Table 1.

Characteristics and physiological relevance of common biospecimen used to study metabolomics of environmental response, asthma pathogenesis, and asthma phenotypes and endotypes.

Biospecimen	Characteristics and physiological relevance to airway infection and diseases	Advantage	Disadvantage
Urine	Stable composition Relatively less complex than serum and plasma52 Reflects both physiological and pathological changes in proximal tissues and from blood perfusing distant organs53 Composition differs by age, gender, and seasons of collection53 Low concentration of total protein and high concentration of salts54 Composed of both endogenous and exogenous metabolites	◆Noninvasive ◆Easy pediatric collection ◆Abundant for repeated collection ◆Integrative view of physiological and environmental metabolites	▪Lack of proximity and specificity to airway physiology ▪Requires transport and short-term storage on ice ▪Low concentration of total protein and high concentration of salts is challenging for MS technologies
Blood	Composed of all molecules that are being secreted, excreted or discarded by different tissues in response to different physiological needs or stresses Metabolomics studies often use plasma and serum. Whole blood is commonly used for inborn errors of metabolism Maintains a normal homeostasis in the body by constant regulatory mechanisms Contains a substantial portion of large molecular weight proteins and lipoproteins 55 Mostly composed of endogenous metabolites56	◆Provides an integrative view of the instantaneous metabolic status ◆Amenable to most analytic techniques and platforms	▪Invasive collection ▪Lack of specificity to airway physiology ▪Less abundance for repeated pediatric collection ▪Analytes are tube-additive dependent ▪Identification of small molecule metabolites, especially using NMR is 55 difficult
Induced Sputum	Complex biofluid Has high viscosity and uneven consistency57 Composed of a mixture of mucins and other exudates Composed of protein/peptide components that may reflect disease presence or severity58	◆Relatively less invasive ◆Can be easily repeated ◆Physiologically relevant to the airways physiology	▪Sample collection requires trained personnel ▪Inducing saline solution may irritate airways ▪Sampling is variable ▪Contaminated with plasma, cells, saliva, and microbes58 ▪High viscosity requires further processing
Saliva	Clear and complex biofluid Equivalent to serum in reflecting the physiological state of the body Contains a variety of secreted enzymes, hormones, antibodies, antimicrobial constituents, growth factors, and low molecular weight molecules59 Dominated by short-chain organic acids, with acetic acid being the most abundant60	◆Noninvasive ◆Easy collection ◆Abundant for repeated collection ◆Easy transport	▪Endogenous metabolites concentrations are low compared with levels in the blood ▪Contaminated by metabolites from food and oral microflora, especially bacterial putrefaction
Exhaled breath (condensates and non-condensates)	EB represents the airway lining fluid, which makes it very useful to study the biochemical and inflammatory molecules in the airway62 Relatively simple composition and contains both volatile and nonvolatile molecules63 VOC can be measured with GC-MS from condensates or non-condensates EB and directly with SOM from non-condensates EB	◆Non-invasive and easily obtainable ◆Can be repeated ◆Relevant to airway physiology ◆Suitable to analyze both volatile and non-volatile metabolites64	▪Sample collection is difficult in pediatric population ▪Affected by exercise, mode and rate of breathing, nasal contamination, environmental temperature, and humidity ▪Contaminated by exogenous environmental exposures and ammonia and sulfur-containing compounds from the oral cavity
Nasal lavage fluid (NLF)	Obtained either via direct suction of nasal secretions, or using a nasal wash The upper respiratory tract is the barrier against environmental exposure Composed of large quantity of serum proteins and low concentration of nasal proteins and small molecules66 Contains secretions that are involved during early stages of viral infection and inflammation	◆Relatively accessible ◆Relatively noninvasive sample collection ◆Can be repeated ◆Relevant to airway physiology	▪Sample collection requires trained personnel ▪Use of hypertonic saline solution may irritate and produce mucus (high total protein concentration) ▪Low concentration nasal wash proteins ▪Contains contaminants from environmental exposures ▪Variation in concentration
Broncho aveolar lavage fluid (BALF)	Thin liquid layer containing peptides and proteins that contribute to host defense and other functions67 Represents the extracellular alveolar excretion from airway epithelial cells68 The small molecule metabolites in BALF represent both those measured in serum and those that are lung specific69	◆Most physiologically relevant sample for studying lower airway respiratory diseases	▪Inaccessible ▪Sample collection requires highly trained personnel ▪Very invasive ▪Requires the introduction of exogenous fluid into alveolar space ▪High protein and salt concentration and low concentrations of metabolites
Stool	Stool is comprised of endogenous human metabolites, gut microbiota metabolites, and residues or metabolites of digested materials	◆Noninvasive ◆Easy collection ◆Abundant for repeated collection ◆Metabolites represent chemical interactions between host and gut microbiota	▪Less relevant to respiratory diseases ▪Not commonly obtained in non clinical setting ▪Difficulty distinguishing nutrition, endogenous, and microbiota metabolites