measurements taken at different points in time.
Continuum Data
Spectral Data
Analytical data in which the adjacency of variables is significant. Examples include NMR spectra, or mass-spectra recorded in continuum mode.
Correction Batch
In the ideal case, analytical batch and run-order effects are detected and corrected based on the analytical batches into which the study has been divided. However in the event of unplanned interruptions to an analysis, it may be necessary to further sub-divide the run into a series of correction batches.
Correlation to Dilution
The Correlation to Dilution provides a measurement of analytical accuracy, expressed as a value between -1 and 1, where the closer the value to 1 the more accurately the feature is measured with respect to its expected concentration. The Correlation to Dilution for feature $$x$$, is the Pearson correlation coefficient between the feature’s measured concentration, and the expected concentration of the sample, calculated from the Serial Dilution Sample set.
Discrete Data
Analytical data in which the adjacency of variables is unimportant to their interpretation. Peak-picked UPLC-MS, targeted, and clinical measures are typically of this type.
Feature
Measured entity from a specific assay, that proxies the abundance of a chemical in the assayed sample. Each chemical in a sample may give rise to none, one, or several features in the dataset generated from a specific assay.
Long-Term Reference
LTR
A specific sample type/assay role combination consisting of samples with External Reference and Precision Reference assignment. These represent a type of QC sample useful, for example, for between-study comparisons.
Mass Accuracy
The precision by which the m/z of an ion can be measured in mass spectrometry. Typically expressed in ppm and calculated by: $$\Delta m_i = \frac{ (\mathit{m_\mathrm{i}} - \mathit{m_\mathrm{a}}) }{\mathit{m_\mathrm{a}}} \times 10^6$$ where $$\mathit{m_\mathrm{i}}$$ is the observed mass and $$\mathit{m_\mathrm{a}}$$ is the true mass.
Mass Spectrometry
MS
Analytical technology that assays a sample in terms of the observed mass-to-charge ratio of the constituent compounds.
Mass-to-Charge Ratio
m/z
Mass Spectrometry term describing the measurement of an ions mass relative to its charge.
Matrix
The source of a specimen, for example, urine, blood-plasma, or serum.
Notation conventions (code)
Matrices are set $$UPPERCASE$$, vectors $$lowercase$$, and scalar values $$\mathit{italic}$$.
Nuclear Magnetic Resonance Spectroscopy
NMR
Analytical technology for assaying samples by detection the resonance of atomic nuclei in a magnetic field.
Participant
Subject
Sample Source
The source of a study sample (generated at a sampling event), which could represent an individual, experimental site or condition, or other.
ppm (MS)
Parts-per-Million, used as a measure of mass accuracy in mass spectrometry.
ppm (NMR)
Parts-per-Million, a measurement of the chemical shift of a nucleus ($$\nu$$) in NMR, expressed as a ratio to the spectrometer frequency ($$\nu_\mathrm{ref}$$) by: $$\delta = \frac{ \mathit{\nu} - \mathit{\nu_\mathrm{ref}}}{ \mathit{\nu_\mathrm{ref}}}$$.
Preparative Batch
A group of one or more sample batches handled and prepared together, using a single batch of reagents.
Reference Sample
Reference samples are measured to characterise the stability of assays during the course of an acquisition, and account for platform dependent analytical variability. There are several common forms of reference sample, including Study Reference, Long-Term Reference.
Relative Standard Deviation
RSD
The RSD provides a measurement of analytical precision, expressed as a percentage. The RSD is calculated for feature $$x$$, from repeated measurements (typically of the study reference samples), by: $$\mathit{rsd(x)} = \frac{\mathit{\sigma_{x}}}{\mathit{\mu_{x}}} \times 100$$.
Repeat Assay
Replicate analytical data acquired from a sample that augments any data previously acquired. For example an interruption in the acquisition of an MS batch may cause an additional dilution series to be acquired when analysis resumes.
Rerun Assay
Replicate analytical data acquired from a sample that obsoletes any data previously acquired. For example, study samples reacquired following analytical issues are reruns.
Resolution

The ability of an instrument to separate two signals.

In NMR resolution is directly related to the magnetic field strength, and typically expressed in terms of the resonant frequency of the hydrogen nuclei in H2O at room temperature.

In MS resolution is measured and calculated by $$r = \frac{\mathit{m_\mathrm{i}}}{\mathit{w_\mathrm{1/2}}}$$, where $$\mathit{m_\mathrm{i}}$$ is the nominal mass of an ion, and $$\mathit{w_\mathrm{1/2}}$$ is the measured peak-width at half-height.

Retention Time
Measurement of the time of elution of a feature as observed in a specific UPLC-MS chromatographic method. Internally, all nPYc toolbox retention times are expressed in seconds unless otherwise noted.
Run Order
The sequence in which samples are assayed.
Run-Order Effects
Analytical factors that may affect the measurement of features in a dataset by introducing progressive assay-to-assay biases in measurement. Examples include the gradual decline in observed intensity of measurement in ToF MS detectors.
Sample
A single specimen to be assayed. May be divided into two broad classes, study samples which form the core of an analysis, and reference samples, that allow that characterisation of analytical performance.
Sample Assay
Analytical data acquired by a single assay, from a single physical specimen.
Sample Base Name
Common name for all comparable assays of the same sample. For example, reacquisitions of the same sample will share an identical Base Name.
Sample Batch
A collection of study samples (typically 80, to allow formatting onto a 96-well plate with room for reference samples) plus some number of reference samples, prepared and analysed together.
Sample File Name
Unique name of an assay data file. Two sample assays acquired from the sample physical sample (for example, a rerun), will have unique Sample File Names.
Sample Type
The overarching compositional class of a specific sample (see SampleType).
Sampling Event
The specific point in time at which a sample was generated. One sampling event may produce several equivalent aliquots. Note that obtaining samples of blood-plasma and urine from a participant at the same time is considered two sampling events, as the biofluids obtained are not interchangeable.
Serial Dilution Sample
SRDS
A specific sample type/assay role combination consisting of samples with Study Pool and Linearity Reference assignment. Serial Dilution Samples consist of a number of pooled QC samples diluted to known concentrations and acquired to asses the linearity of response of features during analysis.
Study
A collection of samples for analysis, constituting a single project.
Study Reference
SR
A specific sample type/assay role combination consisting of samples with Study Sample and Precision Reference assignment. These represent the classic QC sample used in profiling studies to assess analytical stability.
Study Sample
SS
Samples comprising the study.
Ultra-Performance Liquid Chromatography Mass-Spectrometry
UPLC-MS
Analytical technology for assaying samples, coupling chromatographic separation with mass detection.

Units

Where unspecified units used in the nPYc toolbox are as follows:
Variable Unit Datatype Interpretation
Sample inclusion   bool True == included, False == excluded
Feature inclusion   bool True == included, False == excluded
Run order   int Ascending rank order
Times & Dates   datetime Export / import as RFC 3339
Fluid volumes Milliliters (ml) float
Ionisation Mode   Polarity
Ionisation Type   Ionisation
Retention Time Seconds (s) float
Atomic Mass Unified atomic mass units (u) float
NMR Chemical Shift PPM float
Collision Energy Volts (v) float