The biological interpretation of metabolomic data can be misled by the extraction method used

Duportet, Xavier; Aggio, Raphael; Carneiro, Sônia Maria Marchiorato; Villas‐Bôas, Silas G.

doi:10.1007/s11306-011-0324-1

Cited by 93 publications

(63 citation statements)

References 33 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…This method improved metabolite coverage compared with water extraction (1,863 compared with 1,055 features in positive ESI mode and 762 compared with 561 in negative ESI for the MCF-7 line), with particular improvement in detection of nonpolar metabolites. Results obtained by Duportet et al also support the idea of use of multiple solvents, with the authors advocating sequential extraction of metabolites with solvents of decreasing or increasing polarity, while maintaining low temperature, followed by pooling of extracts before analysis as a way of ensuring more complete extraction of most metabolites and resolving the problem of contradictory biological interpretation [34]. Detailed recovery studies will further aid the development of optimum sample-preparation strategies for cell metabolomics.…”

Section: Cell Lysis and Extraction In Cell Metabolomicsmentioning

confidence: 86%

“…For example, Canelas et al showed that even the relative levels of metabolites (up or downregulation when comparing two conditions) could be distorted by the sample-preparation method, leading to erroneous conclusions [33]. Duportet et al showed that extraction of the same quenched samples by use of four different extraction methods could result in significantly different metabolite levels and contradictory biological interpretation of active metabolite pathways [34]. For instance, the aminoacyl t-RNA pathway was shown to be up-regulated when using metabolite profiles obtained from boiling ethanol and freeze-thaw extractions, and seemed to be down-regulated when using cold methanol or cold methanol with sonication extraction.…”

Section: Importance Of Sample Preparation In Global Metabolomicsmentioning

confidence: 99%

See 1 more Smart Citation

Current trends and challenges in sample preparation for global metabolomics using liquid chromatography–mass spectrometry

2012

View full text Add to dashboard Cite

The choice of sample-preparation method is extremely important in metabolomic studies because it affects both the observed metabolite content and biological interpretation of the data. An ideal sample-preparation method for global metabolomics should (i) be as non-selective as possible to ensure adequate depth of metabolite coverage; (ii) be simple and fast to prevent metabolite loss and/or degradation during the preparation procedure and enable high-throughput; (iii) be reproducible; and (iv) incorporate a metabolism-quenching step to represent true metabolome composition at the time of sampling. Despite its importance, sample preparation is often an overlooked aspect of metabolomics, so the focus of this review is to explore the role, challenges, and trends in sample preparation specifically within the context of global metabolomics by liquid chromatography-mass spectrometry (LC-MS). This review will cover the most common methods including solvent precipitation and extraction, solid-phase extraction and ultrafiltration, and discuss how to improve analytical quality and metabolite coverage in metabolomic studies of biofluids, tissues, and mammalian cells. Recent developments in this field will also be critically examined, including in vivo methods, turbulent-flow chromatography, and dried blood spot sampling.

show abstract

Section: Cell Lysis and Extraction In Cell Metabolomicsmentioning

confidence: 86%

Section: Importance Of Sample Preparation In Global Metabolomicsmentioning

confidence: 99%

Current trends and challenges in sample preparation for global metabolomics using liquid chromatography–mass spectrometry

2012

View full text Add to dashboard Cite

show abstract

“…To successfully profile a broad concentration range of chemically diverse metabolites, metabolites were extracted by fractionating plasma samples into pools of species with similar physicochemical properties, using appropriate combinations of organic solvents [32,33]. Three separate UPLC-MS platforms were used to ensure optimal metabolite profiling.…”

Section: Metabolomics Analysesmentioning

confidence: 99%

A Blood-Based, 7-Metabolite Signature for the Early Diagnosis of Alzheimer's Disease

Olazarán

Gil-de-Gómez²,

Rodríguez-Martín³

et al. 2015

JAD

View full text Add to dashboard Cite

Abstract. Accurate blood-based biomarkers of Alzheimer's disease (AD) could constitute simple, inexpensive, and non-invasive tools for the early diagnosis and treatment of this devastating neurodegenerative disease. We sought to develop a robust AD biomarker panel by identifying alterations in plasma metabolites that persist throughout the continuum of AD pathophysiology. Using a multicenter, cross-sectional study design, we based our analysis on metabolites whose levels were altered both in AD patients and in patients with amnestic mild cognitive impairment (aMCI), the earliest identifiable stage of AD. UPLC coupled to mass spectrometry was used to independently compare the levels of 495 plasma metabolites in aMCI (n = 58) and AD (n = 100) patients with those of normal cognition controls (NC, n = 93). Metabolite alterations common to both aMCI and AD patients were used to generate a logistic regression model that accurately distinguished AD from NC patients. The final panel consisted of seven metabolites: three amino acids (glutamic acid, alanine, and aspartic acid), one non-esterified fatty acid .918). Importantly, the model also distinguished aMCI from NC patients (AUC, 0.826), indicating its potential diagnostic utility in early disease stages. These findings describe a sensitive biomarker panel that may facilitate the specific detection of early-stage AD through the analysis of plasma samples.

show abstract

“…7 mg cell dry weight (CDW)) was sampled from each culture in a tube from Greiner (Frickenhausen, Germany) containing 12 mL methanol at −20°C in order to quench the metabolism. A freeze-thaw method (adapted from Duportet et al [24]) was applied to extract the cells, as follows: the quenched cell suspension was pelleted via centrifugation at 4000g at −20°C for 5 min using a Sorvall RC 6+ centrifuge from Thermo Scientific. The cell pellets were washed by re-suspension in 3 mL of 80 % (v/v) methanol (−20°C) and were again centrifuged, discarding the supernatant.…”

Section: Sampling and Extraction Of M Elsdeniimentioning

confidence: 99%

LC-MS/MS-based analysis of coenzyme A and short-chain acyl-coenzyme A thioesters

et al. 2015

View full text Add to dashboard Cite

Absolute quantification of intracellular coenzyme A (CoA), coenzyme A disulfide, and short-chain acyl-coenzyme A thioesters was addressed by developing a tailored metabolite profiling method based on liquid chromatography in combination with tandem mass spectrometric detection (LC-MS/MS). A reversed phase chromatographic separation was established which is capable of separating a broad spectrum of CoA, its corresponding derivatives, and their isomers despite the fact that no ion-pairing reagent was used (which was considered as a key advantage of the method). Excellent analytical figures of merit such as high sensitivity (LODs in the nM to sub-nM range) and high repeatability (routinely 4 %; N = 15) were obtained. Method validation comprised a study on standard purity, stability, and recoveries during sample preparation. Uniformly labeled U(13)C yeast cell extracts offered ideal internal standards for validation purposes and for a quantification exercise in the rumen bacterium Megasphaera elsdenii.

show abstract

The biological interpretation of metabolomic data can be misled by the extraction method used

Cited by 93 publications

References 33 publications

Current trends and challenges in sample preparation for global metabolomics using liquid chromatography–mass spectrometry

Current trends and challenges in sample preparation for global metabolomics using liquid chromatography–mass spectrometry

A Blood-Based, 7-Metabolite Signature for the Early Diagnosis of Alzheimer's Disease

LC-MS/MS-based analysis of coenzyme A and short-chain acyl-coenzyme A thioesters

Contact Info

Product

Resources

About