Proteogenomics
Encyclopedia
Proteogenomics is an emerging field of biological research at the intersection of proteomics
and genomics
. While this intersection is large and can be defined in multiple ways, the term proteogenomics commonly refers to studies that use proteomic information, often derived from mass spectrometry
, to improve gene
annotations.
Since then, the approach has been extended to other species
including Arabidopsis thaliana
, humans, multiple species of Shewanella
bacteria,
chicken
, among many others.
Besides improving gene annotations, proteogenomic studies can also provide valuable information about the presence of programmed frameshifts, N-terminal methionine
excision, signal peptide
s, proteolysis
and other posttranslational modification
s.
Comparative proteogenomics is a branch of proteogenomics that compares proteomic data from multiple related species concurrently and exploits the homology between their proteins to improve annotations with higher statistical confidence.
Proteomics
Proteomics is the large-scale study of proteins, particularly their structures and functions. 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 to make an analogy with...
and genomics
Genomics
Genomics is a discipline in genetics concerning the study of the genomes of organisms. The field includes intensive efforts to determine the entire DNA sequence of organisms and fine-scale genetic mapping efforts. The field also includes studies of intragenomic phenomena such as heterosis,...
. While this intersection is large and can be defined in multiple ways, the term proteogenomics commonly refers to studies that use proteomic information, often derived from mass spectrometry
Mass spectrometry
Mass spectrometry is an analytical technique that measures the mass-to-charge ratio of charged particles.It is used for determining masses of particles, for determining the elemental composition of a sample or molecule, and for elucidating the chemical structures of molecules, such as peptides and...
, to improve gene
Gene
A gene is a molecular unit of heredity of a living organism. It is a name given to some stretches of DNA and RNA that code for a type of protein or for an RNA chain that has a function in the organism. Living beings depend on genes, as they specify all proteins and functional RNA chains...
annotations.
Practical applications
Proteogenomics has been applied to improve the gene annotations of various organisms. The term proteogenomics was first used in this context by a Harvard team in 2004, although the research in this field had been building up in the previous decade.Since then, the approach has been extended to other species
Species
In biology, a species is one of the basic units of biological classification and a taxonomic rank. A species is often defined as a group of organisms capable of interbreeding and producing fertile offspring. While in many cases this definition is adequate, more precise or differing measures are...
including Arabidopsis thaliana
Arabidopsis thaliana
Arabidopsis thaliana is a small flowering plant native to Europe, Asia, and northwestern Africa. A spring annual with a relatively short life cycle, arabidopsis is popular as a model organism in plant biology and genetics...
, humans, multiple species of Shewanella
Shewanella
Shewanella is the sole genus included in the Shewanellaceae family of marine bacteria. Shewanella is a marine bacterium capable of modifying metals, by saturating them with electrons causing the metal to expand and soften, allowing them to process it, which in turn releases an electrical charge...
bacteria,
chicken
Chicken
The chicken is a domesticated fowl, a subspecies of the Red Junglefowl. As one of the most common and widespread domestic animals, and with a population of more than 24 billion in 2003, there are more chickens in the world than any other species of bird...
, among many others.
Besides improving gene annotations, proteogenomic studies can also provide valuable information about the presence of programmed frameshifts, N-terminal methionine
Methionine
Methionine is an α-amino acid with the chemical formula HO2CCHCH2CH2SCH3. This essential amino acid is classified as nonpolar. This amino-acid is coded by the codon AUG, also known as the initiation codon, since it indicates mRNA's coding region where translation into protein...
excision, signal peptide
Signal peptide
A signal peptide is a short peptide chain that directs the transport of a protein.Signal peptides may also be called targeting signals, signal sequences, transit peptides, or localization signals....
s, proteolysis
Proteolysis
Proteolysis is the directed degradation of proteins by cellular enzymes called proteases or by intramolecular digestion.-Purposes:Proteolysis is used by the cell for several purposes...
and other posttranslational modification
Posttranslational modification
Posttranslational modification is the chemical modification of a protein after its translation. It is one of the later steps in protein biosynthesis, and thus gene expression, for many proteins....
s.
Methodology
The main idea behind the proteogenomic approach is to identify peptides in a biological sample using mass spectrometry by searching the six-frame translation of the genome sequence, as opposed to searching the protein database. This enables identification of protein regions that are absent from or incorrectly represented in current gene annotations, and thus allows improvement of the gene annotations.Comparative proteogenomics is a branch of proteogenomics that compares proteomic data from multiple related species concurrently and exploits the homology between their proteins to improve annotations with higher statistical confidence.