GNPS - Metabolomics data for Matrix Method
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Q Exactive
ORGANISM(S): Homo Sapiens (ncbitaxon:9606)
SUBMITTER: 
Pieter C. Dorrestein
PROVIDER: MSV000095260 | GNPS | Fri Jul 05 11:57:00 BST 2024
REPOSITORIES: GNPS
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Project description:Matrix effect from various constituents in biological samples can reduce the accuracy of quantitative metabolomics. Differential chemical isotope labeling liquid chromatography mass spectrometry (CIL LC-MS) can overcome the matrix effect on MS detection based on measuring the intensity ratios of metabolite peak pairs detected in a mixture of a light-isotope labeled sample and a heavy-isotope labeled reference sample. However, the chemical labeling process itself may encounter matrix effect which can influence the overall quantitative results. In this work, we report the effects of salts and buffers commonly present in metabolomic samples on dansylation labeling. It is shown that high concentrations of NaCl and phosphate buffer (>50 mM) or PBS can reduce or enhance the labeling efficiencies of metabolites. By maintaining similar matrix contents in an individual sample vs. a reference sample, relative quantification of metabolites can be performed without compromising the metabolomic profiling results. For samples containing varying amounts of high salts such as urine, we demonstrate that the matrix effect can be largely overcome by diluting the original sample before dansylation labeling (e.g., 4-fold dilution for urine).
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Project description:Alcohol intake is a risk factor for development of osteopenia. Ethanol perturbs gene expression in osteoblasts and osteoclasts and disrupts growth plate morphology. Hepatic metabolism of ethanol to acetate elevates concentrations of acetate in the circulation. We investigated whether acetate could mediate the toxicity of ethanol on gene expression in bone and on chondrocyte differentiation. When ethanol and acetate were compared by gavage for four consecutive days, none of eleven genes involved in bone homeostasis showed expression significantly affected by acetate, but the acetate responses significantly correlated with ethanol responses. Intraperitoneal injection with acetate to transiently elevate serum acetate for four consecutive days significantly increased expression of two markers of osteoclast differentiation, calcitonin receptor (Calcr) and Ocstamp. Early chondrogenic differentiation of ATDC5 cells for 7 days in vitro characterized by aggrecan (Acan) and collagen 2a1 (Col2a1) mRNA expression and proteoglycan production was inhibited by both 50 mM ethanol and 5 mM acetate. Ethanol effects were not blocked by the alcohol dehydrogenase inhibitor 4-methylpyrazole. 50 mM ethanol retarded both ATDC5 cell growth and culture medium acidification. Inhibition of chondrogenic differentiation by 5 mM acetate was associated with elevated phosphorylation of Erk1 and Erk2 and decreased expression of transcription factors Sox9 and Runx2. In acetate-exposed cells, blocking of Erk1 and Erk2 phosphorylation with Trametinib prevented further reduction of Acan and Col2a1 mRNA expression. We conclude that ethanol-derived acetate mediates at least part of the induction of Calcr and Ocstamp expression, and that acetate mimics effects of ethanol on early chondrogenic differentiation.
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