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Term	Abbreviation	Description
Proton leak		Flux of protons driven by the protonmotive force across the inner mt-membrane, bypassing the ATP synthase and thus contributing to LEAK respiration. Proton leak-flux depends non-linearly (non-ohmic) on the protonmotive force. Compare: Proton slip.
Proton pump		Mitochondrial proton pumps are large enzyme complexes (CI, CIII, CIV, CV) spanning the inner mt-membrane, partially encoded by mtDNA. CI, CIII and CIV are proton pumps that drive protons against the electrochemical protonmotive force, driven by electron transfer from reduced substrates to oxygen. In contrast, ATP synthase (also known as CIV) is a proton pump that utilizes the energy of proton flow along the protonmotive force to drive phosphorylation of ADP to ATP.
Proton slip		Proton slip is a property of the proton pumps (Complexes CI, CIII, and CIV) when the proton slips back to the matrix side within the proton pumping process. Slip is different from the proton leak, which depends on Δp and is a property of the inner mt-membrane (including the boundaries between membrane-spanning proteins and the lipid phase). Slip is an uncoupling process that depends mainly on flux and contributes to a reduction in the biochemical coupling efficiency of ATP production and oxygen consumption. Together with proton leak and cation cycling, proton slip is compensated for by LEAK respiration or LEAK oxygen flux, L. Compare: Proton leak.
Q calibration - DatLab		Q calibration
Q-junction		The Q-junction is a junction for convergent electron flow in the Electron transfer pathway (ET-pathway) from type N substrates and mt-matrix dehydrogenases through Complex I (CI), from type F substrates and FA oxidation through electron-transferring flavoprotein Complex (CETF), from succinate (S) through Complex II (CII), from glycerophosphate (Gp) through glycerophosphate dehydrogenase Complex (CGpDH), from choline through choline dehydrogenase, from dihydro-orotate through dihydro-orotate dehydrogenase, and other enzyme Complexes into the Q-cycle (ubiquinol/ubiquinone), and further downstream to Complex III (CIII) and Complex IV (CIV). The concept of the Q-junction, with the N-junction and F-junction upstream, provides the rationale for defining Electron-transfer-pathway states and categories of SUIT protocols.
ROUTINE respiration	R	In the living cell, ROUTINE respiration (R) or ROUTINE activity in the physiological coupling state is controlled by cellular energy demand, energy turnover and the degree of coupling to phosphorylation (intrinsic uncoupling and pathological dyscoupling). The conditions for measurement and expression of respiration vary (oxygen flux in state R, J_O₂R or oxygen flow in state R, I_O₂R). If these conditions are defined and remain consistent within a given context, then the simple symbol R for respiratory state can be used to substitute the more explicit expression for respiratory activity. R and growth of cells is supported by exogenous substrates in culture media. In media without energy substrates, R depends on endogenous substrates. R cannot be measured in permeabilized cells or isolated mitochondria. R is corrected for residual oxygen consumption (ROX), whereas R´ is the uncorrected apparent ROUTINE respiration or total cellular oxygen consumption of cells including ROX.
Respiratory acceptor control ratio	RCR	The respiratory acceptor control ratio (RCR) is defined as State 3/State 4 [1]. If State 3 is measured at saturating [ADP], RCR is the inverse of the OXPHOS control ratio, L/P (when State 3 is equivalent to the OXPHOS state, P). RCR is directly but non-linearly related to the P-L control efficiency, j_P-L = 1-L/P, with boundaries from 0.0 to 1.0. In contrast, RCR ranges from 1.0 to infinity, which needs to be considered when performing statistical analyses. In living cells, the term RCR has been used for the ratio State 3u/State 4o, i.e. for the inverse L/E ratio [2,3]. Then for conceptual and statistical reasons, RCR should be replaced by the E-L coupling efficiency, 1-L/E [4].
Respiratory chain	RC	The mitochondrial respiratory chain (RC) consists of enzyme complexes arranged to form a metabolic system of convergent pathways for oxidative phosphorylation. In a general sense, the RC includes (1) the electron transfer pathway (ET-pathway), with transporters for the exchange of reduced substrates across the inner mitochondrial membrane, enzymes in the matrix space (particularly dehydrogenases of the tricarboxylic acid cycle), inner membrane-bound electron transfer complexes, and (2) the inner membrane-bound enzymes of the phosphorylation system.
Respiratory complexes	CI, CII, CIII, CIV, CETF, CGpDH, ..	Respiratory Complexes are membrane-bound enzymes consisting of several subunits which are involved in energy transduction of the respiratory system. » MiPNet article
Respiratory state		Respiratory states of mitochondrial preparations and living cells are defined in the current literature in many ways and with a diversity of terms. Mitochondrial respiratory states must be defined in terms of both, the coupling-control state and the electron-transfer-pathway state.
Respirometry		Respirometry is the quantitative measurement of respiration. Respiration is therefore a combustion, a very slow one to be precise (Lavoisier and Laplace 1783). Thus the basic idea of using calorimetry to explore the sources and dynamics of heat changes were present in the origins of bioenergetics (Gnaiger 1983). Respirometry provides an indirect calorimetric approach to the measurement of metabolic heat changes, by measuring oxygen uptake (and carbon dioxide production and nitrogen excretion in the form of ammonia, urea, or uric acid) and converting the oxygen consumed into an enthalpy change, using the oxycaloric equivalent. Liebig (1842) showed that the substrate of oxidative respiration was protein, carbohydrates, and fat. The sum of these chemical changes of materials under the influence of living cells is known as metabolism (Lusk 1928). The amount (volume STP) of carbon dioxide expired to the amount (volume STP) of oxygen inspired simultaneously is the respiratory quotient, which is 1.0 for the combustion of carbohydrate, but less for lipid and protein. Voit (1901) summarized early respirometric studies carried out by the Munich school on patients and healthy controls, concluding that the metabolism in the body was not proportional to the combustibility of the substances outside the body, but that protein, which burns with difficulty outside, metabolizes with the greatest ease, then carbohydrates, while fats, which readily burns outside, is the most difficultly combustible in the organism. Extending these conclusions on the sources of metabolic heat changes, the corresponding dynamics or respiratory control was summarized (Lusk 1928): The absorption of oxygen does not cause metabolism, but rather the amount of the metabolism determines the amount of oxygen to be absorbed. .. metabolism regulates the respiration.
STPD	STPD	At standard temperature and pressure dry (STPD: 0 °C = 273.15 K and 1 atm = 101.325 kPa = 760 mmHg), the molar volume of an ideal gas, V_m, and V_m,O₂ is 22.414 and 22.392 L∙mol^-1, respectively. Rounded to three decimal places, both values yield the conversion factor of 0.744 from units used in spiroergometry (V_O₂max [mL O₂·min^-1]) to SI units [µmol O₂·s^-1]. For comparison at normal temperature and pressure dry (NTPD: 20 °C), V_m,O₂ is 24.038 L∙mol^-1. Note that the SI standard pressure is 100 kPa, which corresponds to the standard molar volume of an ideal gas of 22.711 L∙mol^-1 and 22.689 L∙mol^-1 for O₂.
SUIT	SUIT	SUIT is the abbreviation for Substrate-Uncoupler-Inhibitor Titration. SUIT protocols are used with mt-preparations to study respiratory control in a sequence of coupling and pathway control states induced by multiple titrations within a single experimental assay. These studies use biological samples economically to gain maximum information with a minimum amount of cells or tissue.
SUIT-001	RP1
SUIT-001 O2 ce-pce D003	RP1 ce-pce
SUIT-001 O2 ce-pce D004	RP1 ce-pce blood
SUIT-001 O2 mt D001	RP1 mt
SUIT-001 O2 pfi D002	RP1 pfi
SUIT-002	RP2
SUIT-002 O2 ce-pce D007	RP2 ce-pce
SUIT-002 O2 ce-pce D007a	RP2 ce-pce blood
SUIT-002 O2 mt D005	RP2 mt
SUIT-002 O2 pfi D006	RP2 pfi
SUIT-003	CCP-ce
SUIT-003 AmR ce D058	AmR effect on ce
SUIT-003 AmR ce D059	AmR effect on ce - control
SUIT-003 Ce1;ce1P;ce3U;ce4Glc;ce5M;ce6Rot;ce7S;1Dig;1c;2Ama;3AsTm;4Azd	cePMGlc,S
SUIT-003 Ce1;ce2U-	ce
SUIT-003 Ce1;ce3U-	ce
SUIT-003 O2 ce D009	CCP-ce short
SUIT-003 O2 ce D012	CCP-ce(P)
SUIT-003 O2 ce D028	CCP-ce S permeability test
SUIT-003 O2 ce D037	CCP-ce Crabtree_R
SUIT-003 O2 ce D038	CCP-ce Crabtree_E
SUIT-003 O2 ce D039	CCP-ce microalgae
SUIT-003 O2 ce D050	CCP-ce Snv
SUIT-003 O2 ce D060	CCP-ce Snv,Mnanv
SUIT-003 O2 ce D061	CCP-ce Snv,Mnanv - control
SUIT-003 O2 ce D062	CCP-ce Snv - control
SUIT-003 O2 ce-pce D013	CCVP-Glc,M
SUIT-003 O2 ce-pce D018	CCVP-Glc
SUIT-003 O2 ce-pce D020	CCVP
SUIT-003 pH ce D067	CCP-Crabtree with glycolysis inhibition
SUIT-004	RP1-short
SUIT-004 O2 pfi D010	RP1-short pfi
SUIT-005	RP2-short
SUIT-005 O2 pfi D011	RP2-short pfi
SUIT-006	CCP-mtprep
SUIT-006 O2 ce-pce D029	CCP ce-pce PM
SUIT-006 O2 mt D022	CCP mt S(Rot)
SUIT-006 O2 mt D047	CCP mt PM
SUIT-006 Q ce-pce D073	CCP ce-pce S(Rot)
SUIT-006 Q mt D071	CCP mt S(Rot)
SUIT-007	Glutamate anaplerosis
SUIT-007 O2 ce-pce D030	Glutamate anaplerotic pathway
SUIT-008	PM+G+S_OXPHOS+Rot_ET
SUIT-008 O2 ce-pce D025	Q-junction ce-pce
SUIT-008 O2 mt D026	Q-junction mtprep
SUIT-008 O2 pce D25	NS(PGM)
SUIT-008 O2 pfi D014
SUIT-009 O2 ce-pce D016
SUIT-009 O2 mt D015
SUIT-010	Digitonin test
SUIT-010 O2 ce-pce D008	Dig titration-pce
SUIT-011	GM+S_OXPHOS+Rot_ET
SUIT-011 O2 pfi D024	NS physiological maximum capapcity in fibres
SUIT-012	PM+G_OXPHOS
SUIT-012 O2 ce-pce D052	N(PGM)
SUIT-012 O2 mt D027	N CCP mtprep
SUIT-013 AmR ce D023	O_{2 dependence of H₂O₂ production ce}
SUIT-014	GM+P+S_OXPHOS+Rot_ET
SUIT-014 O2 pfi D042	NS(PGM)
SUIT-015	F+G+P+S_OXPHOS+Rot_ET
SUIT-015 O2 pti D043	FNS(Oct,PGM)
SUIT-016	F+G+S+Rot_OXPHOS+Omy
SUIT-016 O2 pfi D044	FNS(Oct,GM)
SUIT-017	F+G+S_OXPHOS+Rot_ET
SUIT-017 O2 mt D046	FNS(Oct,GM)
SUIT-017 O2 pfi D049	FNS(Oct,GM)
SUIT-018 O2 mt D054
SUIT-019	Pal+Oct+P+G_OXPHOS+S+Rot_ET
SUIT-019 O2 pfi D045	FNS(PalOct,PGM)
SUIT-020	PM+G+S+Rot_OXPHOS+Omy
SUIT-020 O2 mt D032	Q-junction additivity and respiratory control for membrane potential
SUIT-021	OXPHOS (GM+S+Rot+Omy)
SUIT-021 O2 mt D035	NS(GM)
SUIT-022	AOX (ce CN+SHAM)
SUIT-022 O2 ce D051	AOX-ce CN+SHAM
SUIT-023	AOX-ce SHAM+CN
SUIT-023 O2 ce D053	AOX-ce SHAM+CN
SUIT-024	ATPase (PM)
SUIT-024 O2 ce-pce D056	N(PM)
SUIT-025	OXPHOS (F+M+P+G+S+Rot)
SUIT-025 O2 mt D057	FNS(Oct,PGM)
SUIT-027	Malate anaplerosis
SUIT-029 O2 mt D066	QC_imt_PM_T+OXPHOS+c+Omy_ET_G+S+Rot
SUIT-031	PM+S+Rot
SUIT-031 O2 ce-pce D079	PM+S+Rot
SUIT-031 O2 mt D075	PM+S+Rot
SUIT-031 Q ce-pce D074	PM+S+Rot
SUIT-031 Q mt D072	PM+S+Rot
SUITbrowser		Use the SUITbrowser to find the substrate-uncoupler-inhibitor-titration (SUIT) protocol most suitable for addressing your research questions. Open the SUITbrowser: http://suitbrowser.oroboros.at/ How to find a DL-Protocol (DLP)
Select O2k - DatLab		Select O2k - DatLab
Selectivity		Selectivity is the ability of a sensor or method to quantify accurately and specifically the analyte or analytes in the presence of other compounds.
Sensitivity		Sensitivity refers to the response obtained for a given amount of analyte and is often denoted by two factors: the limit of detection and the limit of quantification.
Smoothing		Various methods of smoothing can be applied to improve the signal-to-noise ratio. For instance, data points recorded over time [s] or over a range of wavelengths [nm] can be smoothed by averaging n data points per interval. Then the average of the n points per smoothing interval can be taken for each successively recorded data point across the time range or range of the spectrum to give a n-point moving average smoothing. This method decreases the noise of the signal, but clearly reduces the time or wavelength resolution. More advanced methods of smoothing are applied to retain a higher time resolution or wavelength resolution.
Stability		Stability determines the accuracy of intensity and absorbance measurements as a function of time. Instability (see drift introduces systematic errors in the accuracy of fluorescence and absorbance measurements.
Startup O2k-Respirometer		Startup O2k-Respirometer - the experimental system complete for basic high-resolution respirometry (HRR). The O2k-Respirometer includes the O2k-Main Unit with stainless steel housing, O2k-Assembly Kit, two OroboPOS (polarographic oxygen sensors) and OroboPOS-Service Kit, DatLab software, the ISS-Integrated Suction System, the O2k-Titration Set, and for performing high-resolution respirometry with reduced amounts of biological sample the O2k-sV-Module. The O2k is a sole source apparatus with no other instruments meeting its specifications.
Steady state		A system is in a steady state if the state variables of a dynamic system do not change over time due to exchange processes with the environment, which compensate for internal dissipative transformations — such as chemical reactions or diffusion — and thus prevent any changes of the system and externalize dissipative changes to the environment. The dynamic nature of the steady state differentiates it from the thermodynamic equilibrium state. {Quote} Steady states can be obtained only in open systems, in which changes by internal transformations, e.g., O₂ consumption, are instantaneously compensated for by external fluxes across the system boundary, e.g., O₂ supply, thus preventing a change of O₂ concentration in the system (Gnaiger 1993). Mitochondrial respiratory states monitored in closed systems satisfy the criteria of pseudo-steady states for limited periods of time, when changes in the system (concentrations of O₂, fuel substrates, ADP, P_i, H⁺) do not exert significant effects on metabolic fluxes (respiration, phosphorylation). Such pseudo-steady states require respiratory media with sufficient buffering capacity and substrates maintained at kinetically-saturating concentrations, and thus depend on the kinetics of the processes under investigation. {end of Quote: BEC 2020.1}. Whereas fluxes may change at a steady state over time, concentrations are maintained constant. The 'respiratory steady state' (Chance and Williams 1955) is characterized by constant fluxes (O₂ flux, H₂O₂ flux) and measured variables of state (cytochrome redox states, Q redox state, NADH redox state, mitochondrial membrane potential). High-resolution respirometry allows for the measurement of several parameters (e.g. O₂ flux, H₂O₂ flux, mitochondrial membrane potential) at pseudo-steady states, when changes of concentrations in the closed system do not exert any control on fluxes. Combination with the Titration-Injection microPump (TIP2k) allows operation with programmable titration regimes at steady-state ADP concentration (Gnaiger 2001), oxygen concentration (oxystat mode; Gnaiger et al 2000, Harrison et al 2015) or steady-state pH (pH-stat more), yielding an expanded flexibility in experimental design by combining the technical advantages of closed and open systems approaches.
Substrate control state		See Electron-transfer-pathway state
Substrate-uncoupler-inhibitor titration	SUIT	Mitochondrial Substrate-uncoupler-inhibitor titration (SUIT) protocols are used with mitochondrial preparations to study respiratory control in a sequence of coupling and substrates states induced by multiple titrations within a single experimental assay.
TIP2k-Module		TIP2k-Module - Titration-Injection microPump (TIP2k) for two-channel operation with the O2k-FluoRespirometer with automatic control by DatLab of programmable titration regimes and feedback control (oxystat, pH-stat).
TPP+ inhibitory effect		A major task in establishing a procedure for measurement of mitochondrial membrane potential using probe molecules is the evaluation of inhibitory concentrations of the probe molecule on the activity of respiration. The TPP⁺ inhibitory effect (this also applies to TPMP⁺ and other indicator molecules) is frequently ignored. Accurate knowledge of a threshold concentration is required to evaluate the necessary limit of detection of TPP⁺, and for restriction of experimental TPP⁺ concentrations below the inhibitory range.
Taurine		Taurine, or 2-Aminoethan sulfonic acid, is one of the most abundant low-molecular-weight organic constituents in animals and humans. It has a multitude of functions in different types of tissue, one of which is the stabilization of membranes. Because of this and its antioxidative effect, taurine is a component of the respiration media MiR05 and MiR06 to preserve mitochondrial function.
Tetraphenylphosphonium	TPP⁺	Tetraphenylphosphonium (TPP⁺). A lipophilic molecular probe in conjunction with an ion selective electrode (ISE) for measuring the mitochondrial membrane potential.
Time resolution		Time resolution in respirometric measurements is influenced by three parameters: the response time of the POS, the data sampling interval and the number of points used for flux calculation.
Uncoupler titrations		In uncoupler titrations various uncouplers, such as CCCP, FCCP or DNP are applied to uncouple mitochondrial electron transfer from phosphorylation (ATP synthase, ANT and phosphate carrier), particularly with the aim to measure ET capacity. ET capacity is maximum oxygen flux measured as noncoupled respiration with optimum uncoupler concentration.
Uncoupling-control ratio	UCR	The uncoupling-control ratio UCR is the ratio of ET-pathway/ROUTINE-respiration (E/R) in living cells, evaluated by careful uncoupler titrations (Steinlechner et al 1996). Compare ROUTINE-control ratio (R/E) (Gnaiger 2008).
Unspecific binding of TPP+		Unspecific binding of the probe molecule TPP⁺ in the matrix phase of mitochondria is taken into account as a correction for measurement of the mitochondrial membrane potential. External unspecific binding is the binding outside of the inner mt-membrane or on the outer side of the inner mt-membrane, in contrast to internal unspecific binding.
VO2max	V_O₂max; V_O₂max/M	Maximum oxygen consumption, V_O₂max, is and index of cardiorespiratory fitness, measured by spiroergometry on human and animal organisms capable of controlled physical exercise performance on a treadmill or cycle ergometer. V_O₂max is the maximum respiration of an organism, expressed as the volume of O₂ at STPD consumed per unit of time per individual object [mL.min^-1.x^-1]. If normalized per body mass of the individual object, M [kg.x^-1], mass specific maximum oxygen consumption, V_O₂max/M, is expressed in units [mL.min^-1.kg^-1].
Warburg effect		Recently, controversies had a renaissance on the much neglected Crabtree effect (aerobic glycolysis in a large range of cells exposed to glucose or fructose, with fully functional mitochondria; Crabtree 1929; Gnaiger and Kemp 1990) versus the Warburg effect (loss of mitochondrial function inducing cancer and stimulating compensatory aerobic glycolysis in the presence of oxygen; Warburg 1956; see list of references for reviews). Today it is widely accepted that ‘the Warburg effect is not consistent across all cancer types’ (Potter et al 2016) and reprogramming of mitochondrial energy metabolism represents a functional adjustment of cancer cells (Schöpf et al 2020).
Zero calibration	R0	Zero calibration is, together with air calibration, one of the two steps of the POS calibration. It is performed in the closed chamber after all the oxygen has been depleted by the addition of dithionite or by respiration of imt or cells. Any incubation medium can be used for zero calibration with dithionite or sample. Unlike air calibration, it is not necessary to perform a zero calibration on each experimental day. After performing a zero calibration, it is recommended not running other experiments on the same day. Even after standard cleaning of the O2k-chambers, there might be residual amounts of reduced dithionite in the chamber, affecting the oxygen flux in subsequent experiments performed on the same day.

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