adninightingale2.Rd
ADMC Nightingale Platform NMR Post-Unblinding Re-Analysis of Lipoproteins and Metabolites
data(adninightingale2)
A data frame with 1697 rows and 277 variables
A dataset with variables as follows:
RID -4 -4 Participant roster ID
VISCODE -4 -4 Visit code
VISCODE2 -4 -4 Translated visit code
EXAMDATE -4 -4 Examination Date
SAMPLEID -4 -4 -4
GLOBAL.SPEC.ID -4 -4 -4
EDTA_PLASMA -4 -4 Detected EDTA anticoagulant. This indicates a EDTA plasma sample. EDTA anticoagulant interferes with the quantification of glycerol, glycine and pyruvate. Also, metabolites may behave differently (mainly in absolute concentration terms, but potentially also in association terms) in serum and EDTA plasma due to the different biological matrices.
CITRATE_PLASMA -4 -4 A non-physiological citrate concentration. This may result from the sample being citrate plasma.
LOW_ETHANOL -4 -4 This arises potentially due to disinfectant contaminations in the blood donation/collection process and/or contamination in air from lab handling, such as cleaning of well-plates. In higher concentrations, ethanol prohibits the quantification of glycerol, and therefore the sample has been flagged with a "TAG", and no concentration has been provided for the sample. In lower concentrations, it may interfere with the reliable quantification of glycerol and result in artificially distorted glycerol levels. We recommend caution when interpreting absolute glycerol concentrations. It is also good to note that high alcohol in the sample might artificially increase the acetate concentration.
MEDIUM_ETHANOL -4 -4 This arises potentially due to disinfectant contaminations in the blood donation/collection process and/or contamination in air from lab handling, such as cleaning of well-plates. In higher concentrations, ethanol prohibits the quantification of glycerol and 3-hydroxybutyrate, and therefore the sample has been flagged with a "TAG", and no concentration has been provided for the sample. In lower concentrations, it may interfere with the reliable quantification of glycerol and 3-hydroxybutyrate and result in artificially distorted glycerol and 3-hydroxybutyrate levels. We recommend caution when interpreting absolute glycerol and 3-hydroxybutyrate concentrations. It is also good to note that high alcohol in the sample might artificially increase the acetate concentration.
HIGH_ETHANOL -4 -4 This arises potentially due to disinfectant contaminations in the blood donation/collection process and/or contamination in air from lab handling, such as cleaning of well-plates. In higher concentrations, ethanol prohibits the quantification of glycerol, 3-hydroxybutyrate and valine, and therefore the sample has been flagged with a "TAG", and no concentration has been provided for the sample. In lower concentrations, it may interfere with the reliable quantification of glycerol, 3-hydroxybutyrate and valine and result in artificially distorted glycerol, 3-hydroxybutyrate and valine levels. We recommend caution when interpreting absolute glycerol, 3-hydroxybutyrate and valine concentrations. It is also good to note that high alcohol in the sample might artificially increase the acetate concentration.
ISOPROPYL_ALCOHOL -4 -4 Isopropyl alcohol signals detected. In higher concentrations, this compound prohibits the quantification of creatinine, and therefore the sample has been flagged with a "TAG", and no concentration has been provided for the sample. In lower concentrations, it may interfere with the reliable quantification of creatinine and result in artificially distorted creatinine levels. We recommend caution when interpreting absolute creatinine concentrations.
N_METHYL_2_PYRROLIDONE -4 -4 A compound that can be used in sample collection processes. In higher concentrations, it prohibits the quantification of glutamine, and therefore the sample has been flagged with a "TAG", and no concentration has been provided for the sample. In lower concentrations, it may interfere with the reliable quantification of glutamine and result in artificially distorted glutamine levels. We recommend caution when interpreting absolute glutamine concentrations.
POLYSACCHARIDES -4 -4 Polysaccharide or some other type of carbohydrate signals detected. Most commonly observed along with other signs of suboptimal sample quality, but may also indicate presence of heparin. In higher concentrations, this compound prohibits the quantification of creatinine, and therefore the sample has been flagged with a "TAG", and no concentration has been provided for the sample. In lower concentrations, it may interfere with the reliable quantification of creatinine and result in artificially distorted creatinine levels. We recommend caution when interpreting absolute creatinine concentrations.
AMINOCAPROIC_ACID -4 -4 Aminocaproic acid detected in the sample; this compound is an antifibrinolytic agent. In higher concentrations, it prohibits the quantification of acetone, and therefore the sample has been flagged with a "TAG", and no concentration has been provided for the sample.
LOW_GLUCOSE -4 -4 Low glucose is tagged since the physiological concentration is commonly well controlled, particularly in the low concentration end. However, glucose is metabolised to pyruvate and lactate if the blood sample is kept with the cells during the sample collection process, in particular at room temperature but also to some extent at fridge temperature. The low glucose tag thus commonly reflects extended time periods prior to preparation to serum/plasma. As a result of the glycolysis, high lactate and/or high pyruvate is commonly observed along with low glucose levels.
HIGH_LACTATE -4 -4 Low glucose is tagged since the physiological concentration is commonly well controlled, particularly in the low concentration end. However, glucose is metabolised to pyruvate and lactate if the blood sample is kept with the cells during the sample collection process, in particular at room temperature but also to some extent at fridge temperature. The low glucose tag thus commonly reflects extended time periods prior to preparation to serum/plasma. As a result of the glycolysis, high lactate and/or high pyruvate is commonly observed along with low glucose levels.
HIGH_PYRUVATE -4 -4 Low glucose is tagged since the physiological concentration is commonly well controlled, particularly in the low concentration end. However, glucose is metabolised to pyruvate and lactate if the blood sample is kept with the cells during the sample collection process, in particular at room temperature but also to some extent at fridge temperature. The low glucose tag thus commonly reflects extended time periods prior to preparation to serum/plasma. As a result of the glycolysis, high lactate and/or high pyruvate is commonly observed along with low glucose levels.
LOW_GLUTAMINE_OR_HIGH_GLUTAMATE -4 -4 In these samples most of the glutamine appears to have degraded into glutamate. This can take place, e.g. during the sample collection process, if the sample is kept at room temperature for a prolonged period of time, there are multiple freeze-thaw cycles, or there are oxidative conditions / oxidation occurs in the sample. In these samples glutamine is not quantified. In higher concentrations, glutamate prohibits the quantification of pyruvate, and therefore the sample has been flagged with a "TAG", and no concentration has been provided for the sample. In lower concentrations, glutamate may interfere with the reliable quantification of pyruvate and result in artificially distorted pyruvate levels. We recommend caution when interpreting absolute pyruvate concentrations.
GLUCONOLACTONE -4 -4 Gluconolactone is an oxidation product of glucose and is not normally detected in samples. Interferes with the quantification of creatinine.
LOW_PROTEIN -4 -4 Unexpected protein features have been identified during the analysis. This quality observation is related to unexpectedly low total protein concentration in the sample and may be an indication of potential sample dilution. Sample dilution may occur due to water contamination, or prolonged storage in freezer in combination with loosely closed tube caps, which exposes the sample to collect ice and increases the chances of dilution.In case there is reason to assume sample dilution, we recommend caution when analyzing absolute concentrations.
UNEXPECTED_AMINO_ACID_SIGNALS -4 -4 These are signals that we do not typically observe in normal samples. It is likely that they relate to protein breakage due to non optimal storage.Interferes with the reliable quantification of citrate and glycerol, and may result in artificially distorted metabolite concentrations.
UNIDENTIFIED_MACROMOLECULES -4 -4 Signals from abnormal macromolecule(s)/protein(s).Interferes with the quantification of phenylalanine, acetate, acetone, glutamine and pyruvate.
UNIDENTIFIED_SMALL_MOLECULE_A -4 -4 Untypical signals from unknown small molecule(s); potentially xenobiotics.
UNIDENTIFIED_SMALL_MOLECULE_B -4 -4 Untypical signals from unknown small molecule(s); potentially xenobiotics. Interferes with the quantification of acetate.
UNIDENTIFIED_SMALL_MOLECULE_C -4 -4 Unidentified signals at 2.27 ppm and various other spectral areas. Interferes with the reliable quantification of albumin, creatinine, glycerol, glycine and acetone.
BELOW_LIMIT_OF_QUANTIFICATION -4 -4 Below Limit-Of-Quantification (LOQ) means that the concentration of the given biomarker is smaller than the range where the Nightingale platform offers highly accurate quantification. For instance, the LOQ for lipoprotein lipid measures is < 0.01 mmol/L. The estimated biomarker concentration is reported for use in certain epidemiological analyses, but it may be advisable to conduct sensitivity analyses with all values below LOQ excluded.
TOTAL_C -4 mmol/l Total cholesterol
NON_HDL_C -4 mmol/l Total cholesterol minus HDL-C
REMNANT_C -4 mmol/l Remnant cholesterol (non-HDL, non-LDL -cholesterol)
VLDL_C -4 mmol/l VLDL cholesterol
CLINICAL_LDL_C -4 mmol/l Clinical LDL cholesterol
LDL_C -4 mmol/l LDL cholesterol
HDL_C -4 mmol/l HDL cholesterol
TOTAL_TG -4 mmol/l Total triglycerides
VLDL_TG -4 mmol/l Triglycerides in VLDL
LDL_TG -4 mmol/l Triglycerides in LDL
HDL_TG -4 mmol/l Triglycerides in HDL
TOTAL_PL -4 mmol/l Total phospholipids in lipoprotein particles
VLDL_PL -4 mmol/l Phospholipids in VLDL
LDL_PL -4 mmol/l Phospholipids in LDL
HDL_PL -4 mmol/l Phospholipids in HDL
TOTAL_CE -4 mmol/l Total esterified cholesterol
VLDL_CE -4 mmol/l Cholesteryl esters in VLDL
LDL_CE -4 mmol/l Cholesteryl esters in LDL
HDL_CE -4 mmol/l Cholesteryl esters in HDL
TOTAL_FC -4 mmol/l Total free cholesterol
VLDL_FC -4 mmol/l Free cholesterol in VLDL
LDL_FC -4 mmol/l Free cholesterol in LDL
HDL_FC -4 mmol/l Free cholesterol in HDL
TOTAL_L -4 mmol/l Total lipids in lipoprotein particles
VLDL_L -4 mmol/l Total lipids in VLDL
LDL_L -4 mmol/l Total lipids in LDL
HDL_L -4 mmol/l Total lipids in HDL
TOTAL_P -4 mmol/l Total concentration of lipoprotein particles
VLDL_P -4 mmol/l Concentration of VLDL particles
LDL_P -4 mmol/l Concentration of LDL particles
HDL_P -4 mmol/l Concentration of HDL particles
VLDL_SIZE -4 nm Average diameter for VLDL particles
LDL_SIZE -4 nm Average diameter for LDL particles
HDL_SIZE -4 nm Average diameter for HDL particles
PHOSPHOGLYC -4 mmol/l Phosphoglycerides
TG_BY_PG -4 ratio Ratio of triglycerides to phosphoglycerides
CHOLINES -4 mmol/l Total cholines
PHOSPHATIDYLC -4 mmol/l Phosphatidylcholines
SPHINGOMYELINS -4 mmol/l Sphingomyelins
APOB -4 g/l Apolipoprotein B
APOA1 -4 g/l Apolipoprotein A1
APOB_BY_APOA1 -4 ratio Ratio of apolipoprotein B to apolipoprotein A1
TOTAL_FA -4 mmol/l Total fatty acids
UNSATURATION -4 degree Degree of unsaturation
OMEGA_3 -4 mmol/l Omega-3 fatty acids
OMEGA_6 -4 mmol/l Omega-6 fatty acids
PUFA -4 mmol/l Polyunsaturated fatty acids
MUFA -4 mmol/l Monounsaturated fatty acids
SFA -4 mmol/l Saturated fatty acids
LA -4 mmol/l Linoleic acid
DHA -4 mmol/l Docosahexaenoic acid
OMEGA_3_PCT -4
OMEGA_6_PCT -4
PUFA_PCT -4
MUFA_PCT -4
SFA_PCT -4
LA_PCT -4
DHA_PCT -4
PUFA_BY_MUFA -4 ratio Ratio of polyunsaturated fatty acids to monounsaturated fatty acids
OMEGA_6_BY_OMEGA_3 -4 ratio Ratio of omega-6 fatty acids to omega-3 fatty acids
ALA -4 mmol/l Alanine
GLN -4 mmol/l Glutamine
GLY -4 mmol/l Glycine
HIS -4 mmol/l Histidine
TOTAL_BCAA -4 mmol/l Total concentration of branched-chain amino acids (leucine + isoleucine + valine)
ILE -4 mmol/l Isoleucine
LEU -4 mmol/l Leucine
VAL -4 mmol/l Valine
PHE -4 mmol/l Phenylalanine
TYR -4 mmol/l Tyrosine
GLUCOSE -4 mmol/l Glucose
LACTATE -4 mmol/l Lactate
PYRUVATE -4 mmol/l Pyruvate
CITRATE -4 mmol/l Citrate
GLYCEROL -4 mmol/l Glycerol
BOHBUTYRATE -4 mmol/l 3-Hydroxybutyrate
ACETATE -4 mmol/l Acetate
ACETOACETATE -4 mmol/l Acetoacetate
ACETONE -4 mmol/l Acetone
CREATININE -4 ?mol/l Creatinine
ALBUMIN -4 g/l Albumin
GLYCA -4 mmol/l Glycoprotein acetyls
XXL_VLDL_P -4 mmol/l Concentration of chylomicrons and extremely large VLDL particles
XXL_VLDL_L -4 mmol/l Total lipids in chylomicrons and extremely large VLDL
XXL_VLDL_PL -4 mmol/l Phospholipids in chylomicrons and extremely large VLDL
XXL_VLDL_C -4 mmol/l Cholesterol in chylomicrons and extremely large VLDL
XXL_VLDL_CE -4 mmol/l Cholesteryl esters in chylomicrons and extremely large VLDL
XXL_VLDL_FC -4 mmol/l Free cholesterol in chylomicrons and extremely large VLDL
XXL_VLDL_TG -4 mmol/l Triglycerides in chylomicrons and extremely large VLDL
XL_VLDL_P -4 mmol/l Concentration of very large VLDL particles
XL_VLDL_L -4 mmol/l Total lipids in very large VLDL
XL_VLDL_PL -4 mmol/l Phospholipids in very large VLDL
XL_VLDL_C -4 mmol/l Cholesterol in very large VLDL
XL_VLDL_CE -4 mmol/l Cholesteryl esters in very large VLDL
XL_VLDL_FC -4 mmol/l Free cholesterol in very large VLDL
XL_VLDL_TG -4 mmol/l Triglycerides in very large VLDL
L_VLDL_P -4 mmol/l Concentration of large VLDL particles
L_VLDL_L -4 mmol/l Total lipids in large VLDL
L_VLDL_PL -4 mmol/l Phospholipids in large VLDL
L_VLDL_C -4 mmol/l Cholesterol in large VLDL
L_VLDL_CE -4 mmol/l Cholesteryl esters in large VLDL
L_VLDL_FC -4 mmol/l Free cholesterol in large VLDL
L_VLDL_TG -4 mmol/l Triglycerides in large VLDL
M_VLDL_P -4 mmol/l Concentration of medium VLDL particles
M_VLDL_L -4 mmol/l Total lipids in medium VLDL
M_VLDL_PL -4 mmol/l Phospholipids in medium VLDL
M_VLDL_C -4 mmol/l Cholesterol in medium VLDL
M_VLDL_CE -4 mmol/l Cholesteryl esters in medium VLDL
M_VLDL_FC -4 mmol/l Free cholesterol in medium VLDL
M_VLDL_TG -4 mmol/l Triglycerides in medium VLDL
S_VLDL_P -4 mmol/l Concentration of small VLDL particles
S_VLDL_L -4 mmol/l Total lipids in small VLDL
S_VLDL_PL -4 mmol/l Phospholipids in small VLDL
S_VLDL_C -4 mmol/l Cholesterol in small VLDL
S_VLDL_CE -4 mmol/l Cholesteryl esters in small VLDL
S_VLDL_FC -4 mmol/l Free cholesterol in small VLDL
S_VLDL_TG -4 mmol/l Triglycerides in small VLDL
XS_VLDL_P -4 mmol/l Concentration of very small VLDL particles
XS_VLDL_L -4 mmol/l Total lipids in very small VLDL
XS_VLDL_PL -4 mmol/l Phospholipids in very small VLDL
XS_VLDL_C -4 mmol/l Cholesterol in very small VLDL
XS_VLDL_CE -4 mmol/l Cholesteryl esters in very small VLDL
XS_VLDL_FC -4 mmol/l Free cholesterol in very small VLDL
XS_VLDL_TG -4 mmol/l Triglycerides in very small VLDL
IDL_P -4 mmol/l Concentration of IDL particles
IDL_L -4 mmol/l Total lipids in IDL
IDL_PL -4 mmol/l Phospholipids in IDL
IDL_C -4 mmol/l Cholesterol in IDL
IDL_CE -4 mmol/l Cholesteryl esters in IDL
IDL_FC -4 mmol/l Free cholesterol in IDL
IDL_TG -4 mmol/l Triglycerides in IDL
L_LDL_P -4 mmol/l Concentration of large LDL particles
L_LDL_L -4 mmol/l Total lipids in large LDL
L_LDL_PL -4 mmol/l Phospholipids in large LDL
L_LDL_C -4 mmol/l Cholesterol in large LDL
L_LDL_CE -4 mmol/l Cholesteryl esters in large LDL
L_LDL_FC -4 mmol/l Free cholesterol in large LDL
L_LDL_TG -4 mmol/l Triglycerides in large LDL
M_LDL_P -4 mmol/l Concentration of medium LDL particles
M_LDL_L -4 mmol/l Total lipids in medium LDL
M_LDL_PL -4 mmol/l Phospholipids in medium LDL
M_LDL_C -4 mmol/l Cholesterol in medium LDL
M_LDL_CE -4 mmol/l Cholesteryl esters in medium LDL
M_LDL_FC -4 mmol/l Free cholesterol in medium LDL
M_LDL_TG -4 mmol/l Triglycerides in medium LDL
S_LDL_P -4 mmol/l Concentration of small LDL particles
S_LDL_L -4 mmol/l Total lipids in small LDL
S_LDL_PL -4 mmol/l Phospholipids in small LDL
S_LDL_C -4 mmol/l Cholesterol in small LDL
S_LDL_CE -4 mmol/l Cholesteryl esters in small LDL
S_LDL_FC -4 mmol/l Free cholesterol in small LDL
S_LDL_TG -4 mmol/l Triglycerides in small LDL
XL_HDL_P -4 mmol/l Concentration of very large HDL particles
XL_HDL_L -4 mmol/l Total lipids in very large HDL
XL_HDL_PL -4 mmol/l Phospholipids in very large HDL
XL_HDL_C -4 mmol/l Cholesterol in very large HDL
XL_HDL_CE -4 mmol/l Cholesteryl esters in very large HDL
XL_HDL_FC -4 mmol/l Free cholesterol in very large HDL
XL_HDL_TG -4 mmol/l Triglycerides in very large HDL
L_HDL_P -4 mmol/l Concentration of large HDL particles
L_HDL_L -4 mmol/l Total lipids in large HDL
L_HDL_PL -4 mmol/l Phospholipids in large HDL
L_HDL_C -4 mmol/l Cholesterol in large HDL
L_HDL_CE -4 mmol/l Cholesteryl esters in large HDL
L_HDL_FC -4 mmol/l Free cholesterol in large HDL
L_HDL_TG -4 mmol/l Triglycerides in large HDL
M_HDL_P -4 mmol/l Concentration of medium HDL particles
M_HDL_L -4 mmol/l Total lipids in medium HDL
M_HDL_PL -4 mmol/l Phospholipids in medium HDL
M_HDL_C -4 mmol/l Cholesterol in medium HDL
M_HDL_CE -4 mmol/l Cholesteryl esters in medium HDL
M_HDL_FC -4 mmol/l Free cholesterol in medium HDL
M_HDL_TG -4 mmol/l Triglycerides in medium HDL
S_HDL_P -4 mmol/l Concentration of small HDL particles
S_HDL_L -4 mmol/l Total lipids in small HDL
S_HDL_PL -4 mmol/l Phospholipids in small HDL
S_HDL_C -4 mmol/l Cholesterol in small HDL
S_HDL_CE -4 mmol/l Cholesteryl esters in small HDL
S_HDL_FC -4 mmol/l Free cholesterol in small HDL
S_HDL_TG -4 mmol/l Triglycerides in small HDL
XXL_VLDL_PL_PCT -4
XXL_VLDL_C_PCT -4
XXL_VLDL_CE_PCT -4
XXL_VLDL_FC_PCT -4
XXL_VLDL_TG_PCT -4
XL_VLDL_PL_PCT -4
XL_VLDL_C_PCT -4
XL_VLDL_CE_PCT -4
XL_VLDL_FC_PCT -4
XL_VLDL_TG_PCT -4
L_VLDL_PL_PCT -4
L_VLDL_C_PCT -4
L_VLDL_CE_PCT -4
L_VLDL_FC_PCT -4
L_VLDL_TG_PCT -4
M_VLDL_PL_PCT -4
M_VLDL_C_PCT -4
M_VLDL_CE_PCT -4
M_VLDL_FC_PCT -4
M_VLDL_TG_PCT -4
S_VLDL_PL_PCT -4
S_VLDL_C_PCT -4
S_VLDL_CE_PCT -4
S_VLDL_FC_PCT -4
S_VLDL_TG_PCT -4
XS_VLDL_PL_PCT -4
XS_VLDL_C_PCT -4
XS_VLDL_CE_PCT -4
XS_VLDL_FC_PCT -4
XS_VLDL_TG_PCT -4
IDL_PL_PCT -4
IDL_C_PCT -4
IDL_CE_PCT -4
IDL_FC_PCT -4
IDL_TG_PCT -4
L_LDL_PL_PCT -4
L_LDL_C_PCT -4
L_LDL_CE_PCT -4
L_LDL_FC_PCT -4
L_LDL_TG_PCT -4
M_LDL_PL_PCT -4
M_LDL_C_PCT -4
M_LDL_CE_PCT -4
M_LDL_FC_PCT -4
M_LDL_TG_PCT -4
S_LDL_PL_PCT -4
S_LDL_C_PCT -4
S_LDL_CE_PCT -4
S_LDL_FC_PCT -4
S_LDL_TG_PCT -4
XL_HDL_PL_PCT -4
XL_HDL_C_PCT -4
XL_HDL_CE_PCT -4
XL_HDL_FC_PCT -4
XL_HDL_TG_PCT -4
L_HDL_PL_PCT -4
L_HDL_C_PCT -4
L_HDL_CE_PCT -4
L_HDL_FC_PCT -4
L_HDL_TG_PCT -4
M_HDL_PL_PCT -4
M_HDL_C_PCT -4
M_HDL_CE_PCT -4
M_HDL_FC_PCT -4
M_HDL_TG_PCT -4
S_HDL_PL_PCT -4
S_HDL_C_PCT -4
S_HDL_CE_PCT -4
S_HDL_FC_PCT -4
S_HDL_TG_PCT -4
https://adni.bitbucket.io/reference/docs/ADNINIGHTINGALE2/10.1515_ijb-2020-0107.pdf, https://adni.bitbucket.io/reference/docs/ADNINIGHTINGALE2/ADMC_Nightingale_Platform-Methods_Description-2020-update.pdf, https://adni.bitbucket.io/reference/docs/ADNINIGHTINGALE2/Nightingale_2020_quantification.pdf
if (FALSE) { describe(adninightingale2) }