Proteomics in the context of "Mass spectrometry"

Bioinformatics (/ˌbaɪ.oʊˌɪnfərˈmætɪks/ ) is an interdisciplinary field of science that develops computational methods and software tools for understanding biological data, especially when the data sets are large and complex. Bioinformatics uses biology, chemistry, physics, computer science, data science, computer programming, information engineering, mathematics and statistics to analyze and interpret biological data. This process can sometimes be referred to as computational biology, however the distinction between the two terms is often disputed. To some, the term computational biology refers to building and using models of biological systems.

Computational, statistical, and computer programming techniques have been used for computer simulation analyses of biological queries. They include reused specific analysis "pipelines", particularly in the field of genomics, such as by the identification of genes and single nucleotide polymorphisms (SNPs). These pipelines are used to better understand the genetic basis of disease, unique adaptations, desirable properties (especially in agricultural species), or differences between populations. Bioinformatics also includes proteomics, which aims to understand the organizational principles within nucleic acid and protein sequences.

Predictive medicine is a field of medicine that entails predicting the probability of disease and instituting preventive measures in order to either prevent the disease altogether or significantly decrease its impact upon the patient (such as by preventing mortality or limiting morbidity).

While different prediction methodologies exist, such as genomics, proteomics, and cytomics, the most fundamental way to predict future disease is based on genetics. Although proteomics and cytomics allow for the early detection of disease, much of the time those detect biological markers that exist because a disease process has already started. However, comprehensive genetic testing (such as through the use of DNA arrays or full genome sequencing) allows for the estimation of disease risk years to decades before any disease even exists, or even whether a healthy fetus is at higher risk for developing a disease in adolescence or adulthood. Individuals who are more susceptible to disease in the future can be offered lifestyle advice or medication with the aim of preventing the predicted illness.

In evolutionary biology, conserved sequences are identical or similar sequences in nucleic acids (DNA and RNA) or proteins across species (orthologous sequences), or within a genome (paralogous sequences), or between donor and receptor taxa (xenologous sequences). Conservation indicates that a sequence has been maintained by natural selection.

A highly conserved sequence is one that has remained relatively unchanged far back up the phylogenetic tree, and hence far back in geological time. Examples of highly conserved sequences include the RNA components of ribosomes present in all domains of life, the homeobox sequences widespread amongst eukaryotes, and the tmRNA in bacteria. The study of sequence conservation overlaps with the fields of genomics, proteomics, evolutionary biology, phylogenetics, bioinformatics and mathematics.

The Harbin cranium is a nearly complete skull of an archaic human found in sediments of the Songhua River near Harbin on the Northeast China Plain, dating to at minimum 146,000 years ago during the Middle Pleistocene. It was described in 2021, and that year it was assigned as the holotype of the new human species Homo longi ("dragon man") named after Long Jiang, where the fossil skull was discovered . The Harbin cranium was initially hypothesized to belong to the same species as the Denisovans, and subsequent proteomics and mitochondrial DNA analyses confirmed its Denisovan affinities.

The Harbin cranium is broadly anatomically similar to other Middle Pleistocene Chinese specimens. Like other archaic humans, the skull is low and long, with massively developed brow ridges, wide eye sockets, and a large mouth. The skull is the longest ever found from any human species. Like modern humans and the much earlier Homo antecessor, the face is rather flat, but with a larger nose. The brain volume was 1,420 cc, within the range of modern humans and Neanderthals.

Omics is the collective characterization and quantification of entire sets of biological molecules and the investigation of how they translate into the structure, function, and dynamics of an organism or group of organisms. The branches of science known informally as omics are various disciplines in biology whose names end in the suffix -omics, such as genomics, proteomics, metabolomics, metagenomics, phenomics and transcriptomics.

The related suffix -ome is used to address the objects of study of such fields, such as the genome, proteome or metabolome respectively. The suffix -ome as used in molecular biology refers to a totality of some sort; it is an example of a "neo-suffix" formed by abstraction from various Greek terms in -ωμα, a sequence that does not form an identifiable suffix in Greek.

Metabolomics is the scientific study of chemical processes involving metabolites, the small molecule substrates, intermediates, and products of cell metabolism. Specifically, metabolomics is the "systematic study of the unique chemical fingerprints that specific cellular processes leave behind", the study of their small-molecule metabolite profiles. The metabolome represents the complete set of metabolites in a biological cell, tissue, organ, or organism, which are the end products of cellular processes. Messenger RNA (mRNA), gene expression data, and proteomic analyses reveal the set of gene products being produced in the cell, data that represents one aspect of cellular function. Conversely, metabolic profiling can give an instantaneous snapshot of the physiology of that cell, and thus, metabolomics provides a direct "functional readout of the physiological state" of an organism. There are indeed quantifiable correlations between the metabolome and the other cellular ensembles (genome, transcriptome, proteome, and lipidome), which can be used to predict metabolite abundances in biological samples from, for example mRNA abundances. One of the ultimate challenges of systems biology is to integrate metabolomics with all other -omics information to provide a better understanding of cellular biology.

Molecular pathology is an emerging discipline within pathology which is focused in the study and diagnosis of disease through the examination of molecules within organs, tissues or bodily fluids. Molecular pathology shares some aspects of practice with both anatomic pathology and clinical pathology, molecular biology, biochemistry, proteomics and genetics, and is sometimes considered a "crossover" discipline. It is multi-disciplinary in nature and focuses mainly on the sub-microscopic aspects of disease. A key consideration is that more accurate diagnosis is possible when the diagnosis is based on both the morphologic changes in tissues (traditional anatomic pathology) and on molecular testing.

It is a scientific discipline that encompasses the development of molecular and genetic approaches to the diagnosis and classification of human diseases, the design and validation of predictive biomarkers for treatment response and disease progression, the susceptibility of individuals of different genetic constitution to develop disorders.

A 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 is the study of the proteome.

A cancer biomarker refers to a substance or process that is indicative of the presence of cancer in the body. A biomarker may be a molecule secreted by a tumor or a specific response of the body to the presence of cancer. Genetic, epigenetic, proteomic, glycomic, and imaging biomarkers can be used for cancer diagnosis, prognosis, and epidemiology. Ideally, such biomarkers can be assayed in non-invasively collected biofluids like blood or serum.

While numerous challenges exist in translating biomarker research into the clinical space; a number of gene and protein based biomarkers have already been used at some point in patient care; including, AFP (liver cancer), BCR-ABL (chronic myeloid leukemia), BRCA1 / BRCA2 (breast/ovarian cancer), BRAF V600E (melanoma/colorectal cancer), CA-125 (ovarian cancer), CA19.9 (pancreatic cancer), CEA (colorectal cancer), EGFR (Non-small-cell lung carcinoma), HER-2 (Breast Cancer), KIT (gastrointestinal stromal tumor), PSA (prostate specific antigen) (prostate cancer), S100 (melanoma), and many others. Mutant proteins themselves detected by selected reaction monitoring (SRM) have been reported to be the most specific biomarkers for cancers because they can only come from an existing tumor. About 40% of cancers can be cured if detected early through examinations.