MitoPedia: Oroboros QM

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MitoPedia

MitoPedia: Oroboros QM

MitoPedia - high-resolution terminology - matching measurements at high-resolution.
The MitoPedia terminology is developed continuously in the spirit of Gentle Science.

Template NextGen-O2k.jpg
Work in progress
The MitoFit Quality Control System was officially introduced at the MitoFit Science Camp 2016 Kuehtai AT. At present, this page and the corresponding links are work in progress.
Quality management

Aims

MitoFit Quality Control (MitoFit QC) was initiated to develop and implement standards in respirometric OXPHOS analysis, applied in comparative mitochondrial physiology, mitochondrial medicine, and clinical diagnosis.


Definitions

For a high-quality data repository, a QCS is required, based on a consistent and accessible terminology. Terms are defined in the MitoPedia system; these definitions will be formally approved by the MitoFit accreditation panel (to be formed), and will be labelled as MitoFit accredited for consistent use in the MitoFit data repository (under construction).
Examples of terms that require definition and approval are listed below:


  1. Project
  2. Experiment
    1. Assay, Experimental assay
    2. Replica
    3. Repetitions
  3. Population (or group)
    1. Sample
    2. Subsample
    3. Sample type
    4. Sample size
    5. Dataset
  4. MitoFit protocols
    1. Harmonization protocols (Begley, Ioannidis 2015)
    2. Normalization protocols
    3. Subprotocols
    4. Laboratory protocols
    5. Solution protocols: media, substrates, uncouplers, inhibitors used in SUIT protocols, permeabilization agents, etc.
    6. Instrumental performance protocols
    7. Mitochondrial preparation protocols including biopsy sampling, tissue storage, cell preparation protocols, etc.
    8. Respirometric OXPHOS data acquisition and analysis protocols
  5. MitoFit registered project
    1. MitoFit pre-registered project
    2. Publicly deposited protocols (Begley, Ioannidis 2015)
    3. Prespecified protocols (Begley, Ioannidis 2015)
    4. Time-stamped protocols (Begley, Ioannidis 2015)
  6. Standardization
    1. Standard operating procedures
    2. Harmonization
  7. MitoFit proficiency test
    1. SUIT reference protocol
Quality management

MitoPedia terms and definitions: MitoFit Quality Control

TermAbbreviationDescription
AccuracyThe accuracy' of a method is the degree of agreement between an individual test result generated by the method and the true value.
AssayAn experimental assay is a method to obtain a measurement with a defined instrument on a sample or subsample. Multiple assay types may be applied on the same sample or subsample, if the measurement does not destroy it. For instance, the wet weight of a permeabilized muscle fibre preparation can be determined based on a specific laboratory protocol (gravimetric assay), maintaining the functional integrity of the sample, which then can be used in a respirometric assay, followed by a spectrophotometric assay for measurement of protein content. The experimental design determines which types of assays have to be applied for a complete experiment. Destructive assays, such as determination of protein content or dry weight, can be applied on a sample only after performing a respirometric assay, or on a separate subsample. The experimental variability is typically dominated by the assay with the lowest resolution or signal to noise ratio. The signal to noise ratio may be increased by increasing the number, n, of repetitions of measurements on subsamples. Evaluation of procedural variation ('experimental noise') due to instrumental resolution and handling requires subsampling from homogenous samples.
AttributeAttribute in general is a characteristic or property. In databases an attribute describes a column in a table. Rows then represent the according attribute values.
Biological reference intervalBiological reference interval or reference interval is the central 95% interval of the distribution of reference values.
CECECE marking is a mandatory conformity marking for certain products sold within the European Economic Area (EEA).
ClassificationClassification of in vitro diagnostic medical devices (IVD) describes the category to which an IVD belongs.
DatasetA dataset is a collection of data. In the context of databases a dataset represents the collection of entries in a database-table. In this table columns represent attributes and rows display the according values of the entries.
DetectorA detector is a device that converts the light falling upon it into a current or voltage that is proportional to the light intensity. The most common devices in current use for fluorometry and spectrophotometry are photodiodes and photodiode arrays.
DirectiveA directive is a legal act of the European Union, which requires member states to achieve a particular result without dictating the means of achieving that result.
ExaminationAn examination is a set of operations having the object of determining the value or characteristics of a property. In some disciplines (e.g. microbiology) an examination is the total activity of a number of tests, observations or measurements.
ExperimentA number of replica, N, of experiments on one sample type is designed to obtain statistical information about the involved population(s) and to test hypotheses about a population and about differences between populations, when experiments are carried out on different sample types. An experiment may involve various assays, e.g., a respirometric assay and an assay for protein determination.
GroupSee population.
HarmonizationHarmonization is the process of minimizing redundant or conflicting standards which may have evolved independently. To obtain a common basis in reaching a defined objective, critical requirements are identified that need to be retained.
Harmonized European normEN-normHarmonized European norms are norms valid for all members of the European Union. They are mandatory parts of the individual national collections of norms.
Harmonized standardA harmonised standard is a European standard developed by a recognised European Standards Organisation: CEN, CENELEC, or ETSI.
ISO 10012:2003 Measurement management systemsISO 10012:2003ISO 10012:2003 Measurement management systems — Requirements for measurement processes and measuring equipment: An effective measurement management system ensures that measuring equipment and measurement processes are fit for their intended use and is important in achieving product quality objectives and managing the risk of incorrect measurement results. The objective of a measurement management system is to manage the risk that measuring equipment and measurement processes could produce incorrect results affecting the quality of an organization’s product. The methods used for the measurement management system range from basic equipment verification to the application of statistical techniques in the measurement process control.
ISO 13528:2015 Statistical methods for use in proficiency testing by interlaboratory comparisonISO 13528:2015ISO 13528:2015 Statistical methods for use in proficiency testing by interlaboratory comparison: Proficiency testing involves the use of interlaboratory comparisons to determine the performance of participants (which may be laboratories, inspection bodies, or individuals) for specific tests or measurements, and to monitor their continuing performance. There are a number of typical purposes of proficiency testing ISO/IEC 17043:2010. These include the evaluation of laboratory performance, the identification of problems in laboratories, establishing effectiveness and comparability of test or measurement methods, the provision of additional confidence to laboratory customers, validation of uncertainty claims, and the education of participating laboratories. The statistical design and analytical techniques applied must be appropriate for the stated purpose(s).
ISO 15189:2012 Medical laboratories — Particular requirements for quality and competenceISO 15189:2012ISO 15189:2012 Medical laboratories — Particular requirements for quality and competence: This International Standard is for use by medical laboratories in developing their quality management systems and assessing their own competence, and for use by accreditation bodies in confirming or recognising the competence of medical laboratories. While this International Standard is intended for use throughout the currently recognised disciplines of medical laboratory services, those working in other services and disciplines could also find it useful and appropriate.
ISO 17511:2003 In vitro diagnostic medical devicesISO 17511:2003ISO 17511:2003 In vitro diagnostic medical devices -- Measurement of quantities in biological samples -- Metrological traceability of values assigned to calibrators and control materials: For measurements of quantities in laboratory medicine, it is essential that the quantity is adequately defined and that the results reported to the physicians or other health care personel and patients are adequately accurate (true and precise) to allow correct medical interpretation and comparability over time and space.
ISO 9001:2015 Quality management systems - requirementsISO 9001:2015ISO 9001:2015 Quality management systems - requirements: The adoption of a quality management system is a strategic decision for an organization that can help to improve its overall performance and provide a sound basis for sustainable development initiatives. Consistently meeting requirements and addressing future needs and expectations poses a challenge for organizations in an increasingly dynamic and complex environment. To achieve this objective, the organization might find it necessary to adopt various forms of improvement in addition to correction and continual improvement, such as breakthrough change, innovation and re-organization.
ISO/IEC 17025:2005 Competence of testing and calibration laboratoriesISO/IEC 17025:2005ISO/IEC 17025:2005 General requirements for the competence of testing and calibration laboratories: The use of this International Standard will facilitate cooperation between laboratories and other bodies, and assist in the exchange of information and experience, and in the harmonization of standards and procedures. This International Standard specifies the general requirements for the competence to carry out tests and/or calibrations, including sampling. It covers testing and calibration performed using standard methods, non-standard methods, and laboratory-developed methods.
ISO/IEC 17043:2010 General requirements for proficiency testingISO/IEC 17043:2010ISO/IEC 17043:2010 Conformity assessment — General requirements for proficiency testing: The use of interlaboratory comparisons is increasing internationally. This International Standard provides a consistent basis to determine the competence of organizations that provide proficiency testing.
Improvement scoreRISThe relative improvement score, RIS, provides a measure of improvement of a trait from a value measured at baseline, B, to a value measured after treatment, T, expressing the total improvement, T-B, in relation to the theoretical scope of improvement and the level of the trait observed at baseline. RIS incorporates the concept of diminishing returns and consideres maintaining a high value of a trait as an improvement relative to the potential loss.
In vitro diagnostic medical deviceIVDA medical device is an in vitro diagnostic medical device (IVD) if it is a reagent, calibrator, control material, kit, specimen receptacle, software, instrument, apparatus, equipment or system, whether used alone or in combination with other diagnostic goods for in vitro use.
Intended useIntended use or Intended purpose is the objective intend of a medical device manufacturer regarding the use of a product, process or service as it is documented by the manufacturer.
Interlaboratory comparisonAn interlaboratory comparison is the organization, performance and evaluation of measurements or tests on the same or similar items by two or more laboratories in accordance with predetermined conditions.
LinearityLinearity is the ability of the method to produce test results that are proportional, either directly or by a well-defined mathematical transformation, to the concentration of the analyte in samples within a given range. This property is inherent in the Beer-Lambert law for absorbance alone, but deviations occur in scattering media. It is also a property of fluorescence, but a fluorophore may not exhibit linearity, particularly over a large range of concentrations.
Measurement processA measurement process or a measurement is a set of operations to determine the value of a quantity.
Measuring equipmentA measuring equipment is a measuring instrument, software, measurement standard, reference material or auxiliary apparatus, or a combination thereof, necessary to realize a measurement process.
Medical deviceA medical device is an instrument, apparatus, implement, machine, contrivance, implant, in vitro reagent, or other similar or related article, including a component part, or accessory which is:
  • intended for use in the diagnosis of disease or other conditions, or in the cure, mitigation, treatment, or prevention of disease, in man or other animals, or
  • intended to affect the structure or any function of the body of man or other animals, and which does not achieve any of its primary intended purposes through chemical action within or on the body of man or other animals and which is not dependent upon being metabolized for the achievement of any of its primary intended purposes.
MetrologyMetrology is the science of measurement, including all aspects both theoretical and practical with reference to measurements, whatever their uncertainty, and in whatever fields of science or technology they occur [SOURCE: VIM:1993, 2.2].
ModelA model regarding databases is the representation of a real world object in a computer understandable language. A model can be defined by the structure of its dataset and the relations to other models.
National Standards BodyA National Standards Body is the national member of the International Organization for Standardization (ISO).
NoiseIn fluorometry and spectrophotometry, noise can be attributed to the statistical nature of the photon emission from a light source and the inherent noise in the instrument’s electronics. The former causes problems in measurements involving samples of analytes with a low extinction coefficient and present only in low concentrations. The latter becomes problematic with high absorbance samples where the light intensity emerging from the sample is very small.
NormA norm is a rule that is enforced by members of a community.
Notified BodyA Notified Body is an organisation designated by an EU country to assess the conformity of certain products before being placed on the market.
OutlierAn outlier is a member of a set of values which is inconsistent with other members of that set. An outlier can arise by chance from the expected population, originate from a different population, or be the result of an incorrect recording or other blunder. Many schemes use the term outlier to designate a result that generates an action signal. This is not the intended use of the term. While outliers will usually generate action signals, it is possible to have action signals from results that are not outliers [SOURCE: ISO 5725‑1:1994, modified].
OverfittingOverfitting in statistics is the act of mistaking noise for a signal. Overfitting makes a model look ‘’better’’ on paper but perform ‘’worse’’ in the real world. This may make it easier to get the model published in an academic journal or to sell to a client, crowding out more honest models from the marketplace. But if the model is fitting noise, it has the potential to hurt the science (quoted from Silver 2012 Penguin Press).
PopulationA population (or group) defines the sample type of an experiment, before sample preparation. The population (or group) size represents the upper limit of the sample size, N.
Post-examination proceduresPost-examination procedures, in the postanalytical phase, are processes following the examination including systematic review, formatting and interpretation, authorization for release, reporting and transmission of the results, and storage of samples of the examinations.
Pre-examination proceduresPre-examination procedures, in the preanalytical phase, are steps starting, in chronological order, from the clinician’s request and including the examination requisition, preparation of the patient, collection of the primary sample, and transportation to and within the laboratory, and ending when the analytical examination procedure begins.
PrecisionPrecision of measurement is the closeness of agreement between independent results of measurements obtained under stipulated conditions [SOURCE: ISO 3534-1:1993, 3.14]. Precision of measurement cannot be given a numerical value in terms of the measurand, only descriptions such as 'sufficient' or 'insufficient' for a stated purpose. The degree of precision is usually expressed numerically by the statistical measures of imprecision of measurements, such as standard deviation and coefficient of variation, that are inversely related to precision. "Precision" of a given measurement procedure is subdivided according to the specified precision conditions. "Repeatability" relates to essentially unchanged conditions and is often termed "withinserial" or "within-run precision". "Reproducibility" relates to changes in conditions, e.g. time, different laboratories, operators, and measuring systems (including different calibrations and reagent batches).
Primary sampleThe primary sample or specimen is a set of one or more parts initially taken from an object. In some countries, the term “specimen” is used instead of primary sample (or a subsample of it), which is the sample prepared for sending to, or as received by, the laboratory and which is intended for examination.
Proficiency testProficiency testing is an evaluation of participant performance against pre-established criteria by means of interlaboratory comparisons. Some providers of proficiency testing in the medical area use the term “External Quality Assessment (EQA)” for their proficiency testing schemes, or for their broader programmes, or both.
ProjectA scientific project is a collection of experiments designed to proof or disproof a specific hypothesis. The experiments will follow the logic of the scientific discovery [1] on which a hypothesis will support a prediction and this will be tested by experimental assays (i.e., observations under controlled conditions). The result of these experiments will proof or disproof the specific hypothesis and, usually, provide new hypotheses to test. A scientific project must be carefully designed to obtain relevant statistical information through enough data collection. [1] Popper K (2002) The logic of scientific discover. Routledge Classics. ISBN: 978-0-415-27843-0
Publicly deposited protocolsPDPResearchers need to be introduced into adhering to publicly deposited protocols. Prespecified and time-stamped protocols that are publicly deposited may help to save Millions of Euros that may otherwise be wasted on research that is lacking coherent standards.
Quality auditA Quality Audit is the process of systematic examination of a quality system carried out by an internal or external quality auditor or an audit team.
QuantityA quantity is the attribute of a phenomenon, body or substance that may be distinguished qualitatively and determined quantitatively.
Reference materialRMReference material (RM) is material or substance one or more of whose property values are sufficiently homogeneous and well established to be used for the calibration of an apparatus, the assessment of a measurement procedure, or for assigning values to materials (adapted from VIM: 1993, 6.13). The adjective 'homogeneous' refers to the physical homogeneity between macroscopic parts of the material, not to any microheterogeneity between molecules of the analyte. Primary reference material is reference material having the highest metrological qualities and whose value is determined by means of a primary reference measurement procedure. The concept "primary calibrator" is subordinate to "calibrator" (see 3.7) and to "primary reference material".
RepetitionsnRepetitions of an experiment or assay are designed to obtain statistical information on the methodological precision of the measurements. A number of repetitions, n, of measurements are performed on the same sample, applying an identical experimental protocol to subsamples, without providing any information on variability between samples.
ReplicaNReplica are designed in scientific studies to evaluate the effect of uncontrolled variability on a result obtained from an experiment on a single sample, to describe the variability and distribution of experimental results, and to obtain statistical information such as the median or average for a defined sample size. It may be useful to make a terminological distinction between replica of experiments, N, designed to obtain statistical information on the population, and repetitions of experiments or assays, n, designed to obtain statistical information on the methodological precision of the measurements. The terms study, experiment and assay have to be defined carefully in this context.
Reproducibility crisisAn experiment or study is reproducible or replicable when subsequent experiments confirm the results. This is re-search. However, we can define different types of reproducibility depending on the conditions that we use to replicate the previous work or in the information available. Our aim is to focus mostly on two different kinds1:

1. Direct: Is when we obtaining the same results using the same experimental conditions, materials, and methods as described in the original experiment. This would be the ideal reproducibility of an experiment however, it requires a very accurate description of how the original experiment was performed. Some journals are trying to resolve the reproducibility crisis improving the rigor and the excellence on the reported methods and results (e.g. STAR Methods in Cell Press).

2. Systematical: Refers to obtaining the same results, but under different conditions; for example, using another cell line or mouse strain, or inhibiting a gene pharmacologically instead of genetically. This open the door to subsequent studies to find the conditions under which an initial finding holds.

But, is there a reproducibility crisis? According to a survey conducted by Nature2 of 1,576 researchers, "52% agree that there is a significant 'crisis' of reproducibility, less than 31% think that failure to reproduce published results means that the result is probably wrong, and most say that they still trust the published literature" (Baker 2016). Chemistry and biology are the subjects with the highest share of failed attempts of reproduction of results.

Asking the researchers for the causes of this inability to reproduce published results, the top three answers are:

  • Selective reporting
  • Publication pressure
  • Low statistical power and poor analysis

The top three mentioned countermeasures are:

  • Better understanding of statistics
  • Better mentoring and supervision
  • More robust design
RequirementA requirement is a singular documented physical or functional need that a particular design, product or process must be able to perform.
ResearchResearch is a term composed of search and re. What does this tell us? The best comparison of the English with a German word is Untersuchung, composed of suchung (search) and unter (below). The term search (suchen) is straightforward to understand and comparable in both languages. The prefix re and unter are more difficult to reconcile, yet in both languages these perfixes reveal complementary if not nearly identical messages. re means {Quote} back to the original place; again, anew, once more {end of Quote} [1], whereas unter means below or underneath. Re-search, therefore, is not simply the search or investigation of some topic or problem, it means essentially doing the search again and again (re -> re-producibility) and penetrating below a simple search by reaching out for an underlying level of the search. The re in re-search and re-producibility has to be extended ultimately from a single re-search group to inter-laboratory re-investigation. This tells us, therefore, that while search is valuable, re-search provides the necessary validation. This re-evaluation of confirmative re-search should be re-cognized as the most important strategy to address the reproducibility crisis.
ResolutionSpectral resolution is a measure of the ability of an instrument to differentiate between two adjacent wavelengths. Two wavelengths are normally considered to be resolved if the minimum detector output signal (trough) between the two peaks is lower than 80% of the maximum. The resolution of a spectrofluorometer or spectrophotometer is dependent on its bandwidth.
Risk managementRisk management is the identification, assessment, and prioritization of risks.
SampleA sample is one or more parts taken from a system and intended to provide information on the system, often to serve as a basis for evaluation of the system (diagnosis) or for a decision on intervention (therapy, production process). Compare: Primary sample.
Sample sizeNThe sample size, N, is the number of samples collected and assayed to obtain a representative statistical information on the population. The population size defines the upper limit of the sample size.
Sample typeAn experimental sample type is the object of an experiment. A sample type is defined by the specifications of the population and by a specific sample preparation (see MitoPedia: Sample preparations).
SelectivitySelectivity is the ability of a sensor or method to quantify accurately and specifically the analyte or analytes in the presence of other compounds.
SensitivitySensitivity 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.
SmoothingVarious 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.
Solution protocolsSolution protocols contain media, substrates, uncouplers, inhibitors used in SUIT protocols, permeabilization agents, etc.
StabilityStability 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.
Stand alone applicationA Stand alone application is computer software that can work offline, i.e. does not necessarily require network connection to function or does not even provide the possibility to connect to a network.
StandardA standard is an established norm or requirement in regard to a defined system. It can consist of a formal document that establishes uniform criteria, methods, processes and practices. See also Harmonized standard.
Standard operating proceduresSOPStandard operating procedures are a set of step-by-step instructions to achieve a predictable, standardized, desired result often within the context of a longer overall process.
SubsamplenSubsamples can be obtained (1) from a homogenous sample (e.g. cell suspension, tissue homogenate, isolated mitochondria), (2) as subsamples obtained by splitting a sample into comparable parts (e.g. permeabilized muscle fibres from a biopsy split into different chambers for repeated measurements), or (3) repetitive sampling (e.g. taking multiple biopsies) at a single time point. Subsamples may be used for (i) application of different types of assay (e.g. for measurement of respiration and enzyme activities), and (ii) a number of repetitions, n, of the same assay on the same sample.
Time resolutionTime 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.
TraceabilityTraceability is the property of the result of a measurement or the value of a standard whereby it can be related to stated references, usually national or international standards, through an unbroken chain of comparisons all having stated uncertainties [SOURCE: VIM:1993, definition 6.10].
Trueness of measurementTrueness of measurement is the closeness of agreement between the average value obtained from a large series of results of measurements and a true value (adapted from ISO 3534-1:1993, definition 3.12). The degree of trueness is usually expressed numerically by the statistical measure bias that is inversely related to trueness and is the difference between the expectation of the results of measurement and a true value of the measurand.
Uncertainty of measurementUncertainty of measurement is a parameter, associated with the result of a measurement, that characterizes the dispersion of the values that could reasonably be attributed to the measurand. The parameter can be, for example, a standard deviation (or a given multiple of it), or the half-width of an interval having a stated level of confidence. The components of uncertainty are evaluated experimentally from statistical distributions (Type A) or evaluated from assumed probability distributions based on experience or other information (Type B). All components are expressed as standard uncertainties that are combined into one final expression.
Web applicationA Web application is a computer software where the user interface gets accessed by the user through a web browser.
Working measurement standardA working measurement standard is a standard that is used routinely to calibrate or check material measures, measuring instruments or reference materials [SOURCE: VIM:1993, 6.7].
Quality management

MitoPedia terms and definitions: Oroboros Quality Management

TermAbbreviationDescription
Air calibrationR1Air calibration of an oxygen sensor (polarographic oxygen sensor) is performed routinely on any day before starting a respirometric experiment. The volume fraction of oxygen in dry air is constant. An aqueous solution in equilibrium with air has the same partial pressure as that in water vapour saturated air. The water vapour is a function of temperature only. The partial oxygen pressure in aqueous solution in equilibrium with air is, therefore, a function of total barometric pressure and temperature. Bubbling an aqueous solution with air generates deviations from barometric pressure within small gas bubbles and is, therefore, not recommended. To equilibrate an aqueous solution ata known partial pressure of oxygen [kPa], the aqueous solution is stirred rigorously in a chamber enclosing air at constant temperature. The concentration of oxygen, cO2 [µM], is obtained at any partial pressure by multiplying the partial pressure by the oxygen solubility, SO2 [µM/kPa]. SO2 is a function of temperature and composition of the salt solution, and is thus a function of the experimental medium. The solubility factor of the medium, FM, expresses the oxygen solubility relative to pure water at any experimental temperature. FM is 0.89 in serum (37 °C) and 0.92 in MiR06 or MiR05 (30 °C and 37 °C).
DatLab oxygen flux: performance and data analysisThe quality of the results are strongly affected by the performance and data analysis. Therefore, we provide guidelines for performing and evaluating respirometric assays.
MitoFit protocolsMitoFit protocols are moderated by the MitoFit moderators (MitoFit team), either as protocols with direct reference to publications available to the scientific communicty, or protocols additionally described and made available in Bioblast with full information on authors (including contact details), author contributions, and editor (moderator) in charge. This is part of the MitoFit Quality Control System for establishing a comprehensive MitoFit data repository, which will require global input and cooperation.
MitoFit registered projectMitoFit-RPMitoFit registered projects are announced in the MitoFit Quality Control System with reference to MitoFit protocols, which are considered to be publicly deposited protocols. Project registration is a two-phase process. Guidelines will be defined. (1) Pre-registration of a project requires submission to a MitoFit moderator (editor), including protocol details with reference to MitoPedia protocols, or with submission of protocols for publication (Open Access) in MitoPedia. The MitoFit (Bioblast) editors will edit the submitted protocols (layout) and insert into Bioblast submitted pre-registrations and protocols. (2) MitoFit moderators (editors) will set up a MitoFit accreditation panel, in which the registrant will be included (perhaps not in the long run, to avoid conflict of interests) and/or for which the registrant can suggest delegates (compare peer review). Accredited MitoFit protocols are labelled as MitoFit accredited, and the pre-registered MitoFit project becomes labelled and listed as MitoFit registered project (MitoFit accredited). This is possible before (advance registration), during progress, and after completion of a study (post-registration). A MitoFit registered project receives a code for feeding data into the MitoFit data repository.
Outlier index - DatLabOIAn outlier index (OI) is defined for DatLab analysis, derived from Pearson’s coefficient of skewness, but more specific in targeting outliers in data series recorded with the O2k. At the limit of a zero value, Y = ABS(Average + Median)/2, the OI equals Pearson’s coefficient of skewness #2 (without the multiplication factor of 3). At high Y with small standard deviation (SD), the outlier index is effectively the difference between the Average and the Median normalized for the absolute value, (Average-Median)/Y. The definition of the outlier index is,
OI = (Average-Median)/(Y + SD)
OI = (Average-Median)/[ABS(Average+Median)/2 + SD]

By comparison,

Pearson’s coefficient of skewness #2 = 3 x (Average-Median)/SD
The threshold of the absolute value of the OI is set at 0.05. If ABS(OI)>0.05 calculated for the data points within a defined Mark, the Mark window indicates the likely occurrence of outliers in the data sequence. The threshold can be set to a lab-specific or session-specific value different from the default value.
Oxygen flux - instrumental backgroundJ°O2Instrumental background oxygen flux, J°O2, in a respirometer is due to oxygen consumption by the POS, and oxygen diffusion into or out of the aqueous medium in the O2k-Chamber. It is a property of the instrumental system, measured in the range of experimental oxygen levels by a standardized instrumental background test. The oxygen regime from air saturation towards zero oxygen is applied generally in experiments with isolated mitochondria and living or permeabilized cells. To overcome oxygen diffusion limitation in permeabilized fibers and homogenates, an elevated oxygen regime is applied, requiring instrumental background test in the same range of elevated oxygen.
Oxygen sensor testPOS testThe O2 sensor test is an important component of the MitoFit Quality Control System. The OroboPOS sensor test is described in detail in MiPNet06.03 POS-calibration-SOP, is performed after switching on the Oroboros O2k, and is required as a basis of technical service of the instrument.
Standard operating proceduresSOPStandard operating procedures are a set of step-by-step instructions to achieve a predictable, standardized, desired result often within the context of a longer overall process.