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Prepare for an experiment
Key elements in the sample
specimens
Define the experiment
A successful experiment requires several key elements to be present in the samples
that are analyzed. The presence of these elements is a reasonable indicator that
data acquired from the samples is suitable for metabolomic analysis to prove or disprove your hypothesis. The samples are taken from a specimen, an individual organism (e.g., a person, animal, plant, or other organism) of a class or group that is used
as a representative of a whole class or group. For clarification on the terms used
throughout the workflow, see “Definitions” on page 180. There are six key elements.
Many chemical constituents: Samples taken from a specimen should contain many
chemical constituents (metabolites) that are naturally expressed by the specimen or
are a product of the specimen during its interaction with controllable externalities.
Complex relationship among the chemical constituents: The relative composition
of the chemical constituents within each sample is the result of complex relationships, such as the biological functions within the specimen as shown in Figure 7 on
page 22.
Subject specimens: The specimens selected for evaluation represent a random set
of specimens selected from a larger population. If the specimens come from organisms subject to specific and known perturbations in their externalities (independent
variables) they are known as subject specimens. If the specimens come from organisms that are not perturbed in their externalities they are known as control specimens.
Control specimens: A sub-group existing within the sample specimen population
that represents the “normal” attributes of the organism under natural, unperturbed,
externalities. The inclusion of control specimens reduces the occurrence of false
positive and false negative correlations and provides a point of reference for assigning a polarity to any observed effect.
Independent variables: The specific and known perturbations that may be made to a
specimen, or quantifiable externalities that affect the specimen, and which are
expected to induce a measurable change in the metabolic profile. The relative concentrations of the chemical constituents may be influenced by attributes, or parameters, that are independently controlled through either, (a) informed selection of the
specimens (controlled sampling), or (b) application of a set of experimentally controlled externalities or attributes (experiments).
Dependent variables: The measurable response of the specimen to the specific and
known perturbations made through variation of the independent variables. The specimen response is manifest in the relative concentration of the chemical constituents
(metabolic profile) with respect to each varied attribute. The data is collected using
hyphenated mass spectrometry techniques. If the response of the metabolic profile
to the independent variables is known and finite, then traditional quantitation techniques may be applicable (for example, GC/MS may be used to study how the abundance of marker metabolites change when organisms are treated versus not treated
for a condition). Otherwise, if the response is unknown or complex, and spans a
large number of chemical constituents, the data is suitable for analysis using the
metabolomic workflow.
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