The proteome is the entire set of proteins expressed by a genome,
cell, tissue, or organism at a certain time. More specifically, it is
the set of expressed proteins in a given type of cell or organism, at
a given time, under defined conditions.
Proteomics is the study of the
3 Size and contents
3.1 Dark proteome
4 Methods to study the proteome
4.1 Separation techniques and electrophoresis
4.2 Mass spectrometry
Protein complementation assays and interaction screens
5 See also
7 External links
The term has been applied to several different types of biological
systems. A cellular proteome is the collection of proteins found in a
particular cell type under a particular set of environmental
conditions such as exposure to hormone stimulation. It can also be
useful to consider an organism's complete proteome, which can be
conceptualized as the complete set of proteins from all of the various
cellular proteomes. This is very roughly the protein equivalent of the
genome. The term "proteome" has also been used to refer to the
collection of proteins in certain sub-cellular biological systems. For
example, all of the proteins in a virus can be called a viral
Marc Wilkins coined the term proteome  in 1994 in a symposium on
"2D Electrophoresis: from protein maps to genomes" held in Siena in
Italy. It appeared in print in 1995, with the publication of part
of Wilkins's PhD thesis. Wilkins used the term to describe the entire
complement of proteins expressed by a genome, cell, tissue or
Size and contents
The proteome can be larger than the genome, especially in eukaryotes,
as more than one protein can be produced from one gene due to
alternative splicing (e.g. human proteome consists 92,179 proteins out
of which 71,173 are splicing variants). On the other hand, not all
genes are translated to proteins, and many known genes encode only RNA
which is the final functional product. Moreover, complete proteome
size vary depending the kingdom of life. For instance, eukaryotes,
Archaea and viruses have on average 15145, 3200, 2358 and 42
proteins respectively encoded in their genomes.
Perdigão and co-workers surveyed the “dark” proteome – that is,
regions of proteins never observed by experimental structure
determination and inaccessible to homology modeling. For 546,000
Swiss-Prot proteins, they found that 44–54% of the proteome in
eukaryotes and viruses was "dark", compared with only ∼14% in
archaea and bacteria. Surprisingly, most of the dark proteome could
not be accounted for by conventional explanations, such as intrinsic
disorder or transmembrane regions. Nearly half of the dark proteome
comprised dark proteins, in which the entire sequence lacked
similarity to any known structure. Dark proteins fulfill a wide
variety of functions, but a subset showed distinct and largely
unexpected features, such as association with secretion, specific
tissues, the endoplasmic reticulum, disulfide bonding, and proteolytic
Methods to study the proteome
Main article: Proteomics
Numerous methods are available to study proteins, sets of proteins, or
the whole proteome. In fact, proteins are often studied indirectly,
e.g. using computational methods and analyses of genomes. Only a few
examples are given below.
Separation techniques and electrophoresis
Proteomics, the study of the proteome, has largely been practiced
through the separation of proteins by two dimensional gel
electrophoresis. In the first dimension, the proteins are separated by
isoelectric focusing, which resolves proteins on the basis of charge.
In the second dimension, proteins are separated by molecular weight
using SDS-PAGE. The gel is dyed with
Coomassie Brilliant Blue
Coomassie Brilliant Blue or
silver to visualize the proteins. Spots on the gel are proteins that
have migrated to specific locations.
Mass spectrometry has augmented proteomics. Peptide mass
fingerprinting identifies a protein by cleaving it into short peptides
and then deduces the protein's identity by matching the observed
peptide masses against a sequence database. Tandem mass spectrometry,
on the other hand, can get sequence information from individual
peptides by isolating them, colliding them with a non-reactive gas,
and then cataloguing the fragment ions produced.
In May 2014, a draft map of the human proteome was published in
Nature. This map was generated using high-resolution
Fourier-transform mass spectrometry. This study profiled 30
histologically normal human samples resulting in the identification of
proteins coded by 17,294 genes. This accounts for around 84% of the
total annotated protein-coding genes.
Protein complementation assays and interaction screens
Protein fragment complementation assays are often used to detect
protein–protein interactions. The yeast two-hybrid assay is the most
popular of them but there are numerous variations, both used in vitro
and in vivo.
List of omics topics in biology
^ Wilkins, Marc (Dec 2009). "
Proteomics data mining". Expert review of
proteomics. England. 6 (6): 599–603. doi:10.1586/epr.09.81.
^ Wasinger VC, Cordwell SJ, Cerpa-Poljak A, Yan JX, Gooley AA, Wilkins
MR, Duncan MW, Harris R, Williams KL, Humphery-Smith I (1995).
"Progress with gene-product mapping of the Mollicutes: Mycoplasma
genitalium". Electrophoresis. 16 (1): 1090–94.
doi:10.1002/elps.11501601185. PMID 7498152.
^ "UniProt: a hub for protein information". Nucleic Acids Research. 43
(D1): D204–D212. 2014. doi:10.1093/nar/gku989. ISSN 0305-1048.
PMC 4384041 . PMID 25348405.
^ Kozlowski, LP (26 October 2016). "Proteome-pI: proteome isoelectric
point database". Nucleic Acids Research. 45: gkw978.
doi:10.1093/nar/gkw978. PMC 5210655 . PMID 27789699.
^ Perdigão, Nelson; et al. (2015). "Unexpected features of the dark
proteome". PNAS. 112 (52): 15898–15903. doi:10.1073/pnas.1508380112.
PMC 4702990 . PMID 26578815.
^ Altelaar, AF; Munoz, J; Heck, AJ (January 2013). "Next-generation
proteomics: towards an integrative view of proteome dynamics". Nature
Reviews Genetics. 14 (1): 35–48. doi:10.1038/nrg3356.
^ "Mass-Spectrometry-Based Draft of the Human Proteome". Nature.
^ Kim, Min-Sik; et al. (May 2014). "A draft map of the human
proteome". Nature. 509 (7502): 575–81. doi:10.1038/nature13302.
PMC 4403737 . PMID 24870542.
Protein structural domains
List of types of proteins
List of proteins
Proteins: key methods of study
Green fluorescent protein
Peptide mass fingerprinting/
Protein mass spectrometry
Surface plasmon resonance
Isothermal titration calorimetry
Freeze-fracture electron microscopy
Protein structure prediction
Protein structural alignment
Protein–protein interaction prediction
Photoactivated localization micr