Metabolomics, peptidomics and proteomics applications of capillary electrophoresis-mass spectrometry in Foodomics: a review.

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.

[1]  E. Ibáñez,et al.  Metabolomics of transgenic maize combining Fourier transform-ion cyclotron resonance-mass spectrometry, capillary electrophoresis-mass spectrometry and pressurized liquid extraction. , 2009, Journal of chromatography. A.

[2]  L. Fricker,et al.  Peptidomics: identification and quantification of endogenous peptides in neuroendocrine tissues. , 2006, Mass spectrometry reviews.

[3]  Hyun Pyo Kim,et al.  Antioxidant and antigenotoxic activities of Korean fermented soybean. , 2008, Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association.

[4]  Hiroshi Matsuno,et al.  Glycogen is the primary source of glucose during the lag phase of E. coli proliferation. , 2012, Biochimica et biophysica acta.

[5]  W. Van Criekinge,et al.  Peptidomics coming of age: a review of contributions from a bioinformatics angle. , 2010, Journal of proteome research.

[6]  E. J. Song,et al.  CE at the omics level: Towards systems biology – An update , 2008, Electrophoresis.

[7]  E. Fukusaki,et al.  Profiling of primary metabolite by means of capillary electrophoresis-mass spectrometry and its application for plant science , 2009 .

[8]  G. Cagney,et al.  Sequential interval motif search: unrestricted database surveys of global MS/MS data sets for detection of putative post-translational modifications. , 2008, Analytical chemistry.

[9]  F. Foret,et al.  On‐line CE/ESI/MS interfacing: Recent developments and applications in proteomics , 2012, Proteomics.

[10]  A. Segura‐Carretero,et al.  Comparative metabolomic study of transgenic versus conventional soybean using capillary electrophoresis-time-of-flight mass spectrometry. , 2008, Journal of chromatography. A.

[11]  A. Cifuentes,et al.  Chiral analysis of amino acids from conventional and transgenic yeasts. , 2008, Journal of chromatography. B, Analytical technologies in the biomedical and life sciences.

[12]  Matej Oresic,et al.  MZmine 2: Modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data , 2010, BMC Bioinformatics.

[13]  Jianguo Xia,et al.  Web-based inference of biological patterns, functions and pathways from metabolomic data using MetaboAnalyst , 2011, Nature Protocols.

[14]  K. Lemr,et al.  Capillary electrophoresis‐mass spectrometry – a fast and reliable tool for the monitoring of milk adulteration , 2008, Electrophoresis.

[15]  A. Cifuentes,et al.  Advances in Nutrigenomics research: novel and future analytical approaches to investigate the biological activity of natural compounds and food functions. , 2010, Journal of pharmaceutical and biomedical analysis.

[16]  Y. Mechref Analysis of glycans derived from glycoconjugates by capillary electrophoresis‐mass spectrometry , 2011, Electrophoresis.

[17]  E. Ibáñez,et al.  New Analytical Techniques in Food Science , 2001, Critical reviews in food science and nutrition.

[18]  Bas van Breukelen,et al.  Current challenges in software solutions for mass spectrometry-based quantitative proteomics , 2012, Amino Acids.

[19]  Kazuki Saito,et al.  GC-TOF-MS- and CE-TOF-MS-based metabolic profiling of cheonggukjang (fast-fermented bean paste) during fermentation and its correlation with metabolic pathways. , 2012, Journal of agricultural and food chemistry.

[20]  A. Cifuentes,et al.  Capillary electrophoresis time-of-flight mass spectrometry for comparative metabolomics of transgenic versus conventional maize. , 2008, Analytical chemistry.

[21]  A. Cifuentes,et al.  Chiral separation of amino acids derivatised with fluorescein isothiocyanate by single isomer derivatives 3-monodeoxy-3-monoamino-β- and γ-cyclodextrins: the effect of the cavity size. , 2012, Journal of chromatography. A.

[22]  Lukas N. Mueller,et al.  An assessment of software solutions for the analysis of mass spectrometry based quantitative proteomics data. , 2008, Journal of proteome research.

[23]  Amit Kumar Yadav,et al.  MassWiz: a novel scoring algorithm with target-decoy based analysis pipeline for tandem mass spectrometry. , 2011, Journal of proteome research.

[24]  M. Oimomi,et al.  Increased fructose-lysine of nail protein in diabetic patients , 1984, Klinische Wochenschrift.

[25]  R. Ramautar,et al.  Relevance and use of capillary coatings in capillary electrophoresis–mass spectrometry , 2010, Analytical and bioanalytical chemistry.

[26]  A. Cifuentes,et al.  CE‐TOF MS analysis of complex protein hydrolyzates from genetically modified soybeans – A tool for foodomics , 2010, Electrophoresis.

[27]  Stuart M Phillips,et al.  Differential metabolomics for quantitative assessment of oxidative stress with strenuous exercise and nutritional intervention: thiol-specific regulation of cellular metabolism with N-acetyl-L-cysteine pretreatment. , 2010, Analytical chemistry.

[28]  J. German,et al.  Metabolomics in practice: emerging knowledge to guide future dietetic advice toward individualized health. , 2005, Journal of the American Dietetic Association.

[29]  E. Ibáñez,et al.  Present and future challenges in food analysis: foodomics. , 2012, Analytical chemistry.

[30]  Masaru Tomita,et al.  Changes in the charged metabolite and sugar profiles of pasteurized and unpasteurized Japanese sake with storage. , 2012, Journal of agricultural and food chemistry.

[31]  E. Ibáñez,et al.  MS-based analytical methodologies to characterize genetically modified crops. , 2011, Mass spectrometry reviews.

[32]  E. Maxwell,et al.  Flow-through microvial facilitating interface of capillary isoelectric focusing and electrospray ionization mass spectrometry. , 2011, Analytical chemistry.

[33]  D. Kwon,et al.  Antidiabetic effects of fermented soybean products on type 2 diabetes. , 2010, Nutrition research.

[34]  J. Phillipson,et al.  Herbal Medicines: A Guide for Healthcare Professionals , 1996 .

[35]  B. Winblad,et al.  Toward a predictive model of Alzheimer's disease progression using capillary electrophoresis-mass spectrometry metabolomics. , 2012, Analytical Chemistry.

[36]  Time of flight versus ion trap MS coupled to CE to analyse intact proteins. , 2008, Journal of separation science.

[37]  G. Macfarlane,et al.  Role of intestinal bacteria in nutrient metabolism. , 1997, JPEN. Journal of parenteral and enteral nutrition.

[38]  M. Tomita,et al.  Metabolomic profiles and sensory attributes of edamame under various storage duration and temperature conditions. , 2010, Journal of agricultural and food chemistry.

[39]  N. Voelkel,et al.  Appearance of Urinary Metabolites of LTE4 in Human Subjects a , 1991, Annals of the New York Academy of Sciences.

[40]  Allam Appa Rao,et al.  Techniques for integrating ‐omics data , 2009, Bioinformation.

[41]  M. Moini Simplifying CE-MS operation. 2. Interfacing low-flow separation techniques to mass spectrometry using a porous tip. , 2007, Analytical chemistry.

[42]  Martin Kussmann,et al.  OMICS-driven biomarker discovery in nutrition and health. , 2006, Journal of biotechnology.

[43]  Xi-jun Wang,et al.  Modern analytical techniques in metabolomics analysis. , 2012, The Analyst.

[44]  M. Lean,et al.  Identification of metabolites in human plasma and urine after consumption of a polyphenol-rich juice drink. , 2010, Journal of agricultural and food chemistry.

[45]  A. Cifuentes,et al.  CE‐MS of zein proteins from conventional and transgenic maize , 2007, Electrophoresis.

[46]  M. Gerstein,et al.  RNA-Seq: a revolutionary tool for transcriptomics , 2009, Nature Reviews Genetics.

[47]  Dieter Jahn,et al.  MetaQuant: a tool for the automatic quantification of GC/MS-based metabolome data , 2006, Bioinform..

[48]  D. Arráez-Román,et al.  Characterization of phenolic and other polar compounds in a lemon verbena extract by capillary electrophoresis-electrospray ionization-mass spectrometry. , 2010, Journal of separation science.

[49]  Steffen Neumann,et al.  Highly sensitive feature detection for high resolution LC/MS , 2008, BMC Bioinformatics.

[50]  Andreas Rizzi,et al.  Glycosylation analysis of glycoproteins and proteoglycans using capillary electrophoresis‐mass spectrometry strategies , 2008, Electrophoresis.

[51]  Elena Marchiori,et al.  Tools for computational processing of LC-MS datasets: A user's perspective , 2007, Comput. Methods Programs Biomed..

[52]  A. Alwan Global status report on noncommunicable diseases 2010. , 2011 .

[53]  J. Barbosa,et al.  Identification of bioactive peptides in hypoallergenic infant milk formulas by capillary electrophoresis-mass spectrometry. , 2010, Analytica chimica acta.

[54]  Shoshi Kikuchi,et al.  Integrated transcriptomics, proteomics, and metabolomics analyses to survey ozone responses in the leaves of rice seedling. , 2008, Journal of proteome research.

[55]  G. Gutiérrez-López,et al.  Use of Proteomics and Peptidomics Methods in Food Bioactive Peptide Science and Engineering , 2012, Food Engineering Reviews.

[56]  E. Ban,et al.  Growing trend of CE at the omics level: The frontier of systems biology – An update , 2012, Electrophoresis.

[57]  Philip Britz-McKibbin,et al.  New advances in separation science for metabolomics: resolving chemical diversity in a post-genomic era. , 2013, Chemical reviews.

[58]  H. Mischak,et al.  Capillary electrophoresis coupled to mass spectrometer for automated and robust polypeptide determination in body fluids for clinical use , 2004, Electrophoresis.

[59]  H. Mischak,et al.  A pilot study on the effect of short-term consumption of a polyphenol rich drink on biomarkers of coronary artery disease defined by urinary proteomics. , 2011, Journal of agricultural and food chemistry.

[60]  R. Ramautar,et al.  CE‐MS in metabolomics , 2009, Electrophoresis.

[61]  E. J. Song,et al.  Growing trend of CE at the omics level: The frontier of systems biology , 2010, Electrophoresis.

[62]  Matthew A. Hibbs,et al.  Visualization of omics data for systems biology , 2010, Nature Methods.

[63]  Rawi Ramautar,et al.  CE‐MS for metabolomics: Developments and applications in the period 2008–2010 , 2011, Electrophoresis.

[64]  Russell J. Mumper,et al.  Plant Phenolics: Extraction, Analysis and Their Antioxidant and Anticancer Properties , 2010, Molecules.

[65]  O. Mayboroda,et al.  Ultra-low flow electrospray ionization-mass spectrometry for improved ionization efficiency in phosphoproteomics. , 2012, Analytical chemistry.

[66]  Charles C. Liu,et al.  A sheath-flow nanospray interface for capillary electrophoresis/mass spectrometry. , 2005, Rapid communications in mass spectrometry : RCM.

[67]  C. Barbas,et al.  Metabolomic assessment with CE‐MS of the nutraceutical effect of Cystoseira spp extracts in an animal model , 2011, Electrophoresis.

[68]  S. Kochhar,et al.  Nutritional metabonomics: an approach to promote personalized health and wellness. , 2011, Chimia.

[69]  H. Isoda,et al.  Metabolomics Analysis of Cistus monspeliensis Leaf Extract on Energy Metabolism Activation in Human Intestinal Cells , 2012, Journal of biomedicine & biotechnology.

[70]  S. Salomone,et al.  Isoflavones: estrogenic activity, biological effect and bioavailability , 2012, European Journal of Drug Metabolism and Pharmacokinetics.

[71]  Bin Ma,et al.  De Novo Sequencing Methods in Proteomics , 2010, Proteome Bioinformatics.

[72]  Pei Wang,et al.  Bioinformatics Original Paper a Suite of Algorithms for the Comprehensive Analysis of Complex Protein Mixtures Using High-resolution Lc-ms , 2022 .

[73]  R. Abagyan,et al.  XCMS: processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification. , 2006, Analytical chemistry.

[74]  Pedro Mendes,et al.  Bioinformatics Approaches to Integrate Metabolomics and Other Systems Biology Data , 2006 .

[75]  I. Komuro,et al.  L-Carnitine prevents the development of ventricular fibrosis and heart failure with preserved ejection fraction in hypertensive heart disease , 2012, Journal of hypertension.

[76]  Masaru Tomita,et al.  Bioinformatics Tools for Mass Spectroscopy-Based Metabolomic Data Processing and Analysis , 2012, Current bioinformatics.

[77]  Rawi Ramautar,et al.  CE‐MS for metabolomics: Developments and applications in the period 2010–2012 , 2013, Electrophoresis.

[78]  A. Cravioto,et al.  Nutrition, immunology, and genetics: future perspectives. , 2009, Nutrition reviews.

[79]  John R Yates,et al.  Capillary electrophoresis applied to proteomic analysis. , 2009, Journal of separation science.

[80]  G. D. de Jong,et al.  Capillary electrophoresis–mass spectrometry for the analysis of intact proteins 2007–2010 , 2011, Electrophoresis.

[81]  Vladimir Shulaev,et al.  Metabolomics technology and bioinformatics , 2006, Briefings Bioinform..

[82]  Rawi Ramautar,et al.  High capacity capillary electrophoresis-electrospray ionization mass spectrometry: coupling a porous sheathless interface with transient-isotachophoresis. , 2010, Analytical chemistry.

[83]  John Milner,et al.  Nutrigenomics, proteomics, metabolomics, and the practice of dietetics. , 2006, Journal of the American Dietetic Association.

[84]  Richard J Jacob,et al.  Bioinformatics for LC-MS/MS-based proteomics. , 2010, Methods in molecular biology.

[85]  Ming Li,et al.  PEAKS: powerful software for peptide de novo sequencing by tandem mass spectrometry. , 2003, Rapid communications in mass spectrometry : RCM.

[86]  J Bruce German,et al.  Analytical metabolomics: nutritional opportunities for personalized health. , 2011, The Journal of nutritional biochemistry.

[87]  M. Bustamante-Rangel,et al.  Analysis of isoflavones in soy drink by capillary zone electrophoresis coupled with electrospray ionization mass spectrometry. , 2012, Analytica chimica acta.

[88]  E. Ibáñez,et al.  Capillary electrophoresis‐electrospray‐mass spectrometry in peptide analysis and peptidomics , 2008, Electrophoresis.

[89]  C. Barbas,et al.  Capillary electrophoresis as a metabolomics tool for non-targeted fingerprinting of biological samples. , 2011, Journal of pharmaceutical and biomedical analysis.

[90]  Masaru Tomita,et al.  Differential metabolomics software for capillary electrophoresis-mass spectrometry data analysis , 2010, Metabolomics.

[91]  J. Villard,et al.  Antimicrobial activities of the leaf extracts of two Moroccan Cistus L. species. , 2006, Journal of ethnopharmacology.

[92]  R. Ramautar,et al.  CE-MS for proteomics: Advances in interface development and application. , 2012, Journal of proteomics.

[93]  R. Solà,et al.  Nutritional biomarkers and foodomic methodologies for qualitative and quantitative analysis of bioactive ingredients in dietary intervention studies. , 2011, Journal of chromatography. A.

[94]  A. Cifuentes,et al.  Effect of dietary polyphenols on K562 leukemia cells: A Foodomics approach , 2012, Electrophoresis.

[95]  A. Cifuentes,et al.  Is metabolomics reachable? Different purification strategies of human colon cancer cells provide different CE‐MS metabolite profiles , 2011, Electrophoresis.

[96]  U. Sauer,et al.  Cross-platform comparison of methods for quantitative metabolomics of primary metabolism. , 2009, Analytical chemistry.

[97]  M. MacCoss,et al.  Capillary electrophoresis with Orbitrap-Velos mass spectrometry detection. , 2012, Talanta.

[98]  Ana Conesa,et al.  A multiway approach to data integration in systems biology based on Tucker3 and N-PLS , 2010 .

[99]  E. Ibáñez,et al.  Foodomics: MS-based strategies in modern food science and nutrition. , 2012, Mass spectrometry reviews.

[100]  A. Cifuentes,et al.  CE/LC‐MS multiplatform for broad metabolomic analysis of dietary polyphenols effect on colon cancer cells proliferation , 2012, Electrophoresis.

[101]  D. N. Perkins,et al.  Probability‐based protein identification by searching sequence databases using mass spectrometry data , 1999, Electrophoresis.

[102]  J. Yates,et al.  An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database , 1994, Journal of the American Society for Mass Spectrometry.

[103]  M. Walsh,et al.  METABOLOMICS IN HUMAN NUTRITION: OPPORTUNITIES AND CHALLENGES , 2005 .

[104]  E. Etxeberria,et al.  Metabolomic analysis in food science: a review , 2009 .

[105]  A. Varenne,et al.  Separation and quantitation of milk whey proteins of close isoelectric points by on-line capillary isoelectric focusing--electrospray ionization mass spectrometry in glycerol-water media. , 2010, Journal of chromatography. A.

[106]  A. Dominiczak,et al.  Capillary electrophoresis-mass spectrometry as a powerful tool in biomarker discovery and clinical diagnosis: an update of recent developments. , 2009, Mass spectrometry reviews.

[107]  M. Savitski,et al.  Proteomics-grade de novo sequencing approach. , 2005, Journal of proteome research.

[108]  R. O. Stephen,et al.  Generating precise mechanical stimuli and recording chordotonal organ discharge patterns using a microcomputer , 1990, Comput. Appl. Biosci..

[109]  A. Giuffrida,et al.  Mass spectrometry detection as an innovative and advantageous tool in ligand exchange capillary electrophoresis , 2011, Electrophoresis.

[110]  F. Ahmed The role of capillary electrophoresis-mass spectrometry to proteome analysis and biomarker discovery. , 2009, Journal of chromatography. B, Analytical technologies in the biomedical and life sciences.

[111]  Antonio Segura-Carretero,et al.  Global Foodomics strategy to investigate the health benefits of dietary constituents. , 2012, Journal of chromatography. A.

[112]  Dean P. Jones,et al.  Endoplasmic reticulum stress in nonalcoholic fatty liver disease. , 2012, Annual review of nutrition.

[113]  C. Andrés-Lacueva,et al.  Nutrimetabolomic strategies to develop new biomarkers of intake and health effects. , 2012, Journal of agricultural and food chemistry.

[114]  R. Kostiainen,et al.  Microchip capillary electrophoresis-electrospray ionization-mass spectrometry of intact proteins using uncoated Ormocomp microchips. , 2012, Analytica chimica acta.

[115]  Arjen Lommen,et al.  MetAlign: interface-driven, versatile metabolomics tool for hyphenated full-scan mass spectrometry data preprocessing. , 2009, Analytical chemistry.

[116]  S. Bonny,et al.  Genetically modified glyphosate-tolerant soybean in the USA: adoption factors, impacts and prospects. A review , 2011, Agronomy for Sustainable Development.

[117]  A. Cifuentes Food analysis and foodomics. , 2009, Journal of chromatography. A.

[118]  Rolf Danielsson,et al.  Comparing capillary electrophoresis-mass spectrometry fingerprints of urine samples obtained after intake of coffee, tea, or water. , 2008, Analytical chemistry.

[119]  N. Takahashi,et al.  Metabolomics of Supragingival Plaque and Oral Bacteria , 2010, Journal of dental research.

[120]  Rune Matthiesen,et al.  Methods, algorithms and tools in computational proteomics: A practical point of view , 2007, Proteomics.

[121]  J. Hardie,et al.  Oral microbiology: current concepts in the microbiology of dental caries and periodontal disease , 1992, British Dental Journal.