The Evolution of Analytical Chemistry Methods in Foodomics

Journal of Chromatography A, 1428 (2016) 315
Contents lists available at ScienceDirect
Journal of Chromatography A
journal homepage: www.elsevier.com/locate/chroma
Review article
The evolution of analytical chemistry methods in foodomics

Monica Gallo a , Pasquale Ferranti b,c,
a
Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, via Pansini, 5, Naples I-80131, Italy
Department of Agriculture, University of Naples Federico II, Parco Gussone, Portici I-80055, Italy
c
Institute of Food Science and Technology, National Research Council, Via Roma 64ac, Avellino I-83100, Italy
b
a r t i c l e
i n f o
Article history:
Received 1 June 2015
Received in revised form 26 July 2015
Accepted 2 September 2015
Available online 5 September 2015
Keywords:
Food analysis
Omics
Analytical chemistry
Foodomics
Food biomarkers
Personalized diet
a b s t r a c t
The methodologies of food analysis have greatly evolved over the past 100 years, from basic assays based
on solution chemistry to those relying on the modern instrumental platforms. Today, the development
and optimization of integrated analytical approaches based on different techniques to study at molecular
level the chemical composition of a food may allow to dene a food ngerprint, valuable to assess
nutritional value, safety and quality, authenticity and security of foods. This comprehensive strategy,
dened foodomics, includes emerging work areas such as food chemistry, phytochemistry, advanced
analytical techniques, biosensors and bioinformatics.
Integrated approaches can help to elucidate some critical issues in food analysis, but also to face the
new challenges of a globalized world: security, sustainability and food productions in response to environmental world-wide changes. They include the development of powerful analytical methods to ensure
the origin and quality of food, as well as the discovery of biomarkers to identify potential food safety
problems. In the area of nutrition, the future challenge is to identify, through specic biomarkers, individual peculiarities that allow early diagnosis and then a personalized prognosis and diet for patients
with food-related disorders.
Far from the aim of an exhaustive review of the abundant literature dedicated to the applications of
omic sciences in food analysis, we will explore how classical approaches, such as those used in chemistry
and biochemistry, have evolved to intersect with the new omics technologies to produce a progress in
our understanding of the complexity of foods. Perhaps most importantly, a key objective of the review
will be to explore the development of simple and robust methods for a fully applied use of omics data in
food science.
2015 Elsevier B.V. All rights reserved.
Contents
1.
2.
3.
4.
5.
6.
7.
8.
Introduction: analytical chemistry in food science . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4

Sources of information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
2.1.
Books, reviews and journals . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
2.2.
Web sites and databases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
From classical to instrumental approaches to food analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
The rise of modern analytical platforms: mass spectrometry and spectroscopic techniques . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
Spectroscopy-based methods in food analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Chromatography- and electrophoresis-based omics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
Sample preparation techniques for food analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
Foodomics applications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
8.1.
Detection, classication and use of food microorganisms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
8.2.
Pesticides, toxins and antinutritional factors in food . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
8.3.
Food allergy and digestion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
Corresponding author at: Department of Agriculture, University of Naples Federico II, Parco Gussone, Portici I-80055, Italy.
E-mail address: ferranti@unina.it (P. Ferranti).
http://dx.doi.org/10.1016/j.chroma.2015.09.007
0021-9673/ 2015 Elsevier B.V. All rights reserved.
M. Gallo, P. Ferranti / J. Chromatogr. A 1428 (2016) 315
9.
Perspectives . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
9.1.
The rise of the new integrated omic approaches . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
9.2.
Global changes: food security and sustainability . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
10. Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
1. Introduction: analytical chemistry in food science

In 1894, Wilhelm Ostwald, future Nobel prize in chemistry,
dened analytical chemistry as the art of separating, recognizing
different substances and determine the constituents of a sample.
Since then, analytical chemistry evolved from art to a branch of
chemical science of greatest theoretical and practical utility for
industry, medicine and in general for all applied sciences (Fig. 1).
Over the years, applications in food technology led to the development of analytical approaches aimed to the global characterization
of a food to dene its chemical, physical and sensory characteristics
and to ensure its quality and safety for consumers, supporting and
implementing the laws and regulations of the eld.
Recently, this comprehensive strategy has been termed
foodomics [13]. Foodomics is dened as a discipline that studies the food and nutrition domains through the application and
integration of advanced omics technologies to improve consumers
well-being, health and condence [3]. In the development of the
advanced foodomic platforms, because of their potential to prole
complex mixtures of biomolecules, mass spectrometry techniques
have assumed an unquestionable role. The analytical capability of
MS have made highly resolving, hyphenated separation devices
(HPLC, GC, CE, SFC, PAGE) able to characterize at the molecular
level the entire panel of the components of a complex system.
For these reasons MS, together with NMR and other spectroscopic
techniques, is the core of the omic technologies.
This paper illustrates the development and evolution of analytical methods which led to modern foodomic platforms (MS, NMR,
biosensors and ancillary techniques), based on high-throughput
instrumentation and computational methods, and the revolution
they introduced in food analysis. We also review the signicant
technological advances which are opening new and important
areas in food technology, food biotechnology and nutrigenomics.
2. Sources of information
Researchers in the foodomic eld must identify and select the
best methodology among those available to address their specic
questions. The main sources of information and general approach
to a literature search are detailed below.
2.1. Books, reviews and journals
Recent discoveries in molecular biology, analytical chemistry,
and biochemistry have led to the development of new tools that
are likely to revolutionize the study of foods. The fast development of food chemistry and technology over the last two decades
is described in the book Food Chemistry [4]. The book Foodomics:
Advanced Mass Spectrometry in Modern Food Science and Nutrition presents this rapidly emerging eld [5]. The book OMICS
Technologies: Tools for Food Science explores how these tools
reveal the fundamental pathways and biochemical processes that
drive food and nutrition sciences [6].
Omics methods are gaining in importance for process development and validation in food technology and biotechnology as
well as corresponding quality control of starting materials and
nal products (Fig. 2). Therefore, the number of reviews and journals dealing with use of omics methods in food processing and
nutrition has also rapidly increased, for instance: Food Technology

and Biotechnology, Journal of Agricultural and Food Chemistry (ACS
Publications), Food Chemistry, Food Analytical Methods (Springer),
Food Research International (Elsevier). Special Issues of the most
eminent analytical chemistry journals Journal of Chromatography; Trends in Analytical Chemistry (Elsevier); Electrophoresis
(Wiley) are regularly dedicated to update methods and applications
in food analysis.
2.2. Web sites and databases
Current informatic systems allow the generation, processing,
circulation and storage of various scientic information. Generally,
several websites are available for information on a particular
subject. A non-exhaustive list of relevant sites on foodomics
and its applications includes: (http://www.foodomics.eu; http://
www.chancefood.eu; http://www.foodomics.org; http://www.
allergome.com; http://www.foodchem.it; http://www.safefoods.
nl).
Databases together with statistical systems with thematic
character provide a comprehensive and accurate vision of the phenomenon under investigation. Each database is accompanied by
various information (methodologies, classications, denitions) on
the subject. Foodomics is based on molecular characterization by
metabolomic and proteomic approach; therefore, some databases
are www.expasy.ch; GeneBank, EBI, GEO and also BioPEP, PepBank,
EROP or APD.
3. From classical to instrumental approaches to food
analysis
Food chemistry deals with the themes related to the qualitative
and quantitative characterization of foods and their (bio)chemical
transformations during production, maturation and storage (Fig. 1).
The roots of modern food chemistry trace back to the XIX century,
when chemists began studying foods and isolate their macrocomponents.
Most modern food analysis has been advanced by food safety
issues. The U.S. Food and Drug Administration (FDA) was created in
the early XX century to protect consumers from food adulteration.
In that period, nearly all food analysis was carried out using classical chemistry in solution [for an extensive review see 7], based on
specic chemical reactions and using only chemicals and the basic
equipment easily available in all laboratories. From these bases,
Henneberg developed the classication scheme to determine food
composition in terms of macro-components (moisture, proteins,
carbohydrates, lipids) still in use today (Fig. 3). Later, the basic
Kjeldhal procedure for determining the food protein content, the
golden standard for over 100 years, is based on acidbase titration
after conversion of protein nitrogen to ammonia. The limitation of
the method, demanding and laborious, as also recently exploited by
its inability to identify the poisonous adulteration of feed and milk
powder with melamine, are those common to all the chemistry in
solution
It is not an overstatement to say that the demand from food
and agriculture sector was one of the driving forces for the instrumental developments. The rst electronic, portable pH meter was
built by Beckman to meet the request of a consortium of fruit
Fig. 1. The derivation of foodomics strategies from the analytical chemistry owchart. Modern omic approaches using high-throughput instrumentation and computational
methods for assessing food quality [13].
producers in California to check uniform lemon maturation on eld.

Other milestones were the introduction of electronic spectroscopic
devices between 1940 and 60 [7] (Fig. 3). With the availability of
commercial instruments, these devices soon became essential components of any food research laboratory, as they allowed to obtain
characteristic ngerprints of foods and of their components.
Also the evolution of chromatographic methods, spanning all
the XIX century, had a pivotal role in the development of food analysis methods. Starting from the pivotal work of Martin and Synge [8]
on gas chromatography (GC) (Fig. 3) and the commercialization of
the rst GC instruments in 1952, this technique soon evolved from
the use of packed columns to the more efcient capillary columns

in the 70s at the Hewlett-Packard laboratories, establishing GC as
an invaluable tool in food analysis [9]. Also liquid chromatography (LC), born well before GC but limited by the lack of knowledge
of the basic mechanisms of its functioning as well as by the very
lengthy and solvent-consuming process, was revolutionized in the
same years by the introduction of high performance liquid chromatography (HPLC) [10]. HPLC made possible for the rst time the
high resolution separation of complex mixtures of non-volatile analytes in much lower times (a few minutes) compared to classical LC
analyses.
Fig. 2. Research issues related to the qualitative and quantitative analysis of food products and their (bio)chemical transformations during along the whole supply chain.
Fig. 3. The evolution of the application of analytical chemistry methods to food analysis.
Other chemical/biochemical techniques such as thin layer

and paper chromatography, mono-dimensional (1D) or twodimensional (2D) polyacrylamide gel electrophoresis (PAGE), and,
more recently, capillary electrophoresis (CE) and ELISA have
expanded the arsenal of tools available in either component identication or in adulterant detection in foods. However, although
these techniques constituted a considerable advance in routine
analyses, their merely descriptive character was apparent: all these
methods, in fact, compared a prole with the one expected for a
given food product and therefore could not explain the causes of
an altered outcome at the molecular level. Given the limitations of
the above approaches methods, it soon appeared that conrmatory
strategies were also required to provide an unambiguous identication of markers of foreign food components. These limitations
can be overcome by the combination of the above described separative methods with powerful identication techniques, such as mass
spectrometry (MS), IR and UV spectroscopy and on spectroscopic
techniques such as nuclear magnetic resonance (NMR).
4. The rise of modern analytical platforms: mass
spectrometry and spectroscopic techniques
MS, NMR and a small number of other spectroscopic techniques,
often in combination with separation methods and with statistical
and bioinformatics tools are today the key analytical methodologies on which the recently established omic technologies such as
proteomics ad metabolomics are based.
The basic parts of a mass spectrometer are the ion source (in
which ions are generated), the ion analyzer (where ions are separated and their m/z ratio determined with high accuracy) and the
ion detector. MS data are recorded as mass spectra which are
2D graphs displaying ion intensity vs. the mass-over-charge (m/z)
ratio. The accurate measurement of the m/z enables the access
to a unique characteristic of the molecules, i.e. their molecular
weight. Often combined with data generated by the fragmentation of selected molecules (Tandem MS or MS/MS experiments),
this information allows to identify or structurally characterizes (or

contributes to this aim) the components of a mixture.
The rst commercial mass spectrometers, equipped with electron impact ionization (EI) or chemical ionization (CI) ion sources
and quadrupole (Q) analyzers, date now almost 60 years ago. In
the early 60s, Associated Electrical Industries produced MS-9 and
soon after MS-30 as the rst high resolution instruments, followed
by the MS-50 instrument, able to achieve a working resolution of
10,000 at 1000 m/z. The idea was that if a mass spectrometer would
have been able to measure the mass of a molecule with high enough
accuracy to deduce its elemental composition, this molecular structure would have been unambiguously assigned, with the exception
of the isomeric species. Incidentally, the concept is still the basis of
assignment of the molecular structure of an analyte through high
resolution measurement of molecular weight by the new generation of hybrid instruments, which has opened the gates of the
metabolomic era.
MS was soon applied to the analysis of organic molecules,
including agricultural and food contaminants such as pesticides,
halogenated hydrocarbons, dioxins, bacterial metabolites in matrices. The introduction in the 70s of commercial GCMS instruments
mounting quadrupole analyzers in place of the costly and unstable magnetic sectors by Finnigan Instruments (then Thermo) and
by Hewlett-Packard (now Agilent Technologies), led to a rapid
and wide diffusion of GCMS in routine (food) research. These
developments contributed over the following years up to now.
Still today, in different congurations, e.g. EI and CI ion sources
coupled to quadrupole (Q), ion trap (IT), or time-of-ight (TOF)
analyzers, hyphenated GCMS remains one of the most powerful approaches in food metabolomics, allowing fast and accurate
tracking of metabolite patterns indicative of food quality and
preservation over time. Recent applications concern the distinctive
signature of wine metabolites [11,12].
However, at that stage, determining the largest part of the constituents of a food was still precluded, because GCMS methods
were only able to analyze volatile compounds with a mass not
exceeding 1 kDa. This gap was bridged in the early 80s, by the
introduction of soft ionization techniques, such as fast atom
bombardment (FAB), and then by electrospray ionization (ESI)
and matrix-assisted laser desorption/ionization (MALDI), which
allowed to measure non-volatile, high molecular mass molecules.
In 2002, John Fenn and Koichi Tanaka were awarded the Nobel
Prize in Chemistry for the pioneering application of ESI and MALDI,
respectively, to measure the molecular weight of large proteins
and (bio)polymers. For the rst time it was possible to analyze
with high accuracy intact (poly)peptides, proteins, polysaccharides
and complex lipids, covering the whole range of the food constituents. ESI and MALDI are the two techniques most commonly
used for MS [13]. The way was open for macromolecular analysis and one of the rst applications was actually the assignment
of phosphorylation sites of milk beta-casein [14]. These results did
not remain conned to basic biochemical research, but were soon
recognized as unique tools in applied food science: the detailed
reconstruction of the proteolysis pattern of ripened Parmigiano
cheese [15,16] with identication of the whole set of peptides
enriching the cheese at any age, including those providing typical
sensory attributes and nutritional properties, such as calcium transporter casein-derived phosphopeptides [17]. Other applications
were the structure/function correlation between casein genetic
variants, micelle size and cheese making properties of milk [1820].
Thanks to the availability of the new ionization techniques, MSbased food and nutrition proteomics are today capable to address
a wide range of analytical questions which include issues related
to food quality and safety, certication and traceability of (typical)
products, and denition of the structure/function relationship of
food proteins and peptides.
5. Spectroscopy-based methods in food analysis

Similarly to MS, modern spectroscopic techniques such as IR, UV
and NMR, are all capable of high sample throughput and automated
analysis. Born as tools for structure assignment of compounds in
organic chemistry in the rst half of XX century, their potentiality
were initially either masked by poor knowledge of their theoretical mechanisms or their diffusion limited by the instrumental
complexity and cost. However, they expanded rapidly over the
remaining half of the century after the introduction in the 90s
of relatively low cost but reliable benchtop instruments and by
the development of software able to manage data from complex
component mixtures. One of the greatest advantages of these techniques comes from their capability to deliver fast quantitative data,
thus providing a superior alternative to the long and tedious procedure of the wet chemistry.
In IR and NIR (near infrared), quantitative analysis is made possible by monitoring the vibrational transitions of the characteristic
functional groups of the various food constituents (water, proteins
carbohydrates, lipids). The rst NIR applications in food analysis
date back to the 60s with the determination of water content in various foods. In the 70s the approach was extended to the assay of fat
and protein content in cereals and in derived products and then to
determine low-abundance components in food matrices (caffeine
in tea, oxidized lipids in oil). The turning point was when bench-top
IR and NIR instruments made possible to monitor routinely a full
set of physico-chemical parameters in a single analysis. Immediate applications were the quantitative determination of the various
classes of constituents in a food matrix, as well as, for instance,
the content of nutraceuticals in vegetables, related to the maturation process by monitoring their evolution either on the plants or
post-harvest.
Since then, the diffusion of NIR instruments in food industry and
laboratories has allowed to verify quality and authenticity of food
products or ingredients, as well as the changes caused by technological treatments. In the oil sector, for example, NIR has been used
for typing extra virgin olive oils, differentiating them in terms of
their geographical origin. In cereals, NIR spectroscopy has proved
capable of predicting complex characters of quality. The inuence
of genotype and environment on the characteristics of composition and quality can be derived by analysis of whole wheat grain,
correlating the information derived from the spectra of each sample with chemical and rheological indices, measured by reference
test. Even in the dough fermentation process, NIR has been particularly effective in providing useful information, comparable with
those obtained from traditional approaches, with the advantage of
a higher speed. At industrial level, this provides on line prediction
of the grinding yield, of the bread- or pasta-making quality and the
dough behavior during bread baking.
As mentioned, of particular utility is the availability of on-line
NIR instruments, which allow to automate sampling and analysis
and to monitor the industrial processes, measuring in real time
the parameters of interest, and to decide immediate corrective
actions when needed. Production lines can be followed through
a ber optic system (Fig. 4) able to perform absorption and reectivity measurements. Applications in food production monitoring
are uncountable, form the process of fried chips to baked goods,
just to mention a few.
In the eld of food adulteration, some specic targets may be
used as markers of the production system. NIR enables to discriminate fresh from frozen sh, by detecting the water loss in the
product [21] and is useful to detect fraud replacement, especially in
products prepared from minced sh [22]. Wild from farm sh can
be distinguished by IR determination of the fatty acid prole. For
example, a high level of arachidonic acid, unsaturated n-3 and saturated fatty acids in muscles are distinctive of the product shed,
while a high amount of C18 fatty acids (particularly oleic, linoleic
and -linolenic acid), due to intake of vegetable oils from feedings,
characterizes farm sh. The latter, moreover, have a lower amount
of water and a higher fat, as they move less and receive a richer
feeding.
However, the measure of the progress made with respect to the
times of chemistry-in-solution age, as already noted above about
the pitfalls of the Kjeldhal method for food nitrogen determination,
is the possibility of NIR to detect and quantify in a few second time
the presence of melamine in milk and milk powders. Today NIR
and Fourier transform IR instruments allow quantication of ppb
melamine in infant formula powder and soymilk [2326].
Also NMR was conceived for analysis of organic molecules
in the late 1940s. Whereas NMR is not as sensitive as MS, it
requires minimal sample handling, provides rapid analysis, and
offers the potential to run multiple tests on a single sample. In
food applications, the availability of commercial low size, automated instruments are making NMR useful in routine applications
to determine moisture and the content of other components; it
can be applied to food lipids to measure the degree of conjugated
double bonds in fatty acid mixtures in an easy and non-destructive
manner. More interesting applications, which rely on the measurement of relaxation times, allow quantitative analysis not only of the
various components of a food, but also of the ratio among physical
phases within a single food component, for instance the ratio solid
fat/liquid fat or among the different forms of solid fats within a food
ingredient or a nished product. Information like this is invaluable
for food industry in either production monitoring or in the design
of all-new products to obtain the desired rheological and sensory
characteristics.
In metabolome analysis, NMR allows the acquisition of highly
reproducible and resolved spectra on complex food matrices,
reporting on hundreds metabolites. NMR is being widely used to
characterize wine and nd the association of wine metabolome
Fig. 4. The application of near infrared spectroscopy (NIR) to the food product analysis has allowed automation and continuous monitoring of the whole production chain.
The example refers to the industrial production of chips.
with environmental and fermentative factors in vineyard and

wine-making [27] as well as in the differentiation of wines from
diverse territories or cultivars [28]. The NMR-derived proles are
represented by analytical spectra, which are compared using statistical techniques such as pattern recognition. Further, metabolomic
datasets are combined with their other omic counterparts, providing complete views into the molecular pathways of systems
biology. The continuous miniaturization of NMR instrumentation,
which is already available as on-site portable devices for foodomics
applications, and the development of easy-to-use software for data
processing, ensure that NMR-based metabolomics is destined to
continue to emerge as an analytical tool in future.
Also the applications of electronic biosensors in foodomics are
increasing. These include the possibility of label-free detection and
real-time monitoring. In the past two decades, food science has
seen great advances in the development of biosensors and biochips
capable of characterizing and quantifying food biomolecules [29].
Their simplicity and sensitivity make biosensors an effective means
of characterization and monitoring contamination of food samples
[30].
In particular, antibody-based biosensors are able to perform
very specic and sensitive analyses of molecular interactions. Surface plasmon resonance (SPR) allows qualitative and quantitative
measurements of biomolecular interactions in real-time without
requiring a labeling procedure. Today, the development of SPR is
leading to compact, medium-cost, and sensitive biosensors [31]. In
food science, SPR biosensors are gaining popularity as viable tools
for biomolecular analysis. At the basis there are also the development of electronic tongue (taste sensor) and electronic nose (odor
sensor). A taste sensor is produced by intelligent sensor technology
targeted to pharmaceutical and food companies. The taste sensor
and electronic nose play the role of gustatory and olfactory senses,
respectively. One characteristic of taste sensors, is that each sensor
electrode (lipid/polymer membrane) is specic to each taste.
Coupling of SPR with MS (SPRMS) might efciently allow
molecular food characterization. Among the different strategies
under development, the combination of MALDI-MS with SPR is
opening the metabolomic eld known as sensometabolomics, linking metabolomics compositional data with their impact on the food
sensory prole [32]. Two strategies are possible for MS detection
of the SPR captured ligands; one is based on their recovery by elution from the biochip surface and their subsequent MS analysis,
and the other one consists in the direct on-chip MS analysis. The
former is mainly used because most of the SPR-MS coupling devices
described in literature operate with a ow cell. However, the
microrecovery procedure is known to be time-consuming and leads
to material loss and contamination, while the quantitative elution
could be challenging in the case of a high-afnity interaction. The
direct on-chip MS analysis may overcome these limitations, provided that the SPR surface could be easily interfaced with the mass
spectrometer. This format for rapid, collective, and automated onchip MALDI-MS analysis has numerous potential applications in
food and nutrition.
6. Chromatography- and electrophoresis-based omics
The introduction of GC allowed the separation, identication
and determination of chemical compounds in complex mixtures
and the control of the purity of volatile or volatilized compounds.
On the other side, the potential of LC, which is branched in a series
of methodologies such as reverse phase, ion exchange, afnity, etc.,
has been enormously increased by the introduction of HPLC and
more recently by ultra high performance liquid chromatography
(UPLC). The association of such equipment with a large array of
detectors of different nature has made possible the identication of
most of the constituents of complex mixture and their quantitative
variations and alterations in a food matrix.
When these separation technologies are combined with MS or
tandem MS (MS/MS), the superior identication power of MS in
omic analysis is greatly enhanced. Recently, the urinary metabolic
proling of diet-induced hyperlipidemia in a rat model has been
characterized using UPLC coupled with Q/TOF MS/MS [33].
A key issue is that once the food compounds of interest have
been identied, in most cases the determination of the amount of
compounds of interest is required. Quantitative methods can be targeted or untargeted. The usual approach to this challenge is to apply
targeted methods, which are methods specically aimed to the
determination of specic target compounds, previously decided.
To this aim, specic procedures are developed for extraction,
clean up, separation and detection of the compounds of interest.
However, the lack of available reference standards for many of the

metabolites (particularly the myriad of plant secondary metabolites) is a challenge that can be somehow tackled with the MS-based
untargeted metabolomic approach. A further reason for this is the
capacity of modern MS instruments to acquire process and store
a huge mass of data during analysis. Basically, non-targeted measurement uses generic sample preparation and chromatography,
combined with full-scan mass spectrometric detection. All ions are
detected during the entire chromatography run time and, in this
way, there are no limitations to the number of substances that can
be detected. Untargeted methods have been developed to monitor hundreds metabolites at a given time by using high-sensitivity
techniques.
On his side, electrophoresis is probably the most efcient family
of techniques for obtaining high resolution separation of mixtures of molecules on the basis of their different migration under
the effect of an electric eld. It is extensively used in biological, biochemical and molecular for the separation of proteins,
polynucleotides and other biopolymers. Detection is obtained by
(immuno)staining, or, in CE, by on-line photometric, electrochemical or MS detectors. 1D- or 2D-PAGE of proteins makes possible
either the qualitative or the quantitative analysis of proteome by
adding internal standards and using spectrally distinguishable uorescent dyes (difference gel electrophoresis, DIGE [34]).
Electrophoretic techniques play a basic role in proteomic analysis. To date, 2D-PAGE remains the most reliable and efcient
method to separate one-step a large number of proteins. Once
stained, protein spots excised from the gel are digested in situ
with a protease (usually trypsin) and identied by MS or MS/MS
experiments.
In food science, the application of gel electrophoresis as well as
of advanced electromigration methods, such as capillary zone electrophoresis (CZE), micellar electrokinetic chromatography (MEKC)
to the analysis of proteins, phenolic compounds, heterocyclic
and biogenic amines, mycotoxins, melamine and melatonin, has
opened a very important food research eld, where research
institutions, agencies, regulatory laboratories and instrument manufacturers are combining efforts to develop analytical methods on
food composition, quality and safety [3537].
Similarly to chromatography, in electrophoresis the most powerful on-line approach is that combining the fast and resolutive
CE separation capabilities with MS identication. A CEMS-based
approach was proposed [38] for the detection of adulteration of
caprine and ovine milk, with bovine milk. By analyzing the whey
protein fraction from milk, the method allowed the detection of
added bovine milk into the non-bovine ones within the concentration range of 595%. In CEMS special attention has to be paid
to the selection of MS-compatible volatile separation buffers and
the selection of the adequate strategy when capillary coating is
required to avoid MS signal suppression [39]. A comprehensive
study on the use of CE volatile separation buffers compatible with
ESI-MS detection was carried out in order to obtain as much as
possible information from the zein protein fraction of maize [40,41]
with important applications also in analysis of genetically modied
plants.
7. Sample preparation techniques for food analysis

Sampling is the rst step of the analytical process and is crucial for the correct interpretation of the results; an error at this
stage cannot be corrected in any way and affects the entire analytical process. In essence, even the best available method will lead to
incorrect results and unnecessary if applied to a sample improperly
prepared. Correct sampling is not possible without a deep knowledge either of the food matrix or of the analytical procedure to be
applied. The sample must be representative of the material investigated and homogeneous. It is also important to prevent any possible
alteration of the sample during storage prior to the extraction.
Sampling procedures depend on the physical nature of the sample (gas, liquid or solid) and the purpose of the analysis request.
Foods are very complex matrices, and require specic procedures
for the sample preparation. Rapid extraction of the analytes of interest is essential to minimize or prevent the typical alterations that
occur in food samples as a result of enzymatic activity, lipid oxidation, microbial growth and physical changes. Sampling of uid
food matrices must ensure their uniformity and use non-invasive
methods (for example, avoid the formation of precipitates by mild
heating). In the case of solid samples it may be more difcult to
ensure uniformity. Generally primary samples are collected from
various sites of the material and gathered in a bulk sample which is
homogenized, possibly after grinding. These operations follow precise procedural schemes reported in the reference standards for the
type of food and the type of contaminant [4244].
The choice of the method of sample preparation can be complex,
since it often requires considering several parameters simultaneously. First, it is important to assess the chemical and physical
properties of the compound of interest, including volatility, polarity, solubility and stability (thermal, oxidative, hydrolytic). The
food matrix should also been considered to evaluate the analyte
interacts with the other components in the sample and the possible degradation reactions, for example those by enzymes. Food
chemists tend to speed up sample preparation by single step extraction and purication. The extraction conditions must be optimized
in order to maximize the recovery of the analytes. Recovery tests
should be performed with certied material, when available or on
samples fortied with an appropriate concentration of the standard
mixture. When necessary, before the nal analytical determination a step of ne purication of the sample should be included
to eliminate the interfering molecules co-extracted along with the
analytes. For example, non-polar compounds can be removed by
solvent extraction or by inducing coalescence under low temperature, while proteins can be eliminated by selective precipitation or
dialtration. In other cases, selective depletion of most abundant
interferences may be removed by afnity-based cartridges.
Traditionally, sample preparation methods employed in food
analysis, such as conventional liquidliquid extraction and
solidliquid extraction were long and labor intensive. Today, the
introduction of solid phase extraction (SPE) packed materials has
led to speed handling and extreme versatility [45]. The commercially available cartridges and columns are pre-packed with various
stationary phases (reverse phase C4 , C8 , or C18 , ion exchange,
amino). The range of application includes food peptides and proteins, but also polyphenols and other small compounds. The sample
in liquid phase is loaded through the SPE column where target
analytes are selectively retained in the sorbent while other interfering and matrix components are washed out. The pre-concentrated
analytes are then eluted with a relatively small volume of an appropriate solvent as a puried and relatively concentrated extract
amenable to omic (MS, NMR) analysis. Miniaturized versions of
SPE, specically designed for sample preparation in foodomic analysis, are commercialized by various producers and became popular
in the last years because of their easy and fast use. They allow
single-step desalting, concentration, and purication of food samples for sensitive downstream analyses, for instance proteomics
and metabolomics.
Dispersive SPE (dSPE) is also at the core of the novel extraction procedures commercialized as QuEChERS (quick, easy, cheap,
effective, rugged, and safe), originally developed for the analysis
of pesticides in vegetal samples [46], and now extended to many
other foodomic determinations. This technique offers a fast alternative to traditional liquidliquid and solid phase extractions. The
10
Fig. 5. The QuEChERS methods of sample extraction and preparation for omic analysis are based on SPE.
process involves two simple steps (Fig. 5). First, the homogenized
samples are extracted and partitioned using an organic solvent and
salt solution. Then, the supernatant is further extracted and cleaned
using tubes prelled with dispersive SPE resins (for instance C18),
and is immediately ready for GCMS or LCMS determination.
Solid-phase micro-extraction (SPME) technique is particularly
suitable for the analysis of food and beverage matrices. In SPME,
the diffusion of analytes from the sample matrix to the extraction phase on a solid support, allows to reach equilibrium between
phases and hence efcient extraction. Fibers, the most commonly
used form of solid support, are widely used in metabolomics to
extract volatile compounds for GC applications and non-volatile
compounds for LC. The development of high resolution MS combined with the micro extraction capabilities of SPME, although still
in its early days, is rapidly making SPME-MS a powerful analytical tool. Since its introduction, the number of SPME applications
in food analysis has increased exponentially, from analysis of food
contaminants to evaluation of the aroma compounds or of wine,
fruit and cheese [4750]. Also, the avor prole of processed and
stored foods is an important source of qualitative and quantitative
information, able to characterize and dene the state of preservation of the food itself. The aroma components are generally present
at very low concentrations and belong to heterogeneous classes
of compounds with polarity and reactivity very variable; for these
reasons, SPME is often more advantageous compared to other analytical techniques [51].
8. Foodomics applications
8.1. Detection, classication and use of food microorganisms
Food industry operators and suppliers are required that all procedures under their control satisfy food regulation and law relevant
to their activities at all stages of production, processing, storage
and distribution, and verify that such requirements are always
met. Among the mandatory procedures are those based on Hazard Analysis and Critical Control Points (HACCP), a protocol, a set of
procedures aimed at preventing the risks related to food contamination [52]. The critical issue in this frame is the control of products.
As already observed, the initial impulse to the birth of food analysis in the early age was given by the necessity of providing food
analysts which the appropriate tools to ensure food safety.
The main food spoilage microorganisms are bacteria, yeasts and
molds [53]. They can damage products causing undesirable variations in the organoleptic characteristics (avor, smell and taste)
[54,55]. Traditional means of food bacterial recognition include
microorganism isolation and growth and specic immunological
or genetic assays. These typically take 13 days to complete, a time
detrimental for the product quality. To ll this gap, omic approaches
have been directed to the development of methods for bacterial
proling through MALDITOFMS and ESIMS/MS ngerprinting
of bacterial proteins in order to distinguish among different species
and, in some cases, among strains [56,57]. Through these proling
methods, it is possible fast and sensitive detection of pathogens or
spoilage micro-organisms affecting for instance food quality and
safety during processing and storage. Omic technologies can also
help scientists to derive better understanding of the life cycles of
bacteria. Dening the mode of action of bacteria and the mechanisms that confer stress resistance should enable more rational
design of food preservation techniques. In addition, this information can also be used to pinpoint areas of the food chain that are
most susceptible to microbial contamination.
More accurate description of the contaminating microorganisms has been achieved by integration of different omic approaches
(glycomics, lipidomics, metabolomics, peptidomics) able to provide
either structural or quantitative identication of the specic
metabolites produced by the various micro-organisms. GCMS
based metabolomics has been used to prole food products to identify volatile compounds from pathogen contamination. In a recent
study principal component analysis (PCA) was used to identify
important regions in the GCMS chromatogram that resulted from

the prole of volatile organic compounds from natural spoiled pork
and pork contaminated with Salmonella typhimurium [58]. These
approaches are going to be integrated to design sensitive sensors
on a microchip surface for automated detection. The detection of
microorganisms using MALDI-TOF-MS is already ongoing [59] and
dedicated MS instruments are already available, such as the Bruker
Biotyper Biomerieux.
8.2. Pesticides, toxins and antinutritional factors in food
Pesticides are synthetic chemicals that are used in agriculture to
combat pests, diseases and antagonists of cultivated plants. Many
pesticides may contaminate the food chain and thus have adverse
health effects, also depending on the dose that is ingested [60]. The
pesticide residues in foods should not exceed the amount established for each pesticide. However, the law regulations consider
only the risks related to the assumption of individual pesticides,
while not fully assessing the risk of the presence of several different pesticides on the single product, nor the synergies between
different substances, which can be much greater than the sum of
the negative effects of the individual substances. For these reasons, analytical methods are needed to screen, conrm and quantify
the maximum number of pesticides [61]. Multi-residue MS-based
methods provide the basic tools to the analyst for determining
these residues. For many years, GCMS with quadrupole analyzer has been the technique of choice because of its ability to
resolve a single member of a chemical class and individual analytes in extracts containing potential interferences. Unfortunately,
many pesticides are not amenable to GC analysis as a result of
their thermal instability and polarity [6265]. Therefore, alternative and more selective have been developed, based on MS/MS and,
more recently, on high-resolution time-of-ight (TOF) and orbital
trap/Fourier transform (Orbitrap) mass analyzers. The increasing
interest in the use of HRMS in food contaminant analysis for its suitability for both targeted and untargeted analysis, especially with
the latest Orbitrap Velos and Fusion instruments. Furthermore,
with the same instrument a variety of tasks can be carried out: preand post-target analysis, retrospective analysis, and identication
of transformation products [66].
Mycotoxins and algal biotoxins which are two kinds of natural
toxic substances associated with food safety, have the characteristics of strong toxicity. Among the detection means, LCMS
is being widely used for its sensitive and efcient characteristics. LCMS applications related to food toxin testing have been
recently reviewed, as well as the related sample processing technology progress [67]. For peptide toxins, for instance the algal
hepatotoxic microcystins, MALDI-TOF-MS and ESI-Q-TOF-MS/MS
have been useful for fast screening and quantitative determination
of known toxins, as well as for structural characterization untargeted analysis [6871]. MS analysis has been then extended to the
set-up of a method for quantitative determination of microcystins
in nutraceuticals, food integrators, animal feedings, as well as to
the analysis of biological uids in patients to diagnose toxin poisoning. In this way, qualitative and quantitative information can
be obtained to monitor rivers, lakes and water reservoirs and to
improve current knowledge on algal contamination in the food,
feed and drinking water chain, and also to detect protein markers
to discover the use of unsafe water in sh and seafood aquaculture.
In some foods, especially those of plant origin, often molecules
can be present, which perform different roles as natural defense
molecules against molds, bacteria and predators. These effects
occur especially when the food is not cooked nor subjected to
other physical, chemical or enzymatic treatments, able to deactivate these molecules, eliminating the toxic or anti-nutritional
activity [72]. The anti-nutritional factors are a very large class
11
of compounds that have a depressive effect on the digestion

and utilization of food nutrients (enzyme inhibitors, lectins, phenols, saponins, polyphenols, glycosinolates, organic acids). Among
these, lectins are glycoproteins present in many vegetables where
they are involved in defense functions. The best studied plant
lectins are wheat germ agglutinin and red bean phytohaemagglutinin (PHA). Inaccurate heat treatments of legumes have caused
severe poisoning outbreaks. PHAs present in uncooked legumes
can cause damage to the intestinal mucosa and inhibit digestion
and absorption of nutrients. Bean-derived alpha-amylase inhibitor
preparations (Phaseolus vulgaris), used to decrease starch digestion
in subjects affected by chronic diabetes, obesity (starch-blockers,
weight blockers). MS-based strategies have been applied and optimized to set up proteomic methods for lectin structural and
functional denition and to monitor the structural changes (proteolysis, oxidation, sugar changes) in raw and in industrially treated
products [73]. In this way, it has been possible to optimize a strategy which makes possible both the structural and the quantitative
analysis of PHA residues in food supplements and dietetics.
8.3. Food allergy and digestion
Food allergy is a specic form of intolerance to a food component
that activates the immune system in predisposed individuals [74].
Despite the diversity of the human diet in the various countries,
foods responsible for the majority of food allergies in the world are
relatively few. Nearly 90% of food allergies are due to only eight
foods (the big eights): milk, egg, soy, wheat, peanut, shell fruit
(hazelnut, almond, walnut, pecan, cashew, pistachio), sh, shellsh. All allergenic foods are able to cause anaphylaxis, but some
in particular may cause life-threatening reactions. Milk, egg and
peanut are responsible for the vast majority of food-induced allergic reactions in children, while peanut, nut, sh and shellsh are
responsible for the majority of food-induced allergic reactions in
adults [75]. The management of food allergies continues to consist
of educating patients to avoid relevant allergens, to recognize early
symptoms of an allergic reaction in case of an accidental ingestion,
and to initiate appropriate therapy.
The eld of food allergy is probably the one where the progress
of analytical omics from the early times is more evident. In the
last years proteomic science has started to provide an important
contribution to the disclosure of basic aspects of food-related diseases. Among these, the identication of proteins involved in food
allergy and their mechanism of activation of toxicity. Elucidation
of these issues requires the integration of clinical, immunological,
genomic and proteomic approaches [76]. From the pioneer studies
of Sander [77], electrophoresis-based omics play an irreplaceable
role in the recognition of food allergens. The analysis of seeds proteins (cereal, legume and three nuts) by immunochemical assay,
using sera of allergic subjects as immunoglobulins source, followed
by proteomic approach is producing a deeper characterization of
already known allergic proteins and, at the same time, the detection
of new allergens.
In this context detection of hidden allergens, especially peanut
and hazelnut in commercial products often intended for children,
of gluten proteins in wheat-derived, of residual milk or egg proteins used as ning agents in wine. To detect their presence in
food and food production processes, ELISA methods are by far the
most widely used [78]. These methods represent a fundamental
screening tool, but do not provide information on the content of the
single allergen in the product. On the other hand, the traceability
of allergenic protein in the production chain requires reliable analytical methods, selective and adequately sensitive. Recent studies
have exploited MS-based omics as an alternative to the ELISA
golden standard in complex foodstuff analysis. Interestingly, analysis of a large number of beer samples has shown that gel-free
12
shotgun proteomics enable the multiplexed qualitative and quantitative targeted determination of allergens with limits of detection
and quantication down to the low-ppb range, also allowing detection of unknown allergens by untargeted analysis, at difference of
ELISA [79,80].
An important, and in many respects unexplored issue concerns
the role of metals and their mechanism of action in allergic reactions induced by food, which is being explored by inductively
coupled plasma (ICP). The more recent analytical approach that is
being developed in this area is multi-instrument approach based on
a high sensitivity ICP detector for elemental analysis, on line with
MS (ICP-MS) and with a further MS detector for the structural analysis of proteins. This approach has the potential to provide a reliable
identication and determination of metals, their ion species and of
their binding to proteins in food matrices [81].
Strictly related to food allergy and intolerance, the characterization of the pool of peptides released from the gastrointestinal
digestion and the identication of the epitopes responsible for eliciting the allergic reaction by in vitro and/or in vivo models can make
possible a full understanding of the so-called digestome and the
mapping the IgE-binding region of the proteins. MALDI-TOF and
HPLCESI-Q/TOF-MS/MS analysis allowed the characterization of
the digestion stable domains of wheat prolamins that elicit celiac
disease [82] and the potential epitopes of milk proteins surviving
all the digestion compartments in a complete in vitro model and
are able to cross a cell model of the intestinal epithelium [83,84].
9. Perspectives
9.1. The rise of the new integrated omic approaches
The interaction of modern food science and nutrition with disciplines such as pharmacology, medicine or biotechnology is the basis
of a new landscape of challenges and opportunities, within which
there are new trends in food research toward using of increasingly
integrated advanced strategies, omic approaches, bioinformatics
and clinical assays, to study issues considered not addressable only
a few years ago [3,8590].
Application of the novel omics techniques to food science is
improving our knowledge on the relationship between nutrition
and health status of individuals. Recent studies show that the individual gene expression prole is related to the dietary pattern
[91,92]. Current developments in genomic and genetic technologies
such as the availability of DNA microarrays have pushed strongly
nutritional and toxicological research from epidemiological and
physiological approaches to those genomic- and transcriptomicbased, opening the eld of nutrigenomics, i.e. the study of the
inuence of nutrients or contaminants on the entire genome at the
transcriptional level [93]. Also, genotoxicity induced by the presence of potential endogenous and exogenous substances related
to the diet can be revealed by studying changes in gene expression and identifying specic biomarkers [94,95]. The impact of
toxic substances can be modulated by specic food components
that can act as inducers, activators, inhibitors, suppressors or
substrates of enzymes related to toxicity or detoxication. The
use of DNA microarrays offers the opportunity to study simultaneously the genes that respond to toxic substances, including
those related to the metabolism of xenobiotics, the mechanisms of
DNA repair, cell growth and responses to stress. Present studies are
focused on those enzymes, such as cytochrome P450, glutathione Stransferase, UDP-glucuronosyltransferase, N-acetyltransferase and
sulfotransferase, involved specically or coordinated in response to
toxic substances ingested [96100].
Furthermore, the genomic/proteomic approaches can be used
for analytical purposes to detect the presence of hazardous
ingredients, such as the allergens, based on the detection of specic

sequences, or to provide information on the presence or otherwise
of any pathogenic bacteria [101,102]. In this context, MS techniques
allow the analysis of multiple proteins and peptides on a large scale
and with high yields, even in a single experiment. Because of the
high number of data concerned, the use of advanced statistical tools
for data analysis and correlation, as well as those of bioinformatics,
is an indispensable tool for this research. These advancements are
already providing tools to food and nutrition research [103], by giving, for ensuring the correct information on dietary intake through
recognition of specic food biomarkers in biological samples. This
interest also coincides with the trend of medicine and bioscience to
develop new approaches for the prevention of diseases through the
achievement of adequate food consumption and the development
of valuable functional foods [104106].
9.2. Global changes: food security and sustainability
Another critical theme in food research is related to the security
and sustainability of the food chain, especially urgent in relation to
the global challenges of the modern world, which also include the
drastic climate changes at planetary scale. High-throughput omics
approaches integrated with nanotechnologies are being applied
these issues. Nanomaterials quantum dots, gold nanoparticles,
carbon nanotubes, and nanowires have demonstrated potential to
overcome the challenges of sensitivity for biomarker detection, discovery, and application. On this basis, a framework for assessment
of the potential of nanotechnology for enhancing food security in
India has been recently developed [107]. The model has allowed
identication and prioritization of potential areas for nanotechnology applications to enhance food security in the country.
To meet the challenges to food security and health threatened by
increasing population growth and by depletion of non-renewable
natural resources, plant and crop genetic engineering efforts have
shifted from single pathways to holistic approaches involving multiple genes, made possible by the integration of omics technologies
[108].
In a globally changing world, environmental stress factors such
as drought, elevated temperature, salinity and rising CO2 affect
plant growth and pose a growing threat to sustainable agriculture.
This has become a hot issue due to concerns about the effects of
climate change on plant resources, biodiversity and global food
security. Plant adaptation to stress involves key changes in gene
expression and protein synthesis. Therefore, by disclosing these
pathways, omics are providing clues to understand the physiological and molecular programs active in plant stress adaptation
focusing on how genes, proteins and metabolites change after
individual and multiple environmental stresses. Omics analytical
approaches may nally generate models showing the contribution
of different signaling pathways dening the plant omic architectural responses in relation to climate change events. For instance,
through a systems biology analysis, the photosynthetic metabolism
of C3 plants has been shown to be under highly cooperative regulation in changing environments, and systems-level modeling has
been reviewed as a timely method to explore options for enhanced
photosynthesis in the context of global climate change [109].
The availability of high-throughput omics techniques has
enabled the researchers also to study crop proteome responses
to various stress factors [110]. Very recently, cereals and legume
proteomes have been investigated to relate protein expression in
environmental changing conditions [111113] and in response to
abiotic stress [114,115] by using complementary gel-based and gelfree proteomic approaches. In order to achieve a holistic view of
plant responses to climate changes, and to develop molecular engineering strategies to enhance plant tolerance to different stresses, it
will be important to integrate omic data with bioinformatics based
systems-biology/systems-level modeling and to develop computational models [116119].

Preserving natural genetic variation will be an important
requirement for livestock breeding strategies, to match animals to
a variety of husbandry systems and for adaptation to environmental changes. In addition, genetic diversity of livestock species is of
considerable scientic interest for understanding phenotypic variation [120] and for reconstructing the history of livestock [121,122].
Interest in the conservation of local livestock types has increased
in the last years in response to the expansion of highly productive livestock breeds at the expense of local populations [123].
Molecular-genetic characterization of livestock populations has
now become an active eld of research. So far, it has been assumed
that genetic distinctiveness as estimated with anonymous markers
is indirectly informative for functional diversity, but genome-wide
approaches now allow a more direct study of phenotypic variation. Preservation of genetic diversity [124] will be essential for the
management of breeds. It is also predictable that, like for plants
and crops, proteomics, lipidomics and metabolomics data will play
a decisive role in the future to link livestock genetics and quality of
meat milk and dairy [125127].
10. Conclusions
Tracing the history of the development of analytical techniques
capable of describing the complexity of foods (Fig. 3) highlights the
importance of the information which can be acquired by molecular
food characterization and of the implications in terms of human
well-being. Just like in the case of chemical or pharmaceutical
research, also in food science the necessity of the extensive and
accurate knowledge of a food structure and composition has driven
the development of novel analytical techniques and their application to set up of methodologies for food analysis.
In this progression, three main advancement points can be identied. The rst revolution took place in the second half of XX
century with the development of electronic components which led
to the production and commercialization of MS, NMR and spectroscopy instruments soon applied to food analysis. The second
breakpoint was the introduction of high eld NMR instruments and
of soft MS (FAB, ESI, MALDI) ionization techniques in the 8090s,
a couple of innovations which built the foundations of the future
omic disciplines, whose application to food sciences as well as
to most other research elds permitted to ngerprint the complexity of food matrices. The more recent revolution is taking place
right now by the development of new omic analytical platforms
and by their integration with immunochemical, clinical, biological,
nutritional and toxicological research elds.
The plethora of high-throughput technologies currently available, and their rapid evolution, require the scientic community
to adopt further harmonization and standardization in methods of
generating and analyzing data, and highlight, at the same time, the
existence of extended possibilities of implementation of new data
mining tools. Examples are the complex topic of food digestion,
for which harmonization of in vitro and in vivo models and of the
analytical methods to study the process has been the focus of several international research networks (for example the EU project
www.infogest.eu) or the closely related issue of food allergy (www.
imparas.eu).
In addition, the trend toward increasing integration of knowledge from different disciplines, emphasizes the need to strengthen
existing capacity to generate and share analytical data through
closer collaboration not only within the scientic community, but
also within the industrial world and society in general. The application of methodological approaches and knowledge derived from
the omic sciences will have a signicant impact on the novel
13
technologies of food production in the development, optimization

and validation of processes and products.
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The Evolution of Analytical Chemistry Methods in Foodomics

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The Evolution of Analytical Chemistry Methods in Foodomics

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Journal of Chromatography A, 1428 (2016) 315

Contents lists available at ScienceDirect

The evolution of analytical chemistry methods in foodomics

Introduction: analytical chemistry in food science . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4

M. Gallo, P. Ferranti / J. Chromatogr. A 1428 (2016) 315

1. Introduction: analytical chemistry in food science

nutrition has also rapidly increased, for instance: Food Technology

M. Gallo, P. Ferranti / J. Chromatogr. A 1428 (2016) 315

producers in California to check uniform lemon maturation on eld.

the use of packed columns to the more efcient capillary columns

M. Gallo, P. Ferranti / J. Chromatogr. A 1428 (2016) 315

Other chemical/biochemical techniques such as thin layer

this information allows to identify or structurally characterizes (or

M. Gallo, P. Ferranti / J. Chromatogr. A 1428 (2016) 315

5. Spectroscopy-based methods in food analysis

M. Gallo, P. Ferranti / J. Chromatogr. A 1428 (2016) 315

with environmental and fermentative factors in vineyard and

M. Gallo, P. Ferranti / J. Chromatogr. A 1428 (2016) 315

However, the lack of available reference standards for many of the

7. Sample preparation techniques for food analysis

M. Gallo, P. Ferranti / J. Chromatogr. A 1428 (2016) 315

M. Gallo, P. Ferranti / J. Chromatogr. A 1428 (2016) 315

important regions in the GCMS chromatogram that resulted from

of compounds that have a depressive effect on the digestion

M. Gallo, P. Ferranti / J. Chromatogr. A 1428 (2016) 315

ingredients, such as the allergens, based on the detection of specic

M. Gallo, P. Ferranti / J. Chromatogr. A 1428 (2016) 315

systems-biology/systems-level modeling and to develop computational models [116119].

technologies of food production in the development, optimization

M. Gallo, P. Ferranti / J. Chromatogr. A 1428 (2016) 315

[35] M. Celebier, C. Ibnez,

Exposure to Pesticides and Health Effects, EFSA Supporting Publication, 2013,

M. Gallo, P. Ferranti / J. Chromatogr. A 1428 (2016) 315

[100] G. Magnarelli, N. Guinaz,

[106] C. Sim, A. Cifuentes, V. Garca-Canas,

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