Glossary -------- .. glossary:: :sorted: 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 :term:`features`. Assay Role The rational for acquisition of a specific sample (see :py:class:`~nPYc.enumerations.AssayRole`). Analytical Batch Set of :term:`study` and :term:`reference samples` acquired in a single continuous analytical run, without planned interruption *i.e.* instrument maintenance. Batch Effects Analytical and preparative influences that may cause a systematic difference in measurements taken at different points in time. Correction Batch In the ideal case, analytical :term:`batch` and :term:`run-order` effects are detected and corrected based on the :term:`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 :term:`feature` :math:`x`, is the Pearson correlation coefficient between the feature's measured concentration, and the expected concentration of the sample, calculated from the :term:`Serial Dilution Sample` set. Discrete Data Analytical data in which the adjacency of variables is unimportant to their interpretation. Peak-picked :term:`UPLC-MS`, targeted, and clinical measures are typically of this type. Feature Measured entity from a specific :term:`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 :term:`sample type`/:term:`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 :term:`m/z` of an ion can be measured in :term:`mass spectrometry`. Typically expressed in :term:`ppm` and calculated by: :math:`\Delta m_i = \frac{ (\mathit{m_\mathrm{i}} - \mathit{m_\mathrm{a}}) }{\mathit{m_\mathrm{a}}} \times 10^6` where :math:`\mathit{m_\mathrm{i}}` is the observed mass and :math:`\mathit{m_\mathrm{a}}` is the true mass. Mass-to-Charge Ratio *m/z* :term:`Mass Spectrometry` term describing the measurement of an ions mass relative to its charge. Mass Spectrometry MS Analytical technology that :term:`assays` a sample in terms of the observed :term:`mass-to-charge ratio` of the constituent compounds. Matrix The source of a :term:`specimen`, for example, urine, blood-plasma, or serum. Notation conventions (code) Matrices are set :math:`UPPERCASE`, vectors :math:`lowercase`, and scalar values :math:`\mathit{italic}`. Nuclear Magnetic Resonance Spectroscopy NMR Analytical technology for :term:`assaying` samples by detection the resonance of atomic nuclei in a magnetic field. Participant Subject Sample Source The source of a :term:`study sample` (generated at a :term:`sampling event`), which could represent an individual, experimental site or condition, or other. ppm (NMR) Parts-per-Million, a measurement of the chemical shift of a nucleus (:math:`\nu`) in :term:`NMR`, expressed as a ratio to the spectrometer frequency (:math:`\nu_\mathrm{ref}`) by: :math:`\delta = \frac{ \mathit{\nu} - \mathit{\nu_\mathrm{ref}}}{ \mathit{\nu_\mathrm{ref}}}`. ppm (MS) Parts-per-Million, used as a measure of :term:`mass accuracy` in :term:`mass spectrometry`. Preparative Batch A group of one or more :term:`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 :term:`Study Reference`, :term:`Long-Term Reference`. Rerun Assay Replicate :term:`analytical data` acquired from a sample that obsoletes any data previously acquired. For example, :term:`study samples` reacquired following analytical issues are reruns. Repeat Assay Replicate :term:`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. Relative Standard Deviation RSD The RSD provides a measurement of analytical precision, expressed as a percentage. The RSD is calculated for :term:`feature` :math:`x`, from repeated measurements (typically of the :term:`study reference` samples), by: :math:`\mathit{rsd(x)} = \frac{\mathit{\sigma_{x}}}{\mathit{\mu_{x}}} \times 100`. Resolution The ability of an instrument to separate two signals. In :term:`NMR` resolution is directly related to the magnetic field strength, and typically expressed in terms of the resonant frequency of the hydrogen nuclei in H\ :sub:`2`\ O at room temperature. In :term:`MS` resolution is measured and calculated by :math:`r = \frac{\mathit{m_\mathrm{i}}}{\mathit{w_\mathrm{1/2}}}`, where :math:`\mathit{m_\mathrm{i}}` is the nominal mass of an ion, and :math:`\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 :term:`UPLC-MS` chromatographic method. Internally, all nPYc toolbox retention times are expressed in seconds unless otherwise noted. Run Order The sequence in which :term:`samples` are :term:`assayed`. Sample A single specimen to be :term:`assayed`. May be divided into two :term:`broad classes`, :term:`study samples` which form the core of an analysis, and :term:`reference samples`, that allow that characterisation of analytical performance. Aliquot Aliquots are one or more sub-fractions of a :term:`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 :term:`assay`. Sample Assay Analytical data acquired by a single :term:`assay`, from a single physical specimen. Sample File Name Unique name of an assay data file. Two :term:`sample assays` acquired from the sample physical sample (for example, a :term:`rerun`), will have unique Sample File Names. 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 :term:`study samples` (typically 80, to allow formatting onto a 96-well plate with room for :term:`reference samples`) plus some number of :term:`reference samples`, prepared and analysed together. Sampling Event The specific point in time at which a :term:`sample` was generated. One sampling event may produce several equivalent :term:`aliquots`. Note that obtaining samples of blood-plasma and urine from a :term:`participant` at the same time is considered two sampling events, as the biofluids obtained are not interchangeable. Sample Type The overarching compositional class of a specific sample (see :py:class:`~nPYc.enumerations.SampleType`). Continuum Data Spectral Data Analytical data in which the adjacency of variables is significant. Examples include :term:`NMR` spectra, or mass-spectra recorded in continuum mode. Study A collection of :term:`samples` for analysis, constituting a single project. Study Sample SS Samples comprising the :term:`study`. Study Reference SR A specific :term:`sample type`/:term:`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. Serial Dilution Sample SRDS A specific :term:`sample type`/:term:`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 :term:`features` during analysis. Run-Order Effects Analytical factors that may affect the measurement of :term:`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. Ultra-Performance Liquid Chromatography Mass-Spectrometry UPLC-MS Analytical technology for :term:`assaying` samples, coupling chromatographic separation with :term:`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 :term:`Run order` ``int`` Ascending rank order Times & Dates :class:`~datetime.datetime` Export / import as :rfc:`3339` Fluid volumes Milliliters (ml) ``float`` Ionisation Mode :class:`~nPYc.enumerations.Polarity` Ionisation Type :class:`~nPYc.enumerations.Ionisation` :term:`Retention Time` Seconds (s) ``float`` Atomic Mass Unified atomic mass units (u) ``float`` :term:`NMR Chemical Shift` :term:`PPM` ``float`` Collision Energy Volts (v) ``float`` ===================================== ============================== ======================================= ============================================