What is Proteomics?
The Center
Rationale of the Proteome Center
Technology and Application Development
Post Doctoral Fellow Program
Definitions

Definitions

Electrophoresis:

The separation of ions in an electric field. For macromolecules, this is usually done in a water-swellable matrix like polyacrylamide or agarose which perform sieving functions and reduce convection.

Express Profile:

A time-slice analysis of the gene products (mRNA or protein) present in a cell. Usually implies quantitative analysis of the gene products in response to a change.

Funtional Genomics:

The study of the functions of genes and their interrelationships. Genome sequence is structure only. While bioinformatics allows us to infer function, in some cases, it is necessary.

Genome:

All the DNA in a cell, both chromosomal and extra-chromosomal. A Genome sequence is the sequence of all the DNA in a cell, genes, pseudogenes, as well as DNA that does not code for genes.

Genomics:

The study of the genome. Any study which takes as its basis a complete genome sequence and which deals RNA or DNA.

High Throughput:

A common, compound adjective used to describe many genome and proteome studies. High-throughput technologies are necessary in these disciplines due to the sheer number of genes to be studied.

Ion suppression:

When two proteins are present as a mixture in MALDI analysis, one may predominate over the other in the mass spectrum. In some cases, a protein can be observed if it is loaded as a pure sample, but if it is loaded at the same level in a mixture with other proteins, its intensity will be suppressed. Ion suppression can be quite severe for complex mixtures analyzed from a probe tip, but seems to be somewhat less critical when desorbing directly from gels.

Isoelectric Focusing:

The eletrophoretic migration of proteins in a pH gradient to the pH at which they have no net charge (the isoelectric point). Proteins which diffuse away from the isoelectric pH become charged again and are electrophoresed back to their isoelectric pH (thus isoelectric focussing).

Mass Spectrometry:

Any technique which measures the mass of an ion in a vacuum. This is, in essence, a very accurate and sensitive method to weigh a molecule. It provides the molecular weight of the ionized molecule.

Multiplex mass maps:

These allow simultaneous mass analysis of peptide fragments from more than one protein. Using our technology, the masses of the intact proteins and their pI values are also available, aiding protein identification.

Multiplex sequencing:

Sequence analysis of protein mixtures by Edman degradation results in multiple residues identified at each cycle. It is only effective for simple mixtures (up to 4 or 5 components)

Multivariate analysis:

This refers to analysis of a sample (in this context, a protein) by more than one independent method of analysis. For example, a classical 2-D gel provides two independent, orthogonal parameters, pI and apparent size. MALDI of the intact protein from the gel provides a third dimension, mass, which is an intrinsic property of the protein and is similar, but more useful, than the relative size derived from the SDS dimension. MALDI of the CNBr fragments of the protein directly from the gel provides a true fourth dimension of analysis.

m/z:

Where m = mass and z = charge of the ion in the mass spectrometer. Mass spectrometry measures mass divided by charge (m/z). In MALDI the singly-charged species is usually the most intense ion peak, doubly-charged and the occasional triply-charge ion peaks are less intense. Artifactual dimers and even trimers show up with less frequency and are much less intense than the singly-charged monomers.

Proteome:

All the proteins produced from all the genes of a genome.

Proteomics:

The study of the proteome. Any global analysis of changes in the quantities and post-translational modifications of all the proteins in cells taking genome sequence as the starting point. The changes may be brought about by growth differentiation, senescence, changes in the environment, genetic manipulation, or other events. See detailed discussion elsewhere on this site.

Sequence coverage:

This refers to the fraction of the complete protein sequence analyzed by a method. For example, identification of 4 tryptic peptides corresponding to 50 residues of a 250-residue protein represents 20% coverage by sequence.

Virtual 2-D gels:

These gels are two-dimensional images constructed from sequential mass spectra obtained from a one-dimensional gel.

Lay Summary of the Proteome:

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