Proteomics 935

PROTEOMICS
AND ITS APPLICATION

Proteomics involves the examination of the proteome, which refers to the complete
collection of expressed proteins within a cell. Proteomics encompasses the processes
of identifying and quantifying proteins, as well as determining their localization,
composition, structures, functions, interactions, expression profiling, and modifications
[4]. This field holds significant importance in biomedical research, particularly in
deciphering disease pathogenesis and prognosis, diagnosing diseases, and providing
the foundation for the discovery of biologics .
Types of Proteomics
Proteomics can be categorized into ;-
- expression proteomics,
- structural proteomics,
- and functional proteomics
depending on how protien respond under stress conditions [11, 12].
Xiong J., Essential Bioinformatics, 2006, 1st edition, Cambridge

University press, Cambridge, UK.Google Scholar
Expression Proteomics Structural Proteomics
Expression proteomics involves the The study of proteomics,elucidating

qualitative and quantitative the 3D structure and intricate
examination of the overall protein structural features of functional
expression differences between proteins found within a specific
samples influenced by a specific cellular organelle, is referred to as
factor [11]. This factor might “cell mapping” or structural
encompass a disease, a drug proteomics [11]. In this discipline, the
treatment, or an environmental identification and localization of entire
condition. proteins within a complex system or
organelles are undertaken, and
potential protein-protein interactions
are determined.
Functional Proteomics
Functional proteomics investigates protein functions, molecular mechanisms
within a cell, and interactions among protein partners. The identification of
an unknown protein associating with partners from a specific protein
complex involved in a particular mechanism strongly indicates its biological
function
PROTEOMICS OBJECTIVES
- Protein/Peptides separation
- Identification and characterization of resolved proteins by MS
- Data analysis and application
11 Chandrasekhar K., Dileep A., Lebonah D. E., and Kumari J. P., A short review on proteomics
and its applications, International Letters of Natural Sciences. (2014) 17, no. 1, 77–84,
https://doi.org/10.56431/p-avsz0g.Google Scholar
12 Al-Amrani S., Al-Jabri Z., Al-Zaabi A., Alshekaili J., and Al-Khabori M., Proteomics: concepts
and applications in human medicine, World Journal of Biological Chemistry. (2021) 12, no. 5, 57–
69, https://doi.org/10.4331/wjbc.v12.i5.57.PubMedGoogle Scholar
Procedure of proteomics
Separation of proteins
One dimentional electrophoressis
2 D electrophossis(modern)
Multi-dimensional HPLC (modern)
Analysis of proteins
Mass Spectrometry (modern)
Database utilization
Protein mixture
(eg. body fluid/tissue, food matter
LC-based workflow
Gel-based workflow
In-solution digestion of protein mixture Protein separation on 1D- or

65 82 73
Enter Enter 2D-gel Enter
LC separation of
title peptides title In-gel digestion
title of protein
mixture
MS
analysis of peptides
ESI-MS instruments
MALDI-MS instruments
Data analysis
Protein identification
Protein quantification
Protein validation
Techniques Used in Proteomics
Gel based
– SDS-PAGE
– 1DE ,2-DE

Off gel base
40%
– LC (SCX, RP-LC, Immuno affinity)

MS
– MALDI, LC-MS, CE-MS
Domon B. and Aebersold R., Mass spectrometry and protein analysis, Science. (2006) 312, no. 5771, 212–217,
https://doi.org/10.1126/science.1124619, 2-s2.0-33645813378.CASPubMedWeb of Science®Google Scholar
The entire process involves three steps: first, converting biomolecules in a liquid or
solid phase into gas-phase ions; second, separating these ions using m/z values in
a mass analyzer compartment under the influence of magnetic or electric fields;
and finally, measuring the separated ions and quantifying each species with a
specific m/z value.
Two types of MS instrument used
MALDI AND ESI

Two widely used ionization techniques are electrospray ionization (ESI) and
matrix-assisted laser desorption ionization (MALDI) [24]. Both processes involve
adding or removing protons to transform peptides into ions. The “soft” ionization
techniques, such as ESI and MALDI, allow ion production without significant
compromise to sample integrity, enabling precise mass data collection for
proteins and peptides in their natural forms [6]. While MALDI results in both
positive and negative ionization for different molecule.
Proteomics-based technologies find application in diverse biomedical contexts,
including the detection of diagnostic markers, understanding pathogenesis,
observing changes in protein expression patterns in response to internal or
external signals, and interpreting functional protein pathways in various
diseases.
Application of Proteomics
Applications of Proteomics in Biotechnology,Drug Discovery and Development:
Toxicology: Proteomics can be used to study the effects of drugs on protein

expression and pathways, helping in understanding drug toxicity and side
effects.
Amiri-Dashatan N., Koushki M., Abbaszadeh H. A., Rostami-Nejad M., and Rezaei-Tavirani M., Proteomics applications
in health: biomarker and drug discovery and food industry, Iranian Journal of Pharmaceutical
Target Identification:
Proteomics helps identify potential drug targets by
analyzing protein expression patterns and post-translational modifications in
disease conditions.
Biomarker Discovery:
By studying the differences in protein expression
between healthy and diseased states, proteomics can identify biomarkers for
early diagnosis, prognosis, and therapeutic monitoring of diseases.
Aslam B., Basit M., Nisar M. A., Khurshid M., and Rasool M. H., Proteomics: technologies and their
applications, Journal of Chromatographic Science. (2017) 55, no. 2, 182–196,
https://doi.org/10.1093/chromsci/bmw167, 2-s2.0-85018634209.CASPubMedWeb of Science®Google Scholar
Agricultural Biotechnology:
Crop Improvement:
Proteomics can be applied to understand the protein
changes in plants under different environmental conditions, aiding in the
development of stress-resistant and high-yielding crop varieties.
Pest and Disease Resistance:

By studying the proteome of plants and their
pathogens, proteomics can contribute to the development of plants that are
resistant to pests and diseases.
Personalized Medicine:
Precision Therapeutics:
Proteomics allows for the identification of protein
profiles that are unique to an individual’s disease state, which can lead to
the development of personalized treatment strategies.
Pharmacogenomics:
Integrating proteomics with genomics helps in
understanding how an individual's genetic makeup affects their response to
drugs, enabling the development of more effective and personalized
medications.
Aslam B., Basit M., Nisar M. A., Khurshid M., and Rasool M. H., Proteomics: technologies and their
applications, Journal of Chromatographic Science. (2017) 55, no. 2, 182–196,
https://doi.org/10.1093/chromsci/bmw167, 2-s2.0-85018634209.CASPubMedWeb of Science®Google Scholar
Environmental Biotechnology:
Bioremediation:
Proteomics can be used to study the proteins involved in
the degradation of environmental pollutants by microorganisms, which
can be harnessed for bioremediation purposes.
Biofuel Production:
By studying the proteome of microorganisms
involved in the production of biofuels, proteomics can contribute to
optimizing the production process and improving yield.
Industrial Biotechnology:
Enzyme Engineering:
Proteomics helps in understanding the structure and
function of industrial enzymes, leading to the development of more efficient
and robust enzymes for various industrial processes.
Fermentation Technology:
Proteomics can be applied to monitor and
optimize fermentation processes, ensuring higher yields and quality of
bioproducts such as antibiotics, vitamins, and amino acids.
Disease Mechanism Understanding: Proteomics provides insights into
the molecular mechanisms of diseases, which can lead to the
development of new diagnostic tools.
Protein-based Diagnostics: The identification of specific protein

markers associated with diseases can lead to the development of
protein-based diagnostic tests, such as ELISA (enzyme-linked
immunosorbent assay) or mass spectrometry-based diagnostics.
Overall, proteomics is a powerful tool in biotechnology, offering insights

that are crucial for advancing various fields, from medicine and
agriculture to environmental and industrial applications.
Al-Amrani S., Al-Jabri Z., Al-Zaabi A., Alshekaili J., and Al-Khabori M., Proteomics: concepts and applications in human
medicine, World Journal of Biological Chemistry. (2021) 12, no. 5, 57–69, https://doi.org/10.4331/wjbc.v12.i5.57.
PubMedGoogle Scholar
Future trends in Proteomics
As with the progression of proteomics from human

biomedical research throughout the life sciences, we are
already seeing elements of integrative proteomics being
carried out in non-human systems.
The “Proteomics” technologies have always been

characterised by combining multi-disciplinary expertise’s in
biology, genetics, computer science, and engineering. This
trend is continuing as we are now building the resources to
comprehensively study how mutations affect genome
structure, gene expression, protein function and interactions
to contribute to the complex phenotypic outcomes we
observe in diseases, and to offer new insights into future
treatment.
Refrences
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Blood. (2004) 103, no. 10, 3624–3634, https://doi.org/10.1182/blood-2003-09-3295, 2-s2.0-2342541676.CAS
PubMedWeb of Science®Google Scholar
2 Aslam B., Basit M., Nisar M. A., Khurshid M., and Rasool M. H., Proteomics: technologies and their applications,
Journal of Chromatographic Science. (2017) 55, no. 2, 182–196, https://doi.org/10.1093/chromsci/bmw167, 2-
s2.0-85018634209.CASPubMedWeb of Science®Google Scholar
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Baharvand H., and Hosseini Salekdeh G., Comparative proteome and transcriptome analyses of embryonic stem
cells during embryoid body-based differentiation, Proteomics. (2009) 9, no. 21, 4859–4870,
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via shotgun proteomics, Methods in Molecular Biology. (2013) 1002, 167–179,
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applications in health: biomarker and drug discovery and food industry, Iranian Journal of Pharmaceutical
Research: IJPR. (2018) 17, no. 4, 1523–1536.CASPubMedWeb of Science®Google Scholar
8 Kwon Y. W., Jo H.-S., Bae S., Seo Y., Song P., Song M., and Yoon J. H., Application of proteomics in cancer:
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https://doi.org/10.1126/science.1124619, 2-s2.0-33645813378.CASPubMedWeb of Science®Google Scholar
10 Ceciliani F., Eckersall D., Burchmore R., and Lecchi C., Proteomics in veterinary medicine: applications and
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applications, International Letters of Natural Sciences. (2014) 17, no. 1, 77–84,
https://doi.org/10.56431/p-avsz0g.Google Scholar
12 Al-Amrani S., Al-Jabri Z., Al-Zaabi A., Alshekaili J., and Al-Khabori M., Proteomics: concepts and applications
in human medicine, World Journal of Biological Chemistry. (2021) 12, no. 5, 57–69,
https://doi.org/10.4331/wjbc.v12.i5.57.PubMedGoogle Scholar
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PROTEOMICS

AND ITS APPLICATION

Xiong J., Essential Bioinformatics, 2006, 1st edition, Cambridge

Expression proteomics involves the The study of proteomics,elucidating

In-solution digestion of protein mixture Protein separation on 1D- or

MALDI AND ESI

Applications of Proteomics in Biotechnology,Drug Discovery and Development:

Toxicology: Proteomics can be used to study the effects of drugs on protein

Pest and Disease Resistance:

Protein-based Diagnostics: The identification of specific protein

Overall, proteomics is a powerful tool in biotechnology, offering insights

As with the progression of proteomics from human

The “Proteomics” technologies have always been

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