Proteomics Glossary

Amino Acids

Amino acids are the primary subunit of proteins; chains of amino acids are joined to form peptides. Multicellular organisms use 20 amino acids to create all proteins in body. Substitution or deletion of a single amino acid can alter the function of a protein, and mutations that lead to cancer are many times attributed to changes in amino acid sequence.


A biomarker is any molecule that is associated with a particular pathological or physiological state. Protein biomarkers are often used to identify drug targets or to diagnose and monitor therapy.


A method of separation in which molecules are separated according to chemical characteristics or size.


Conformation refers to protein folding and the effects of three-dimensional structure on protein function. Events that affect protein conformation are the interactions of a protein with other proteins and post-translational modifications.


Proteins that catalyze biochemical reactions in an organism. Enzymes are necessary because they provide the activation energy for chemical reactions that otherwise would occur very slowly.

Mass Spectrometry

A technique used to identify proteins by their mass and electric charge. To utilize mass spectrometry to identify proteins, protein or peptide samples are ionized by an ionization source. Two common sources used in proteomics are matrix-assisted laser desorption ionization (MALDI-) and electrospray ionization (ESI-). The ionization source adds protons to the amino acids in the sample. After ionization, the charged protein enters a mass analyzer, such as time-of-flight (TOF-), or quadropole ion flight, which sorts the peptides according to their mass-to-charge ratio. Finally, a detector notes the number of ions over a range of mass-to-charge ratios. The output may produce a "peptide mass fingerprint" - an amino acid sequence or a pattern of unique peptides.


A device that measures the difference in gene expression or protein expression in biomaterials under different experimental conditions, such as healthy versus diseased tissues or cells. In the typical protein array, the capture reagent, such as a known protein or antibody, is immobilized on a microchip and treated with liquid phase reagents. Binding or interaction of elements of the liquid phase with the capture reagent is quantified by computer software. Protein microarrays measure the variations in protein levels and can be used to determine the protein expression profile in diseases like cancer.


Peptides are short chains of amino acids or protein fragments.


A complex molecule made of amino acids. Proteins are found in all organisms, and are responsible for the majority of biochemical reactions that are essential for a system to function properly. Proteins are often involved in enzymatic reactions and signal transduction.


The biochemical process by which messenger RNA (mRNA) is used as a template by the ribosome to synthesize the respective protein.

Two-Dimensional Electrophoresis

A biochemistry technique (also known as 2-D gel electrophoresis) that separates proteins based on both size and isoelectric point or pI. In the technique, proteins are first separated according to isoelectric point. The proteins are then separated by size. The protein of interest may be isolated and characterized by mass spectrometry.

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