Laboratory of Foodomics

Madrid, Spain

Laboratory of Foodomics

Madrid, Spain

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Ibanez C.,Laboratory of Foodomics | Simo C.,Laboratory of Foodomics | Barupal D.K.,University of California at Davis | Fiehn O.,University of California at Davis | And 3 more authors.
Journal of Chromatography A | Year: 2013

Alzheimer's disease (AD) is the most prevalent cause of dementia among older people. Although AD probably starts 20-30 years before first clinical symptoms become noticeable, nowadays it cannot be diagnosed accurately in its early stages. In this work, we present a new MS-based metabolomic approach based on the use of ultra-high performance liquid chromatography-time-of-flight mass spectrometry (UHPLC-TOF MS) to investigate cerebrospinal fluid (CSF) samples from patients with different AD stages. With the aim to obtain wide metabolome coverage two different chromatographic separation modes, namely reversed phase (RP) and hydrophilic interaction chromatography (HILIC), were used. RP/UHPLC-MS and HILIC/UHPLC-MS methods were optimized and applied to analyze CSF samples from 75 patients related to AD progression. Significant metabolic differences in CSF samples from subjects with different cognitive status related to AD progression were detected using this methodology, obtaining a group of potential biomarkers together with a classification model by means of a multivariate statistical analysis. The proposed model predicted the development of AD with an accuracy of 98.7% and specificity and sensitivity values above of 95%. © 2013 Elsevier B.V.


Simo C.,Laboratory of Foodomics | Cifuentes A.,Laboratory of Foodomics | Kasicka V.,Czech Institute of Organic Chemistry And Biochemistry
Methods in Molecular Biology | Year: 2013

In this chapter, the potential of capillary electrophoresis-mass spectrometry (CE-MS) for peptide analysis is demonstrated by the presentation of two different strategies typically followed in analysis of these biomolecules by CE-MS. The first one is a target-based approach and it is used to detect a toxic oligopeptide in a complex matrix. Namely, CE-MS using an ion trap MS analyzer is applied to detect and quantify γ-glutamyl-S-ethenyl-cysteine (GEC) bioactive dipeptide in a legume plant. The second one is a shotgunlike methodology used for proteomic analysis. Particularly, CE-MS using a time-of- flight MS analyzer is employed to investigate the substantial equivalence between a genetically modified (GM) variety of soybean and its conventional isogenic counterpart. These generic methods have broad applications for the analysis of peptides in a large variety of matrices, including applications in the area of proteomics and peptidomics. © Springer Science+Business Media, LLC 2013.


Ibanez C.,Laboratory of Foodomics | Simo C.,Laboratory of Foodomics | Garcia-Canas V.,Laboratory of Foodomics | Gomez-Martinez A.,University Miguel Hernández | And 2 more authors.
Electrophoresis | Year: 2012

In this study, an analytical multiplatform is presented to carry out a broad metabolomic study on the anti-proliferative effect of dietary polyphenols on human colon cancer cells. CE, RP/UPLC, and HILIC/UPLC all coupled to TOF MS were combined to achieve a global metabolomic examination of the effect of dietary polyphenols on HT29 colon cancer cells. By the use of a nontargeted metabolomic approach, metabolites showing significant different expression after the polyphenols treatment were identified in colon cancer cells. It was demonstrated that this multianalytical platform provided extensive metabolic information and coverage due to its complementary nature. Differences observed in metabolic profiles from CE-TOF MS, RP/UPLC-TOF MS, and HILIC/UPLC-TOF MS can be mainly assigned to their different separation mechanisms without discarding the influence of the different tools used for data processing. Changes in glutathione metabolism with an enhanced reduced glutathione/oxidized glutathione (GSH/GSSG) ratio were detected in polyphenols-treated cells. Moreover, significant alterations in polyamines content with important implications in cancer proliferation were observed after the treatment with polyphenols. These results from metabolomics can explain the chemopreventive effect of the tested dietary polyphenols on colon cancer and may be of importance for future prevention and/or treatment of this disease. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.


Valdes A.,Laboratory of Foodomics | Garcia-Canas V.,Laboratory of Foodomics | Cifuentes A.,Laboratory of Foodomics
Electrophoresis | Year: 2013

Nowadays, new solutions focused on the replacement of reagents hazardous to human health are highly demanded in laboratories and Green Chemistry. In the present work, GelGreen, a new nonhazardous DNA staining reagent, has been assayed for the first time to analyze double-stranded DNA by CGE with LIF detection. The effect of GelGreen concentration on S/N ratio and migration time of a wide concentration range of standard DNA mixtures was evaluated. Under optimum GelGreen concentration in the sieving buffer efficient and sensitive separations of DNA fragments with sizes from 100-500 base pairs (bp) were obtained. A comparison in terms of resolution, time of analysis, LOD, LOQ, reproducibility, sizing performance, and cost of analysis was established between two optimized CGE-LIF protocols for DNA analysis, one based on the dye YOPRO-1 (typically used for CGE-LIF of DNA fragments) and another one using the new GelGreen. Analyses using YOPRO-1 were faster than those using GelGreen (ca. 31 min versus 34 min for the analysis of 100-500 bp DNA fragments). On the other side, sensitivity using GelGreen was twofold higher than that using YOPRO-1. The cost of analysis was significantly cheaper (ninefold) using GelGreen than with YOPRO-1. The resolution values and sizing performance were not significantly different between the two dyes (e.g. both dyes allowed the separation of fragments differing in only 2 bp in the 100-200 bp range). The usefulness of the separation method using GelGreen is demonstrated by the characterization of different amplicons obtained by PCR. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.


Garcia-Canas V.,Laboratory of Foodomics | Simo C.,Laboratory of Foodomics | Herrero M.,Laboratory of Foodomics | Ibanez E.,Laboratory of Foodomics | Cifuentes A.,Laboratory of Foodomics
Analytical Chemistry | Year: 2012

The state-of-the-art of food analysis at the beginning of the 21st century is presented in this work, together with its major applications, current limitations, and present and foreseen challenges. © 2012 American Chemical Society.


Ibanez C.,Laboratory of Foodomics | Simo C.,Laboratory of Foodomics | Martin-Alvarez P.J.,Laboratory of Foodomics | Kivipelto M.,Karolinska Institutet | And 3 more authors.
Analytical Chemistry | Year: 2012

Alzheimer's disease (AD) is the most prevalent form of dementia with an estimated worldwide prevalence of over 30 million people, and its incidence is expected to increase dramatically with an increasing elderly population. Up until now, cerebrospinal fluid (CSF) has been the preferred sample to investigate central nervous system (CNS) disorders since its composition is directly related to metabolite production in the brain. In this work, a nontargeted metabolomic approach based on capillary electrophoresis-mass spectrometry (CE-MS) is developed to examine metabolic differences in CSF samples from subjects with different cognitive status related to AD progression. To do this, CSF samples from 85 subjects were obtained from patients with (i) subjective cognitive impairment (SCI, i.e. control group), (ii) mild cognitive impairment (MCI) which remained stable after a follow-up period of 2 years, (iii) MCI which progressed to AD within a 2-year time after the initial MCI diagnostic and, (iv) diagnosed AD. A prediction model for AD progression using multivariate statistical analysis based on CE-MS metabolomics of CSF samples was obtained using 73 CSF samples. Using our model, we were able to correctly classify 97-100% of the samples in the diagnostic groups. The prediction power was confirmed in a blind small test set of 12 CSF samples, reaching a 83% of diagnostic accuracy. The obtained predictive values were higher than those reported with classical CSF AD biomarkers (Aβ42 and tau) but need to be confirmed in larger samples cohorts. Choline, dimethylarginine, arginine, valine, proline, serine, histidine, creatine, carnitine, and suberylglycine were identified as possible disease progression biomarkers. Our results suggest that CE-MS metabolomics of CSF samples can be a useful tool to predict AD progression. © 2012 American Chemical Society.


Ibanez C.,Laboratory of Foodomics | Simo C.,Laboratory of Foodomics | Garcia-Canas V.,Laboratory of Foodomics | Cifuentes A.,Laboratory of Foodomics | Castro-Puyana M.,Laboratory of Foodomics
Analytica Chimica Acta | Year: 2013

In the current post-genomic era, Foodomics has been defined as a discipline that studies food and nutrition through the application of advanced omics approaches. Foodomics involves the use of genomics, transcriptomics, epigenetics, proteomics, peptidomics, and/or metabolomics to investigate food quality, safety, traceability and bioactivity. In this context, capillary electrophoresis-mass spectrometry (CE-MS) has been applied mainly in food proteomics, peptidomics and metabolomics. The aim of this review work is to present an overview of the most recent developments and applications of CE-MS as analytical platform for Foodomics, covering the relevant works published from 2008 to 2012. The review provides also information about the integration of several omics approaches in the new Foodomics field. © 2013 Elsevier B.V.


Valdes A.,Laboratory of Foodomics | Ibanez C.,Laboratory of Foodomics | Simo C.,Laboratory of Foodomics | Garcia-Canas V.,Laboratory of Foodomics
TrAC - Trends in Analytical Chemistry | Year: 2013

We provide an overview of the recent progress in high-throughput transcriptomics techniques, namely microarray and RNA-seq, and discuss their advantages and drawbacks. Besides, we highlight relevant applications of these technologies in the context of food science to illustrate their impressive potential. We also provide some ideas of the future technological advances and the potential applications of these fast-evolving techniques. © 2013 Elsevier Ltd.


Valdes A.,Laboratory of Foodomics | Simo C.,Laboratory of Foodomics | Ibanez C.,Laboratory of Foodomics | Garcia-Canas V.,Laboratory of Foodomics
TrAC - Trends in Analytical Chemistry | Year: 2013

Advanced tools in transcriptomics, proteomics, and metabolomics in combination with bioinformatics and chemometrics may provide chemical compositional data that may be helpful in studying any effects (intended or not) derived from genetic transformation. In this review, we critically discuss the use of the main omics technologies to characterize genetically-modified organisms at the transcriptome, proteome and metabolome levels. © 2013 Elsevier Ltd.


Ibanez C.,Laboratory of Foodomics | Simo C.,Laboratory of Foodomics | Cifuentes A.,Laboratory of Foodomics
Electrophoresis | Year: 2013

Alzheimer's disease (AD) is a neurodegenerative multifactorial disease whose cause is still unknown. The majority of AD biochemical markers currently available have been developed as an extension of targeted physiological studies on the basis of the "amyloid hypothesis." The potential of metabolomics for the discovery of novel biomarkers and elucidation of new biochemical pathways modified in the progression of AD is highlighted in this review work. A variety of nontargeted metabolomic approaches for the discrimination between healthy subjects and AD patients are described. Moreover, the feasibility of metabolomics to predict progression to AD in individuals with mild cognitive impairment is also presented. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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