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
- Subject
- 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
== excludedFeature inclusion bool
True
== included,False
== excludedRun 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