Proteomics
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For the journal Proteomics, see Proteomics (journal).
Robotic preparation of MALDI mass spectrometry samples on a sample carrier.
Proteomics is the large-scale study of proteins, particularly their structures and functions.[1][2]
Proteins are vital parts of living organisms, as they are the main components of the physiological
metabolic pathways of cells. The term "proteomics" was first coined in 1997[3] to make an
analogy with genomics, the study of the genes. The word "proteome" is a blend of "protein" and
"genome", and was coined by Marc Wilkins in 1994 while working on the concept as a PhD
student.[4][5] The proteome is the entire complement of proteins,[4] including the modifications
made to a particular set of proteins, produced by an organism or system. This will vary with time
and distinct requirements, or stresses, that a cell or organism undergoes.
While proteomics generally refers to the large-scale experimental analysis of proteins, it is often
specifically used for protein purification and mass spectrometry.
Contents
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1 Complexity of the problem
o 1.1 Post-translational modifications
 1.1.1 Phosphorylation
 1.1.2 Ubiquitination
 1.1.3 Additional modifications
o 1.2 Distinct proteins are made under distinct settings
2 Limitations of genomics and proteomics studies
3 Methods of studying proteins
o 3.1 Identifying proteins that are post-translationally modified
o 3.2 Determining the existence of proteins in complex mixtures
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o 3.3 Computational methods in studying protein biomarkers
4 Establishing protein–protein interactions
5 Practical applications of proteomics
o 5.1 Biomarkers
o 5.2 Proteogenomics
o 5.3 Current research methodologies
6 See also
o 6.1 Protein databases
o 6.2 Research centers
7 References
8 Bibliography
9 External links
[edit] Complexity of the problem
After genomics and transcriptomics, proteomics is considered the next step in the study of
biological systems. It is much more complicated than genomics mostly because while an
organism's genome is more or less constant, the proteome differs from cell to cell and from time
to time. This is because distinct genes are expressed in distinct cell types. This means that even
the basic set of proteins which are produced in a cell needs to be determined.
In the past this was done by mRNA analysis, but this was found not to correlate with protein
content.[6][7] It is now known that mRNA is not always translated into protein,[8] and the amount
of protein produced for a given amount of mRNA depends on the gene it is transcribed from and
on the current physiological state of the cell. Proteomics confirms the presence of the protein and
provides a direct measure of the quantity present.
[edit] Post-translational modifications
Not only does the translation from mRNA cause differences, but many proteins are also
subjected to a wide variety of chemical modifications after translation. Many of these posttranslational modifications are critical to the protein's function.
[edit] Phosphorylation
One such modification is phosphorylation, which happens to many enzymes and structural
proteins in the process of cell signaling. The addition of a phosphate to particular amino acids—
most commonly serine and threonine[9] mediated by serine/threonine kinases, or more rarely
tyrosine mediated by tyrosine kinases—causes a protein to become a target for binding or
interacting with a distinct set of other proteins that recognize the phosphorylated domain.
Because protein phosphorylation is one of the most-studied protein modifications, many
"proteomic" efforts are geared to determining the set of phosphorylated proteins in a particular
cell or tissue-type under particular circumstances. This alerts the scientist to the signaling
pathways that may be active in that instance.
[edit] Ubiquitination
Ubiquitin is a small protein that can be affixed to certain protein substrates by enzymes called E3
ubiquitin ligases. Determining which proteins are poly-ubiquitinated can be helpful in
understanding how protein pathways are regulated. This is therefore an additional legitimate
"proteomic" study. Similarly, once it is determined which substrates are ubiquitinated by each
ligase, determining the set of ligases expressed in a particular cell type will be helpful.
[edit] Additional modifications
Listing all the protein modifications that might be studied in a "Proteomics" project would
require a discussion of most of biochemistry; therefore, a short list will serve here to illustrate the
complexity of the problem. In addition to phosphorylation and ubiquitination, proteins can be
subjected to (among others) methylation, acetylation, glycosylation, oxidation and nitrosylation.
Some proteins undergo ALL of these modifications, often in time-dependent combinations, aptly
illustrating the potential complexity one has to deal with when studying protein structure and
function.
[edit] Distinct proteins are made under distinct settings
Even if one is studying a particular cell type, that cell may make different sets of proteins at
different times, or under different conditions. Furthermore, as mentioned, any one protein can
undergo a wide range of post-translational modifications.
Therefore a "proteomics" study can become quite complex very quickly, even if the object of the
study is very restricted. In more ambitious settings, such as when a biomarker for a tumor is
sought – when the proteomics scientist is obliged to study sera samples from multiple cancer
patients – the amount of complexity that must be dealt with is as great as in any modern
biological project.
[edit] Limitations of genomics and proteomics studies
Proteomics typically gives us a better understanding of an organism than genomics. First, the
level of transcription of a gene gives only a rough estimate of its level of expression into a
protein.[10] An mRNA produced in abundance may be degraded rapidly or translated
inefficiently, resulting in a small amount of protein. Second, as mentioned above many proteins
experience post-translational modifications that profoundly affect their activities; for example
some proteins are not active until they become phosphorylated. Methods such as
phosphoproteomics and glycoproteomics are used to study post-translational modifications.
Third, many transcripts give rise to more than one protein, through alternative splicing or
alternative post-translational modifications. Fourth, many proteins form complexes with other
proteins or RNA molecules, and only function in the presence of these other molecules. Finally,
protein degradation rate plays an important role in protein content.[11]
Reproducibility. Proteomics experiments conducted in one laboratory are not easily reproduced
in another. For instance, Peng et al.[12] have identified 1504 yeast proteins in a proteomics
experiment of which only 858 were found in a similar previous study.[13] Similarly, this latter
study identified 607 proteins that were not found by Peng et al. This translates to a
reproducibility of 57% (Peng vs. Washburn) to 59% (Washburn vs. Peng).
[edit] Methods of studying proteins
[edit] Identifying proteins that are post-translationally modified
One way in which a particular protein can be studied is to develop an antibody which is specific
to that modification. For example, there are antibodies which only recognize certain proteins
when they are tyrosine-phosphorylated, known as phospho-specific antibodies; also, there are
antibodies specific to other modifications. These can be used to determine the set of proteins that
have undergone the modification of interest.
For sugar modifications, such as glycosylation of proteins, certain lectins have been discovered
which bind sugars. These too can be used.[citation needed]
A more common way to determine post-translational modification of interest is to subject a
complex mixture of proteins to electrophoresis in "two-dimensions", which simply means that
the proteins are electrophoresed first in one direction, and then in another, which allows small
differences in a protein to be visualized by separating a modified protein from its unmodified
form. This methodology is known as "two-dimensional gel electrophoresis".[14]
Recently, another approach has been developed called PROTOMAP which combines SDSPAGE with shotgun proteomics to enable detection of changes in gel-migration such as those
caused by proteolysis or post translational modification.[15]
[edit] Determining the existence of proteins in complex mixtures
Classically, antibodies to particular proteins or to their modified forms have been used in
biochemistry and cell biology studies. These are among the most common tools used by
practicing biologists today.
For more quantitative determinations of protein amounts, techniques such as ELISAs can be
used.[citation needed]
For proteomic study, more recent techniques such as matrix-assisted laser desorption/ionization
(MALDI)[14] have been employed for rapid determination of proteins in particular mixtures and
increasingly electrospray ionization (ESI).[citation needed]
[edit] Computational methods in studying protein biomarkers
Computational predictive models[16] have shown that extensive and diverse feto-maternal protein
trafficking occurs during pregnancy and can be readily detected non-invasively in maternal
whole blood. This computational approach circumvented a major limitation, the abundance of
maternal proteins interfering with the detection of fetal proteins, to fetal proteomic analysis of
maternal blood. Computational models can use fetal gene transcripts previously identified in
maternal whole blood to create a comprehensive proteomic network of the term neonate. Such
work shows that the fetal proteins detected in pregnant woman’s blood originate from a diverse
group of tissues and organs from the developing fetus. The proteomic networks contain many
biomarkers that are proxies for development and illustrate the potential clinical application of
this technology as a way to monitor normal and abnormal fetal development.
An information theoretic framework has also been introduced for biomarker discovery,
integrating biofluid and tissue information.[17] This new approach takes advantage of functional
synergy between certain biofluids and tissues with the potential for clinically significant findings
not possible if tissues and biofluids were considered individually. By conceptualizing tissuebiofluid as information channels, significant biofluid proxies can be identified and then used for
guided development of clinical diagnostics. Candidate biomarkers are then predicted based on
information transfer criteria across the tissue-biofluid channels. Significant biofluid-tissue
relationships can be used to prioritize clinical validation of biomarkers.[citation needed]
[edit] Establishing protein–protein interactions
Most proteins function in collaboration with other proteins, and one goal of proteomics is to
identify which proteins interact. This is especially useful in determining potential partners in cell
signaling cascades.
Several methods are available to probe protein–protein interactions. The traditional method is
yeast two-hybrid analysis. New methods include protein microarrays, immunoaffinity
chromatography followed by mass spectrometry, dual polarisation interferometry, Microscale
Thermophoresis and experimental methods such as phage display and computational methods
[edit] Practical applications of proteomics
One of the most promising developments to come from the study of human genes and proteins
has been the identification of potential new drugs for the treatment of disease. This relies on
genome and proteome information to identify proteins associated with a disease, which computer
software can then use as targets for new drugs. For example, if a certain protein is implicated in a
disease, its 3D structure provides the information to design drugs to interfere with the action of
the protein. A molecule that fits the active site of an enzyme, but cannot be released by the
enzyme, will inactivate the enzyme. This is the basis of new drug-discovery tools, which aim to
find new drugs to inactivate proteins involved in disease. As genetic differences among
individuals are found, researchers expect to use these techniques to develop personalized drugs
that are more effective for the individual.[18]
[edit] Biomarkers
The FDA defines a biomarker as, "A characteristic that is objectively measured and evaluated as
an indicator of normal biologic processes, pathogenic processes, or pharmacologic responses to a
therapeutic intervention".
Understanding the proteome, the structure and function of each protein and the complexities of
protein–protein interactions will be critical for developing the most effective diagnostic
techniques and disease treatments in the future.
An interesting use of proteomics is using specific protein biomarkers to diagnose disease. A
number of techniques allow to test for proteins produced during a particular disease, which helps
to diagnose the disease quickly. Techniques include western blot, immunohistochemical staining,
enzyme linked immunosorbent assay (ELISA) or mass spectrometry.[14][19] Secretomics, a
subfield of proteomics that studies secreted proteins and secretion pathways using proteomic
approaches, has recently emerged as an important tool for the discovery of biomarkers of
disease.[20]
[edit] Proteogenomics
In what is now commonly referred to as proteogenomics, proteomic technologies such as mass
spectrometry are used for improving gene annotations. Parallel analysis of the genome and the
proteome facilitates discovery of post-translational modifications and proteolytic events,[21]
especially when comparing multiple species (comparative proteogenomics).[22]
[edit] Current research methodologies
Fluorescence two-dimensional differential gel electrophoresis (2-D DIGE)[23] can be used to
quantify variation in the 2-D DIGE process and establish statistically valid thresholds for
assigning quantitative changes between samples.[24]
Comparative proteomic analysis can reveal the role of proteins in complex biological systems,
including reproduction. For example, treatment with the insecticide triazophos causes an increase
in the content of brown planthopper (Nilaparvata lugens (Stål)) male accessory gland proteins
(Acps) that can be transferred to females via mating, causing an increase in fecundity (i.e. birth
rate) of females.[25] To identify changes in the types of accessory gland proteins (Acps) and
reproductive proteins that mated female planthoppers received from male planthoppers,
researchers conducted a comparative proteomic analysis of mated N. lugens females.[26] The
results indicated that these proteins participate in the reproductive process of N. lugens adult
females and males.[27]
Proteome analysis of Arabidopsis peroxisomes[28] has been established as the major unbiased
approach for identifying new peroxisomal proteins on a large scale.[29]
There are many approaches to characterizing the human proteome, which is estimated to contain
between 20,000 and 25,000 non-redundant proteins. The number of unique protein species likely
increase by between 50,000 and 500,000 due to RNA splicing and proteolysis events, and when
post-translational modification are also considered, the total number of unique human proteins is
estimated to range in the low millions.[30][31]
In addition, first promising attempts to decipher the proteome of animal tumors have recently
been reported.[14]
[edit] See also
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Activity based proteomics
Bioinformatics
Bottom-up proteomics
Cytomics
Functional genomics
Genomics
Immunomics
Immunoproteomics
Lipidomics
List of biological databases
List of omics topics in biology
Metabolomics
PEGylation
Phosphoproteomics
Proteogenomics
Proteomic chemistry
Secretomics
Shotgun proteomics
Top-down proteomics
Systems biology
Transcriptomics
Yeast two-hybrid system
[edit] Protein databases
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Cardiac Organellar Protein Atlas Knowledgebase (COPaKB)
Human Protein Reference Database
Model Organism Protein Expression Database (MOPED)
National Center for Biotechnology Information (NCBI)
Protein Data Bank (PDB)
Protein Information Resource (PIR)
Proteomics Identifications Database (PRIDE)
Proteopedia The collaborative, 3D encyclopedia of proteins and other molecules
Swiss-Prot
UniProt
[edit] Research centers
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European Bioinformatics Institute
Netherlands Proteomics Centre (NPC)
[edit] References
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