The proteome is the entire set of proteins that is, or can be, expressed by a genome, cell, tissue, or organism at a certain time. It is the set of expressed proteins in a given type of cell or organism, at a given time, under defined conditions.

Proteomics Proteomics is the large-scale study of proteins. Proteins are vital parts of living organisms, with many functions such as the formation of structural fibers of muscle tissue, enzymatic digestion of food, or synthesis and replication of DNA. In ...

is the study of the proteome.

Types of proteomes

While proteome generally refers to the proteome of an organism, multicellular organisms may have very different proteomes in different cells, hence it is important to distinguish proteomes in cells and organisms. 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 systems, such as organelles. For instance, the

mitochondrial A mitochondrion (; ) is an organelle found in the cells of most Eukaryotes, such as animals, plants and fungi. Mitochondria have a double membrane structure and use aerobic respiration to generate adenosine triphosphate (ATP), which is use ...

proteome may consist of more than 3000 distinct proteins. The proteins in a virus can be called a '' viral proteome''. Usually viral proteomes are predicted from the viral genome but some attempts have been made to determine all the proteins expressed from a virus genome, i.e. the viral proteome. More often, however, virus proteomics analyzes the changes of host proteins upon virus infection, so that in effect ''two'' proteomes (of virus and its host) are studied.

Importance in cancer

The proteome can be used in order to comparatively analyze different cancer cell lines. Proteomic studies have been used in order to identify the likelihood of metastasis in bladder cancer cell lines KK47 and YTS1 and were found to have 36 unregulated and 74 down regulated proteins. The differences in protein expression can help identify novel cancer signaling mechanisms. Biomarkers of cancer have been found by

mass spectrometry Mass spectrometry (MS) is an analytical technique that is used to measure the mass-to-charge ratio of ions. The results are presented as a ''mass spectrum'', a plot of intensity as a function of the mass-to-charge ratio. Mass spectrometry is use ...

based proteomic analyses. The use of proteomics or the study of the proteome is a step forward in personalized medicine to tailor drug cocktails to the patient's specific proteomic and genomic profile. The analysis of ovarian cancer cell lines showed that putative biomarkers for ovarian cancer include "α-enolase (ENOA),

elongation factor Tu EF-Tu (elongation factor thermo unstable) is a prokaryotic elongation factor responsible for catalyzing the binding of an aminoacyl-tRNA (aa-tRNA) to the ribosome. It is a G-protein, and facilitates the selection and binding of an aa-tRNA to ...

, mitochondrial (EFTU), glyceraldehyde-3-phosphate dehydrogenase (G3P), stress-70 protein, mitochondrial (GRP75), apolipoprotein A-1 (APOA1), peroxiredoxin (PRDX2) and annexin A (ANXA)". Comparative proteomic analyses of 11 cell lines demonstrated the similarity between the metabolic processes of each cell line; 11,731 proteins were completely identified from this study. Housekeeping proteins tend to show greater variability between cell lines. Resistance to certain cancer drugs is still not well understood. Proteomic analysis has been used in order to identify proteins that may have anti-cancer drug properties, specifically for the colon cancer drug irinotecan. Studies of adenocarcinoma cell line LoVo demonstrated that 8 proteins were unregulated and 7 proteins were down-regulated. Proteins that showed a differential expression were involved in processes such as transcription,

apoptosis Apoptosis (from grc, ἀπόπτωσις, apóptōsis, 'falling off') is a form of programmed cell death that occurs in multicellular organisms. Biochemical events lead to characteristic cell changes (morphology) and death. These changes incl ...

and cell proliferation/differentiation among others.

The proteome in bacterial systems

Proteomic analyses have been performed in different kinds of bacteria to assess their metabolic reactions to different conditions. For example, in bacteria such as ''

Clostridium ''Clostridium'' is a genus of anaerobic, Gram-positive bacteria. Species of ''Clostridium'' inhabit soils and the intestinal tract of animals, including humans. This genus includes several significant human pathogens, including the causative ag ...

'' and '' Bacillus'', proteomic analyses were used in order to investigate how different proteins help each of these bacteria spores germinate after a prolonged period of dormancy. In order to better understand how to properly eliminate spores, proteomic analysis must be performed.

History

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 his PhD thesis. Wilkins used the term to describe the entire complement of proteins expressed by a genome, cell, tissue or organism.

Size and contents

The genomes of viruses and prokaryotes encode a relatively well-defined proteome as each protein can be predicted with high confidence, based on its open reading frame (in viruses ranging from ~3 to ~1000, in bacteria ranging from about 500 proteins to about 10,000). However, most protein prediction algorithms use certain cut-offs, such as 50 or 100 amino acids, so small proteins are often missed by such predictions. In eukaryotes this becomes much more complicated as more than one protein can be produced from most genes due to

alternative splicing Alternative splicing, or alternative RNA splicing, or differential splicing, is an alternative splicing process during gene expression that allows a single gene to code for multiple proteins. In this process, particular exons of a gene may be ...

(e.g. human proteome encodes about 20,000 proteins, but some estimates predicted 92,179 proteins out of which 71,173 are splicing variants). Proteoforms. There are different factors that can add variability to proteins. SAPs (single amino acid polymorphisms) and non-synonymous single nucleotide polymorphisms (nsSNPs) can lead to different "proteoforms" or "proteomorphs". Recent estimates have found ~135,000 validated nonsynonymous cSNPs currently housed within SwissProt. In dbSNP, there are 4.7 million candidate cSNPs, yet only ~670,000 cSNPs have been validated in the 1,000-genomes set as nonsynonymous cSNPs that change the identity of an amino acid in a protein. Dark proteome. The term dark proteome coined by Perdigão and colleagues, defines regions of proteins that have no detectable

sequence homology Sequence homology is the biological homology between DNA, RNA, or protein sequences, defined in terms of shared ancestry in the evolutionary history of life. Two segments of DNA can have shared ancestry because of three phenomena: either a spe ...

to other proteins of known three-dimensional structure and therefore cannot be modeled by homology. For 546,000 Swiss-Prot proteins, 44–54% of the proteome in

eukaryote Eukaryotes () are organisms whose cells have a nucleus. All animals, plants, fungi, and many unicellular organisms, are Eukaryotes. They belong to the group of organisms Eukaryota or Eukarya, which is one of the three domains of life. Bacte ...

s and viruses was found to be "dark", compared with only ∼14% in

archaea Archaea ( ; singular archaeon ) is a domain of single-celled organisms. These microorganisms lack cell nuclei and are therefore prokaryotes. Archaea were initially classified as bacteria, receiving the name archaebacteria (in the Archaebac ...

and bacteria. Human proteome. Currently, several projects aim to map the human proteome, including th
Human Proteome MapProteomicsDBisoform.io
an
The Human Proteome Project (HPP)
Much like the

human genome project The Human Genome Project (HGP) was an international scientific research project with the goal of determining the base pairs that make up human DNA, and of identifying, mapping and sequencing all of the genes of the human genome from both a ...

, these projects seek to find and collect evidence for all predicted protein coding genes in the human genome. The Human Proteome Map currently (October 2020) claims 17,294 proteins and ProteomicsDB 15,479, using different criteria. On October 16, 2020, the HPP published a high-stringency blueprint covering more than 90% of the predicted protein coding genes. Proteins are identified from a wide range of fetal and adult tissues and cell types, including hematopoietic cells.

Methods to study the proteome

Analyzing proteins proves to be more difficult than analyzing nucleic acid sequences. While there are only 4 nucleotides that make up DNA, there are at least 20 different amino acids that can make up a protein. Additionally, there is currently no known high throughput technology to make copies of a single protein. 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

, the study of the proteome, has largely been practiced through the separation of proteins by

two dimensional gel electrophoresis Two-dimensional gel electrophoresis, abbreviated as 2-DE or 2-D electrophoresis, is a form of gel electrophoresis commonly used to analyze proteins. Mixtures of proteins are separated by two properties in two dimensions on 2D gels. 2-DE was first ...

. 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

stained A stain is a discoloration that can be clearly distinguished from the surface, material, or medium it is found upon. They are caused by the chemical or physical interaction of two dissimilar materials. Accidental staining may make materials app ...

with Coomassie brilliant blue or silver to visualize the proteins. Spots on the gel are proteins that have migrated to specific locations.

Mass spectrometry

Mass spectrometry Mass spectrometry (MS) is an analytical technique that is used to measure the mass-to-charge ratio of ions. The results are presented as a ''mass spectrum'', a plot of intensity as a function of the mass-to-charge ratio. Mass spectrometry is use ...

is one of the key methods to study the proteome. Some important mass spectrometry methods include Orbitrap Mass Spectrometry, MALDI (Matrix Assisted Laser Desorption/Ionization), and ESI (Electrospray Ionization). 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.

Chromatography

Liquid chromatography is an important tool in the study of the proteome. It allows for very sensitive separation of different kinds of proteins based on their affinity for a matrix. Some newer methods for the separation and identification of proteins include the use of monolithic capillary columns, high temperature chromatography and capillary electrochromatography.

Blotting

Western blotting can be used in order to quantify the abundance of certain proteins. By using antibodies specific to the protein of interest, it is possible to probe for the presence of specific proteins from a mixture of proteins.

Protein complementation assays and interaction screens

Protein-fragment complementation assay Within the field of molecular biology, a protein-fragment complementation assay, or PCA, is a method for the identification and quantification of protein–protein interactions. In the PCA, the proteins of interest ("bait" and "prey") are each cov ...

s 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''. Pull-down assays are a method to determine what kinds of proteins a protein interacts with.

Protein structure prediction

Protein structure prediction can be used to provide three-dimensional protein structure predictions of whole proteomes. In 2022, a large-scale collaboration between EMBL-EBI and

DeepMind DeepMind Technologies is a British artificial intelligence subsidiary of Alphabet Inc. and research laboratory founded in 2010. DeepMind was List of mergers and acquisitions by Google, acquired by Google in 2014 and became a wholly owned subsid ...

provided predicted structures for over 200 million proteins from across the tree of life. Smaller projects have also used protein structure prediction to help map the proteome of individual organisms, for exampl
isoform.io
provides coverage of multiple protein isoforms for over 20,000 genes in the human genome.

Protein databases

Th
Human Protein Atlas
contains information about the human proteins in cells, tissues, and organs. All the data in the knowledge resource is open access to allow scientists both in academia and industry to freely access the data for exploration of the human proteome. The organizatio
ELIXIR
has selected the protein atlas as a core resource due to its fundamental importance for a wider life science community. Th
Plasma Proteome database
contains information on 10,500 blood plasma proteins. Because the range in protein contents in plasma is very large, it is difficult to detect proteins that tend to be scarce when compared to abundant proteins. There is an analytical limit that may possibly be a barrier for the detections of proteins with ultra low concentrations. Databases such a
neXtprot
an
UniProt
are central resources for human proteomic data.

References

External links

PIR database

UniProt database
* {{Protein topics Proteomics