Methods
Key data of our analytical platforms are described below and include PubChem numbers, reported biomarker concentrations, LODs, CVs, ICCs, sample matrix and method description for most of our biomarkers.*
Analytical platforms
- A
- B
- C
- D
- E
- F
- G
- H
- I
Short-chain fatty acids.
GC-MS/MS: 50 µL vol.
All concentrations are reported in µmol/L.
Acetate | Ace | Short-chain fatty acid | 175-176 | 5-300 | s, p |
Butyrate | But | Short-chain fatty acid | 264 | 1-30 | s, p |
Formate | Frm | Short-chain fatty acid | 284 | 8-100 | s, p, csf |
Isobutyrate | iBut | Short-chain fatty acid | 6590 | 0.7-6 | s, p, csf |
Isovalerate | iVlr | Short-chain fatty acid | 10430 | 0.3-3 | s, p |
Propionate | Pro | Short-chain fatty acid | 1042 | 1-13 | s, p |
Valerate | Vlr | Short-chain fatty acid | 7991 | 0.2-1 | s, p |
α-Methylbutyrate | aMB | Short-chain fatty acid | 8314 | 0.3-3 | s, p |
Amino- and carboxylic acids. TCA metabolites and intermediates.
GC-MS/MS: 50 µL vol.
All concentrations are reported in µmol/L.
*Sarcosine cannot be measured in EDTA-tubes from some suppliers because of the presence of sarcosine in these tubes; **BCAA, Branched chain amino acid; ***AGE, Advanced glycation end product.
aXiaofei Yin, Orla Prendiville, Aoife E. McNamara, and Lorraine Brennan. Targeted Metabolomic Approach to Assess the Reproducibility of
Plasma Metabolites over a Four Month Period in a Free-Living Population. J. Proteome Res. 2022, 21, 683−690.
Choline derivatives. Charged, methylated or sulfur amino acids. Short- and medium-chain acylcarnitines.
LC-MS/MS: 35 µL vol.
All concentrations are reported in µmol/L.
*Measured in a separate assay after sample treatment with phospholipase D that does not affect the other metabolites of platform C, which are obtainable; **Measured in a separate assay involving alkaline hydrolysis of acylcarnitines.
aFloegel A, Drogan D, Wang-Sattler R, Prehn C, Illig T, et al. (2011) Reliability of Serum Metabolite Concentrations over a 4-Month Period Using a
Targeted Metabolomic Approach. PLoS ONE 6(6): e21103. doi:10.1371/journal.pone.0021103
Kynurenine pathway and B vitamins (B1, B2, B3, B6).
LC-MS/MS: 60 µL vol.
Folate species and catabolites.
LC-MS/MS: 60 µL vol.
All concentrations are reported in nmol/L.
Folate (B9) and cobalamin (B12).
Microbiological assay: 15-35 µL vol.
Serum folate | s-Folate | B vitamin | >7.5 nmol/L | 2 | 4 | 5 | 0.56 | s, p | |
Erythrocyte folate | e-Folate | B vitamin | >340 nmol/L | e | |||||
Serum cobalamin | s-B12 | B vitamin | >150 pmol/L | 30 | 4 | 5 | 0.82 | s, p |
Protein biomarkers and variants.
MALDI-TOF MS: 30 µL vol.
*Mass interference of S100A and CnC proteoforms; **ICCs of proteoforms are reported here; *** high sensitive CRP (hs-CRP)
Lipid-soluble vitamins and long-chain acylcarnitines.
LC-MS/MS: 50-100 µL vol.
aFloegel A, Drogan D, Wang-Sattler R, Prehn C, Illig T, et al. (2011) Reliability of Serum Metabolite Concentrations over a 4-Month Period Using a
Targeted Metabolomic Approach. PLoS ONE 6(6): e21103. doi:10.1371/journal.pone.0021103
bXiaofei Yin, Orla Prendiville, Aoife E. McNamara, and Lorraine Brennan. Targeted Metabolomic Approach to Assess the Reproducibility of
Plasma Metabolites over a Four Month Period in a Free-Living Population. J. Proteome Res. 2022, 21, 683−690.
Short-, medium- and long-chain acylcarnitines.
LC (HILIC)-MS/MS. This platform is under development.
All concentrations are reported in µmol/L.
Butyrobetaine | BB | Quarternary ammonium | 725 | 0.4-2 | 0.2 | s, p | |
Carnitine | C0 | Carnitine | 288 | 20-80 | 0.5 | 0.76b | s, p |
Acetylcarnitine | C2 | Acylcarnitine | 7045767 | 3-15 | 0.1 | 0.63 | s, p |
Propionylcarnitine | C3 | Acylcarnitine | 107738 | 0.2-1.5 | 0.05 | 0.62 | s, p |
Butyrylcarnitine | C4 | Acylcarnitine | 213144 | 0.1-0.5 | 0.012 | 0.79b | s, p |
Isovalerylcarnitine | iC5 | Acylcarnitine | 6426851 | 0.06-0.2 | 0.05 | 0.68 | s, p |
Hexanoylcarnitine | C6 | Acylcarnitine | 6426853 | 0.01-1.2 | 0.01 | s, p | |
Octanoylcarnitine | C8 | Acylcarnitine | 123701 | 0.06-0.3 | 0.05 | 0.41 | s, p |
Decanoylcarnitine | C10 | Acylcarnitine | 10245190 | 0.2-1 | 0.02 | 0.67b | s, p |
Dodecanoylcarnitine | C12 | Acylcarnitine | 168381 | < 0.4 | 0.02 | s, p | |
Myristoylcarnitine | C14 | Acylcarnitine | 6426854 | 0.01-0.1 | 0.38a | s, p | |
Palmitoylcarnitine | C16 | Acylcarnitine | 461 | 0.05-0.25 | 0.49a | s, p | |
Stearoylcarnitine | C18 | Acylcarnitine | 52922056 | 0.03-0.1 | 0.40a | s, p | |
Oleoylcarnitine | C18:1 | Acylcarnitine | 46907933 | 0.04-0.2 | s, p | ||
Linoleylcarnitine | C18:2 | Acylcarnitine | 6450015 | 0.01-0.1 | s, p |
Targeted Metabolomic Approach. PLoS ONE 6(6): e21103. doi:10.1371/journal.pone.0021103
bXiaofei Yin, Orla Prendiville, Aoife E. McNamara, and Lorraine Brennan. Targeted Metabolomic Approach to Assess the Reproducibility of
Plasma Metabolites over a Four Month Period in a Free-Living Population. J. Proteome Res. 2022, 21, 683−690.
Short-chain fatty acids.
Volume: 50 µL
All concentrations are reported as µmol/L; CVs (%) shown as within-day (Wtn-day) and between-day (Btw-day) variations; sample matrices: serum (s), plasma (p), cerebrospinal fluid (csf).
Acetate | Ace | Short-chain fatty acid | 175-176 | 5-300 | s, p |
Butyrate | But | Short-chain fatty acid | 264 | 1-30 | s, p |
Formate | Frm | Short-chain fatty acid | 284 | 8-100 | s, p, csf |
Isobutyrate | iBut | Short-chain fatty acid | 6590 | 0.7-6 | s, p, csf |
Isovalerate | iVlr | Short-chain fatty acid | 10430 | 0.3-3 | s, p |
Propionate | Pro | Short-chain fatty acid | 1042 | 1-13 | s, p |
Valerate | Vlr | Short-chain fatty acid | 7991 | 0.2-1 | s, p |
α-Methylbutyrate | aMB | Short-chain fatty acid | 8314 | 0.3-3 | s, p |
Amino- and carboxylic acids. TCA metabolites and intermediates. Volume: 50 µL
All concentrations are reported as µmol/L; CVs (%) shown as within-day (Wtn-day) and between-day (Btw-day) variations; sample matrices: serum (s), plasma (p), urine (u).
*Sarcosine cannot be measured in EDTA-tubes from some suppliers because of the presence of sarcosine in these tubes; **BCAA, Branched chain amino acid; ***AGE, Advanced glycation end product.
aXiaofei Yin, Orla Prendiville, Aoife E. McNamara, and Lorraine Brennan. Targeted Metabolomic Approach to Assess the Reproducibility of
Plasma Metabolites over a Four Month Period in a Free-Living Population. J. Proteome Res. 2022, 21, 683−690.
Choline derivatives. Charged, methylated or sulfur amino acids. Short- and medium-chain acylcarnitines.
Volume: 35 µL
All concentrations are reported as µmol/L; CVs (%) shown as within-day (Wtn-day) and between-day (Btw-day) variations; sample matrices: serum (s), plasma (p), urine (u).
*Measured in a separate assay after sample treatment with phospholipase D that does not affect the other metabolites of platform C, which are obtainable; **Measured in a separate assay involving alkaline hydrolysis of acylcarnitines.
Kynurenine pathway and B vitamins (B1, B2, B3, B6).
Volume: 60 µL
All concentrations are reported as µmol/L or nmol/L. CVs (%) shown as within-day (Wtn-day) and between-day (Btw-day) variations; sample matrices: serum (s), plasma (p), urine (u), cerebrospinal fluid (csf).
Folate species and catabolites.
LC-MS/MS: 60 µL vol.
All concentrations are reported as nmol/L. CVs (%) shown as within-day (Wtn-day) and between-day (Btw-day) variations; sample matrices: serum (s), plasma (p).
Folate (B9) and cobalamin (B12).
Microbiological assay: 15-35 µL vol.
All concentrations are reported as nmol/L or pmol/L.
Serum folate | s-Folate | B vitamin | >7.5 nmol/L | 2 | 4 | 5 | 0.56 | s, p | |
Erythrocyte folate | e-Folate | B vitamin | >340 nmol/L | e | |||||
Serum cobalamin | s-B12 | B vitamin | >150 pmol/L | 30 | 4 | 5 | 0.82 | s, p |
Protein biomarkers and variants.
MALDI-TOF MS: 30 µL vol.
All concentrations are reported as µmol/L or %.
*Mass interference of S100A and CnC proteoforms; **ICCs of proteoforms can be found here.
Lipid-soluble vitamins and long-chain acylcarnitines.
LC-MS/MS: 50-100 µL vol.
All concentrations are reported as µmol/L or nmol/L.
aFloegel A, Drogan D, Wang-Sattler R, Prehn C, Illig T, et al. (2011) Reliability of Serum Metabolite Concentrations over a 4-Month Period Using a
Targeted Metabolomic Approach. PLoS ONE 6(6): e21103. doi:10.1371/journal.pone.0021103
bXiaofei Yin, Orla Prendiville, Aoife E. McNamara, and Lorraine Brennan. Targeted Metabolomic Approach to Assess the Reproducibility of
Plasma Metabolites over a Four Month Period in a Free-Living Population. J. Proteome Res. 2022, 21, 683−690.
This platform is under development.
Short-, medium- and long-chain acylcarnitines.
LC (HILIC)-MS/MS.
All concentrations are reported as µmol/L.
Butyrobetaine | BB | Quarternary ammonium | 725 | 0.4-2 | 0.2 | s, p | |
Carnitine | C0 | Carnitine | 288 | 20-80 | 0.5 | 0.76b | s, p |
Acetylcarnitine | C2 | Acylcarnitine | 7045767 | 3-15 | 0.1 | 0.63 | s, p |
Propionylcarnitine | C3 | Acylcarnitine | 107738 | 0.2-1.5 | 0.05 | 0.62 | s, p |
Butyrylcarnitine | C4 | Acylcarnitine | 213144 | 0.1-0.5 | 0.012 | 0.79b | s, p |
Isovalerylcarnitine | iC5 | Acylcarnitine | 6426851 | 0.06-0.2 | 0.05 | 0.68 | s, p |
Hexanoylcarnitine | C6 | Acylcarnitine | 6426853 | 0.01-1.2 | 0.01 | s, p | |
Octanoylcarnitine | C8 | Acylcarnitine | 123701 | 0.06-0.3 | 0.05 | 0.41 | s, p |
Decanoylcarnitine | C10 | Acylcarnitine | 10245190 | 0.2-1 | 0.02 | 0.67b | s, p |
Dodecanoylcarnitine | C12 | Acylcarnitine | 168381 | < 0.4 | 0.02 | s, p | |
Myristoylcarnitine | C14 | Acylcarnitine | 6426854 | 0.01-0.1 | 0.38a | s, p | |
Palmitoylcarnitine | C16 | Acylcarnitine | 461 | 0.05-0.25 | 0.49a | s, p | |
Stearoylcarnitine | C18 | Acylcarnitine | 52922056 | 0.03-0.1 | 0.40a | s, p | |
Oleoylcarnitine | C18:1 | Acylcarnitine | 46907933 | 0.04-0.2 | s, p | ||
Linoleylcarnitine | C18:2 | Acylcarnitine | 6450015 | 0.01-0.1 | s, p |
aFloegel A, Drogan D, Wang-Sattler R, Prehn C, Illig T, et al. (2011) Reliability of Serum Metabolite Concentrations over a 4-Month Period Using a
Targeted Metabolomic Approach. PLoS ONE 6(6): e21103. doi:10.1371/journal.pone.0021103
bXiaofei Yin, Orla Prendiville, Aoife E. McNamara, and Lorraine Brennan. Targeted Metabolomic Approach to Assess the Reproducibility of
Plasma Metabolites over a Four Month Period in a Free-Living Population. J. Proteome Res. 2022, 21, 683−690.
*Multianalyte determination is carried out in a single aliquot. Volume requirement is independent of the number of metabolites. Reported values are not strictly normal reference range, which depends on the population, and several factors, including age, gender, ethnicity and procedures for sample handling and analytical technology. Reported values are concentrations that we and others have observed or reported in various cohorts of healthy subjects. For some biomarkers the assay performance may be different from those given in published articles. This is due to continuous improvements of the methods. LODs, CVs, and ICCs are not available for all biomarkers.