Review
doi: 10.1021/acs.analchem.0c04698.
Epub 2020 Nov 28.
Recurrent Topics in Mass Spectrometry-Based Metabolomics and Lipidomics-Standardization, Coverage, and Throughput
Affiliations
- PMID: 33249827
- PMCID: PMC7807424
- DOI: 10.1021/acs.analchem.0c04698
Item in Clipboard
Review
Recurrent Topics in Mass Spectrometry-Based Metabolomics and Lipidomics-Standardization, Coverage, and Throughput
Anal Chem.
.
No abstract available
Conflict of interest statement
The authors declare no competing financial interest.
Figures
Accurate
absolute quantification according to the U.S. FDA guideline. Four
requirements need to be fulfilled for calibration: 1, matrix-matched;
2, multipoint; 3, external standardization; 4, internal standardization.
Additionally, their control point, the challenge, and a practical
solution for omics-experiments are given. *The ranking of ISTD follows
the levels of quantification of the Lipidomics Standards Initiative
(LSI).
Fit for purpose internal
standard-based quantification strategies established in the field
of metabolomics and lipidomics. Colors in the graphs symbolize values
from the sample (purple), compound-specific standards (green), and
surrogate standards (orange).
Difference
between enrichment degree and the relative isotopic abundance of a
fully labeled isotopologue. (A) Isoleucine with 6 carbon atoms is
used as an example. (B) Calculation of abundances for carbon as di-isotopic
element is based on the binominal formula. Other elements with more
than one isotope (e.g. H, N) influence the final abundance according
to their natural abundance also based on a binominal formula. Polyisotopic
elements (O) are based on polynomial terms. Usually, the contribution
of H, N, and O to the overall difference is minimal (here 1–2%)
but other elements must be considered (e.g. Cl, Br, S). (C) Determination
of coefficients of a binominal formula for each term according to
the n + 1 line in Pasqual’s triangle (for n = 6:1, 6, 15, 20,
15, 6, 1). (D) Binominal formula for n = 6. Each term is the relative
abundance of the corresponding isotopologue without the consideration
of other elemental isotopes. The last term corresponds to the fully
labeled isotopologue. The sum of all isotopologues is always 100%.
(E) Exemplarily, the effect of 1% enrichment difference (99%-darker
color and 98%-lighter color) on the abundance is shown for PC 34:2
(n = 42, blue) and isoleucine (n = 6, grey). The bar chart shows the
distribution from the fully labeled isotopologue (M′) until
M′ – 4 for both molecules. The difference for the fully
labeled isotopologue to 100% is already 12% for the 98% labeled isoleucine
and 58% for PC 34:2. But even for a better enrichment (99%) the error
for PC 34:2 is still 36%, highlighting the importance to consider
the relative abundance for quantification workflows.
Current in-house library of annotated metabolites and
lipids found in Pichia pastoris (yeast). (A) Metabolite
classes in ethanolic yeast extract classified
using the ClassyFirer annotation system.
(B) Lipid classes annotated in chloroformic yeast extract. GPL, glycerophospholipids; GL, glycerolipids;
SL, sphingolipids; ST. sterols; PR, prenols; Hex1Cer, hexosyl ceramides;
SPH, shingosine bases; SE, steryl esters; Co, coenzyme Q; PG, phosphatidylglycerols;
PA, phosphatidic acids; CL, cardiolipins.
Metabolite (left) and lipid (right) identification
according to the proposed guidelines of the metabolomics society (A–G)
using the examples of leucine and a PC 18:0/16:2(7E,11Z)[R]. The lowest
annotation level corresponds to known accurate mass information (G)
followed by a known compound class (F), known compound sum formula
(E), known functional moieties (D), known structure (isoleucine)/double
bond position (PC 18:0/16:2(7,11) (C), known diastereomer (B), and
the highest level to enantiomer-specific identification (A). *in lipidomics 3 intermediate steps are distinguished at level
D: sum of carbon and double bond number for all fatty acyl chains
(PC 34:2)/known distribution (PC 18:0_16:2) and known position of
the fatty acyl chains (PC 18:0/16:2).
General steps of nontargeted data preprocessing.
Practical setup
solutions for sequential and parallel LC. (A) In valve position A,
the void volume of the first column is transferred to the second column.
Afterward, the valve is switched in position B and the sample is analyzed
on both columns parallel., (B) In valve position
A, the first extract is injected on the first column and analyzed.
Meanwhile, the second column is equilibrated and the mobile phase
is flushed into waste. After separation on the first column, the valve
is switched to position B and the second extract is injected on the
second column and analyzed while the first column is equilibrated. (C) In valve position A, the sample is loaded
and divided into two sample loops equally. In valve position B, both
parts of the sample are injected onto two orthogonal columns and analyzed.
References
-
- González-Riano C.; Dudzik D.; Garcia A.; Gil-de-la-Fuente A.; Gradillas A.; Godzien J.; López-Gonzálvez Á.; Rey-Stolle F.; Rojo D.; Ruperez F. J.; Saiz J.; Barbas C. Recent Developments along the Analytical Process for Metabolomics Workflows. Anal. Chem. 2020, 92 (1), 203–226. 10.1021/acs.analchem.9b04553. - DOI - PubMed
-
- Dunn W. B.; Ellis D. I. Metabolomics: Current Analytical Platforms and Methodologies. TrAC, Trends Anal. Chem. 2005, 24 (4), 285–294. 10.1016/j.trac.2004.11.021. - DOI
-
- Lerma-Ortiz C.; Jeffryes J. G.; Cooper A. J. L.; Niehaus T. D.; Thamm A. M. K.; Frelin O.; Aunins T.; Fiehn O.; de Crécy-Lagard V.; Henry C. S.; Hanson A. D. ‘Nothing of Chemistry Disappears in Biology’: The Top 30 Damage-Prone Endogenous Metabolites. Biochem. Soc. Trans. 2016, 44 (3), 961–971. 10.1042/BST20160073. - DOI - PubMed
Publication types
MeSH terms
LinkOut - more resources
Full Text Sources
