Proteomics

proteomicprotein analysisHuman Proteome Resourceproteomic analysisanalysis of a proteinApplied ProteomicsFunctional Proteomicsproteinprotein profilingproteome
Proteomics is the large-scale study of proteins.wikipedia
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Proteome

proteomesproteomicprotein expression
The proteome is the entire set of proteins that is produced or modified by an organism or system.
Proteomics is the study of the proteome.

Functional genomics

functionalgene functionAP-MS
It is an important component of functional genomics.
The latter comprise a number of "-omics" such as transcriptomics (gene expression), proteomics (protein production), and metabolomics.

Phosphoproteomics

phosphoproteome
Phosphoproteomics is a branch of proteomics that identifies, catalogs, and characterizes proteins containing a phosphate group as a posttranslational modification.

Genomics

genomicgenome biologygenomic analysis
The term proteomics was coined in 1997, in analogy to genomics, the study of the genome. In this way, proteomics can be seen as complementary to genomics, transcriptomics, epigenomics, metabolomics, and other -omics approaches in integrative analyses attempting to define biological phenotypes more comprehensively. After genomics and transcriptomics, proteomics is the next step in the study of biological systems.
The English-language neologism omics informally refers to a field of study in biology ending in -omics, such as genomics, proteomics or metabolomics.

Glycoproteomics

Glycoproteomics is a branch of proteomics that identifies, catalogs, and characterizes proteins containing carbohydrates as a result of posttranslational modification.

Shotgun proteomics

data-dependent acquisitionphospho-shotgun
This causes stochastic differences between experiments due to data-dependent acquisition of tryptic peptides.
The most common method of shotgun proteomics starts with the proteins in the mixture being digested and the resulting peptides are separated by liquid chromatography.

Protein

proteinsproteinaceousstructural proteins
Proteomics is the large-scale study of proteins.
The total complement of proteins present at a time in a cell or cell type is known as its proteome, and the study of such large-scale data sets defines the field of proteomics, named by analogy to the related field of genomics.

Marc Wilkins (geneticist)

Marc Wilkins
The word proteome is a portmanteau of protein and genome, and was coined by Marc Wilkins in 1994 while he was a Ph.D. student at Macquarie University.
In 1997 he co-edited the first book on proteomics, 'Proteome Research: New Frontiers in Functional Genomics' (Wilkins et al. (eds), Springer Verlag), which sold more than 4,000 copies.

Protein mass spectrometry

HX/MSmass spectrometryMudPIT
While the most traditional method is yeast two-hybrid analysis, a powerful emerging method is affinity purification followed by protein mass spectrometry using tagged protein baits.
Its applications include the identification of proteins and their post-translational modifications, the elucidation of protein complexes, their subunits and functional interactions, as well as the global measurement of proteins in proteomics.

Top-down proteomics

top-down
These methods gave rise to the top-down and the bottom-up proteomics workflows where often additional separation is performed before analysis (see below).
Top-down proteomics is capable of identifying and quantitating unique proteoforms through the analysis of intact proteins.

Secretomics

leaderless secretory pathwaysecretosomes
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.
Secretomics is a type of proteomics which involves the analysis of the secretome—all the secreted proteins of a cell, tissue or organism.

Protein microarray

Protein arrayhybridization arraymicroarray
Other methods include surface plasmon resonance (SPR), protein microarrays, dual polarisation interferometry, microscale thermophoresis and experimental methods such as phage display and in silico computational methods.
Protein microarrays were developed due to the limitations of using DNA microarrays for determining gene expression levels in proteomics.

Proteogenomics

proteogenomic
In proteogenomics, proteomic technologies such as mass spectrometry are used for improving gene annotations.
Proteogenomics is a field of biological research that utilizes a combination of proteomics, genomics, and transcriptomics to aid in the discovery and identification of peptides.

Bioinformatics

bioinformaticbioinformaticianbio-informatics
Using bioinformatics techniques, researchers are capable of faster analysis and data storage.
In a less formal way, bioinformatics also tries to understand the organisational principles within nucleic acid and protein sequences, called proteomics.

Bottom-up proteomics

bottom-up
These methods gave rise to the top-down and the bottom-up proteomics workflows where often additional separation is performed before analysis (see below).
The major alternative workflow used in proteomics is called top-down proteomics where intact proteins are purified prior to digestion and/or fragmentation either within the mass spectrometer or by 2D electrophoresis.

Systems biology

molecular physiologysystems biologistbiological systems
Knowledge of protein-protein interactions is especially useful in regard to biological networks and systems biology, for example in cell signaling cascades and gene regulatory networks (GRNs, where knowledge of protein-DNA interactions is also informative).
Therefore, transcriptomics, metabolomics, proteomics and high-throughput techniques are used to collect quantitative data for the construction and validation of models.

Epigenomics

epigenomicepigenomic profilinggenome-wide DNA methylation patterns
In this way, proteomics can be seen as complementary to genomics, transcriptomics, epigenomics, metabolomics, and other -omics approaches in integrative analyses attempting to define biological phenotypes more comprehensively.
The field is analogous to genomics and proteomics, which are the study of the genome and proteome of a cell.

Richard D. Smith

Another quantitative approach is the Accurate Mass and Time (AMT) tag approach developed by Richard D. Smith and coworkers at Pacific Northwest National Laboratory.
In the late 1990s, Smith's group was also extensively involved in the development and application of Fourier transform ion cyclotron resonance (FTICR) mass spectrometry, which provided the basis for much greater MS resolution and mass measurement accuracy, and particularly in the development of these technologies for applications in proteomics.

Transcriptomics technologies

transcriptomicstranscriptomictranscriptomic technique
In this way, proteomics can be seen as complementary to genomics, transcriptomics, epigenomics, metabolomics, and other -omics approaches in integrative analyses attempting to define biological phenotypes more comprehensively. After genomics and transcriptomics, proteomics is the next step in the study of biological systems.

Metabolomics

metabolomicmetabolitesmetabonomics
In this way, proteomics can be seen as complementary to genomics, transcriptomics, epigenomics, metabolomics, and other -omics approaches in integrative analyses attempting to define biological phenotypes more comprehensively.
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.

ExPASy

ProtParam ExPASy
A good place to find lists of current programs and databases is on the ExPASy bioinformatics resource portal.
Scientists can access a wide range of resources in many different domains, such as proteomics, genomics, phylogenetics/evolution, systems biology, population genetics, and transcriptomics.

Omics

-omicsomic-ome
In this way, proteomics can be seen as complementary to genomics, transcriptomics, epigenomics, metabolomics, and other -omics approaches in integrative analyses attempting to define biological phenotypes more comprehensively.
The English-language neologism omics informally refers to a field of study in biology ending in -omics, such as genomics, proteomics or metabolomics.

Matrix-assisted laser desorption/ionization

MALDIMALDI-TOFmatrix-assisted laser desorption ionization
More recently implemented methods use mass spectrometry-based techniques, a development that was made possible by the discovery of "soft ionization" methods developed in the 1980s, such as matrix-assisted laser desorption/ionization (MALDI) and electrospray ionization (ESI).
In proteomics, MALDI is used for the rapid identification of proteins isolated by using gel electrophoresis: SDS-PAGE, size exclusion chromatography, affinity chromatography, strong/weak ion exchange, isotope coded protein labelling (ICPL), and two-dimensional gel electrophoresis.

Activity-based proteomics

Activity based proteomicsActivity based protein profilingActivity based probes
Activity-based proteomics, or activity-based protein profiling (ABPP) is a functional proteomic technology that uses chemical probes that react with mechanistically related classes of enzymes.

Immunoproteomics

Immunoproteomics is the study of large sets of proteins (proteomics) involved in the immune response.