| Compound Name |
Compound |
name |
|
The compound name that is commonly used in the laboratory (e.g. "glucose", "C16:0") |
|
|
| Compound Formula |
Compound |
formula |
|
The molecular formula of the compound (e.g. "C6H12O6", "C16H32O2") |
|
|
| HMDB Accession |
Compound |
hmdb_id |
|
A unique identifier for this compound in the Human Metabolome Database |
|
|
| Compound Synonyms |
Compound |
name |
|
Synonyms for the Compound Name found in uploaded raw data or predicted from HMDB. |
|
|
| PeakGroup Name |
PeakGroup |
name |
Detected Compound |
The compound or isomer group name (e.g. "citrate/isocitrate", "glucose") |
|
|
| Measured Compound |
|
|
|
The Compound Name for this PeakGroup or PeakData row |
|
|
| PeakGroup Formula |
PeakGroup |
formula |
|
The molecular formula of the compound (e.g. "C6H12O6") |
|
|
| Total Abundance |
PeakGroup |
total_abundance |
Total Ion Count (tic), Pool Size (AccuCor) |
Sum of the corrected abudance of all PeakData for this PeakGroup (when multiple elements are detected, this includes all combinations of elements) |
|
|
| Enrichment Fraction |
PeakGroup |
enrichment_fraction |
|
A weighted average of the fraction of labeled atoms for this PeakGroup in this Sample (i.e. the fraction of carbons are labeled in this PeakGroup compound). Calculated on a per-element basis (e.g. "C" enrichment and "N" enrichment are independent of each other). Sum of all (PeakData.fraction * PeakData.labeled_count) / PeakGroup.Compound.num_atoms(PeakData.labeled_element) |
|
|
| Enrichment Abundance |
PeakGroup |
enrichment_abundance |
|
The abundance of labeled atoms in this compound, on a per-element basis. PeakGroup.total_abundance * PeakGroup.enrichment_fraction |
|
|
| Normalized Labeling |
PeakGroup |
normalized_labeling |
|
The enrichment in this compound normalized to the enrichment in the tracer compound from the final serum timepoint. ThisPeakGroup.enrichment_fraction / SerumTracerPeakGroup.enrichment_fraction |
|
|
| Labeled Element |
PeakData |
labeled_element |
|
The type of element that is labeled in this observation (e.g. "C", "H", "O") |
|
|
| Labeled Count |
PeakData |
labeled_count |
C_Label (AccuCor) |
The number of labeled atoms (M+) observed relative to the presumed compound referred to in the peak group |
|
|
| Labeled Element:Count |
PeakData |
|
|
Combination of Labeled Element and Labeled Element Count for this peak (e.g. "C:1" indicates labeled element is Carbon and labeled element count is 1) (e.g. "C:2; N:1" indicates labeled carbon count is 2 and labeled nitrogen count is 1) |
|
|
| Raw Abundance |
PeakData |
raw_abudance |
|
The ion count of this observation before correction for natural isotope abundance |
|
|
| Corrected Abundance |
PeakData |
corrected_abundance |
|
The ion counts corrected for natural abundance of isotopomers |
|
|
| Fraction |
PeakData |
fraction |
Normalized (AccuCor) |
The corrected abundance of this peak in PeakData as a fraction of the total abundance of all peaks in this group. This differs "Enrichment Fraction" (PeakGroup): Fraction does not account for the number of labeled atoms or distinguish by the type of Labeled Element. |
|
|
| Median M/Z |
PeakData |
med_mz |
|
The median mass/charge value of this measurement |
|
|
| Median RT |
PeakData |
med_rt |
|
The median retention time value of this measurement |
|
|
| MSRunSequence Date |
MSRunSequence |
date |
|
The date that the mass spectrometer was run |
|
|
| MSRunSequence Owner |
MSRunSequence |
researcher |
|
The name of the researcher who ran the mass spectrometer |
|
|
| Protocol Name |
Protocol |
name |
|
Unique name of the protocol |
|
|
| Procotol Description |
Protocol |
description |
|
Full text of the protocol's methods |
|
|
| Protocol Category |
Protocol |
category |
|
Classification of the protocol (e.g. an animal treatment or mass spec procedure) |
|
|
| Sample Name |
Sample |
name |
|
The unique name of the biological sample |
|
|
| Sample Date |
Sample |
date |
Date Collected |
The date the sample was collected |
|
|
| Sample Owner |
Sample |
researcher |
|
The name of the researcher who prepared the sample (e.g. "Alex Medina"), designated as the person who was responsible for the animal infusion and sample collection. |
|
|
| Collection Time |
Sample |
time_collected |
|
The time, relative to the start of the infusion, that a sample was extracted from a animal (minutes) |
|
|
| Tissue Name |
Tissue |
name |
|
The laboratory standardized name for this tissue type (e.g. "serum", "brain", "liver") |
|
|
| Animal Name |
Animal |
name |
Animal ID |
A unique name or lab identifier of the source animal for a series of studied samples |
|
|
| Infusate Name |
Animal |
name |
Tracer Cocktail |
A unique name describing the tracer compound or mixture of compounds, including Compound Name, Element Labeled, and concentration (mM) |
|
|
| Tracer Group Name |
Animal |
name |
|
A shorthand / nickname description of a specific infusate mixture (e.g. "BCAAs") |
|
|
| Parent Compound |
|
|
|
Primary Compound Name for a Measured Compound or Tracer Compound |
|
|
| Tracer Compound |
Animal |
tracer_compound |
Infusate |
The compound which was used as the tracer, i.e. the labeled compound that was infused into the animal |
|
|
| Tracer Label |
|
|
|
Description of element and position of labeling in a tracer compound (e.g. "13C2") |
|
|
| Labeled Element |
Animal |
tracer_labeled_atom |
|
The type of element that is labeled in the tracer compound or measured compound (e.g. "C", "H", "O", "N") |
|
|
| Tracer Labeled Count |
Animal |
tracer_labeled_count |
|
The number of labeled atoms (M+) in the tracer compound supplied to this animal |
|
|
| Tracer Infusion Rate |
Animal |
tracer_infusion_rate |
|
The rate of tracer infusion in microliters/min/gram of body weight of the animal (ul/min/g) |
|
|
| Tracer Infusion Concentration |
Animal |
tracer_infusion_concentration |
|
The millimolar concentration of the tracer in the solution that was infused (mM) |
|
|
| Genotype |
Animal |
genotype |
|
The laboratory standardized genotype of the animal. |
|
|
| Body Weight |
Animal |
body_weight |
|
The weight (in grams) of the animal at the time of sample collection |
|
|
| Age |
Animal |
age |
|
The age (in weeks) of the animal at the time of sample collection |
|
|
| Sex |
Animal |
sex |
|
The sex of the animal ("male" or "female") |
|
|
| Diet |
Animal |
diet |
chow |
The feeding descriptor for the animal [e.g. "LabDiet Rodent 5001"], listed as exact identifier where possible |
|
|
| Feeding Status |
Animal |
feeding_status |
Animal State |
The laboratory coded dietary state for the animal (e.g. "fasted", "fed", "refed"). Details can be included in Study Description. |
|
|
| Treatment Name |
Animal |
treatment.name |
|
The laboratory controlled label of the actions taken on an animal |
|
|
| Treatment Category |
Animal |
|
|
|
|
|
| Treatment Description |
Animal |
description |
|
A long form description of the treatment given an animal. May encompass dosing, dose timing, etc. |
|
|
| FCirc Intact |
Fcirc |
|
|
Circulatory Flux of the intact tracer, where any change in labeling pattern from the original tracer compound is counted as an endogenous transformation. (e.g. infusion of 13C3-lactate, using 13C3-lactate / (13C3 + 13C2 + 13C1 + 13C0 lactate). Calculated per element (e.g. infusion of [13C3, 15N1]-alanine has FCirc Intact for "C" and "N" seperately). Reported as nmol/minute/gram body weight |
|
|
| FCirc Average |
Fcirc |
|
|
Circulatory Flux of the intact tracer for a given element, based on average labeling of atoms in the tracer compound (aka "Enrichment Fraction"). Calculated per element (e.g. infusion of [13C3, 15N1]-alanine has FCirc Intact for "C" and "N" seperately. Reported as nmol atom/minute/gram body weight |
|
|
| FCirc Intact per Mouse |
Fcirc |
|
|
FCirc Intact not normalized to animal body weight. Reported as nmol/minute/mouse |
|
|
| FCirc Average per Mouse |
Fcirc |
|
|
FCirc Average not normalized to animal body weight. Reported as nmol atom/minute/mouse |
|
|
| FCirc Ra |
Fcirc |
|
|
Circulatory Flux that excludes the tracer infusion, so that it represents the endogenous rate of appearance of the compound |
|
|
| FCirc Rd |
Fcirc |
|
|
Circulatory Flux that includes the tracer infusion, to that it represents the total rate of disposal of the compound (in this experiment). |
|
|
| Serum Sample |
Fcirc |
|
|
Serum Sample used to calculate Fcirc |
|
|
| Serum Tracer Peak Group (rows) |
Fcirc |
|
|
Toggle in Fcirc table used to include only the "Last" serum sample collected, or also the "Previous" serum samples collected. Fcirc is estimated for each serum sample regardless of when it was collected. |
|
|
| Study Name |
Study |
name |
Experiment Name |
A succinct name for the study, which is a collection of one or more series of animals and their associated data. May include any combination of animals (any conditions, tracers, etc) |
|
|
| Study Description |
Study |
description |
Experiment Description |
A long form description for the study which may include the experimental design process, citations, and other relevant details |
|
|
| Tissue Description |
Animal |
|
|
A long form description of the Tissue, used to clearly define and distinguish between different tissues |
|
|