Glossary


2-D gel electrophoresis
Currently used in reference to the gel-based separation of proteins by their isoelectric point in one dimension followed by a molecular weight separation by SDS-polyacrylamide gel electrophoresis perpendicular to the first dimension. Other properties of the proteins can also be used as a means for separation.
2D-LC
Two Dimensional Liquid Chromatography; A preliminary separation technique generating fractions, which are further fractionated on a second column using an orthogonal chromatography technique.
Affinity chromatography
Selective separation of proteins based on their affinity for a particular ligand.

Blue Native gel electrophoresis
A "charge shift" electrophoresis of native membrane protein complexes using negatively-charged Coomassie Blue bound to the polypeptides to allow electrophoretic mobility. Convenient for isolation of complexes of membrane proteins in a native state.

Bottom-up (proteomics)

Method to identify proteins and characterize their amino acid sequences and post-translational modifications. Isolated proteins or proteome mixtures are first completely digested into peptides by proteolysis and then peptides are analysed by mass spectrometry.
Capillary electrophoresis
Solution or gel based electrophoresis performed in micro-glass capillaries.
CE
Capillary Electrophoresis; a protein separation method based upon linear separation within a fine capillary.

CAD

Collision-activated Dissociation

CID
Collision Induced Dissociation.

DIGE
Differential in Gel Electrophoresis: 2D co-separation of protein samples labeled with different fluorescent dyes (GE healthcare)
Edman degradation
Chemical method for determining the amino acid sequence of a protein starting from the N-terminus.
ESI
Electrospray Ionization
FTICR
Fourier Transform Ion Cyclotron Resonance Mass Spectrometry, a high resolution sensitivity MS technique

FWHM

full width half maximum, i.e. where Dm is the peak width of ion m at 50% relative abundance
HPLC
High-performance liquid chromatography; a technique for separating proteins and other molecules
ICAT
Isotope coded affinity tags; proteomic technique based on the use of isotopic reagents for labeling two different populations of proteins. Reacts with cysteinyl residues.

In-gel digestion
Protease digestion of proteins in polyacrylamide gel slices.
Ion Trap
Ion species are confined using dual parabolic trapping potentials to resolve ions by mass prior to detection
Ion-exchange
A chromatographic technique in which analytes are bound to a charged column and differentially eluted off by increasing ionic strength of eluting media
Isoelectric point
pH at which an amphoteric molecule has a net charge equal to zero
Isolectric focusing
Electrophoretic focusing of proteins in a pH gradient
LC/MS
Liquid Chromatography/Mass Spectrometry

iTRAQ

Isobaric Tag for Relative and Absolute Quantitation analysis
MALDI
Matrix assisted laser-desorption ionization; common form of soft-ionisation for proteins

MALDI imaging

A mass spectrometry imaging technique in which the sample, often a thin tissue section, is moved in two dimensions while the mass spectrum is recorded
Matrix
An organic molecule used to cocrystallize with sample, that absorbs laser energy and allows sample to desorb and ionize in MALDI
MDLC
Multi Dimensional Liquid Chromatography

MRM

Multiple-reaction monitoring is a powerful method for the quantitation of specific proteins by MS/MS. The technique involves the selective MS analysis of peptide ions and fragmented product ions from proteins of interest. The ratio of the m/z of a user-specified peptide to that of its chosen product ion is called the MRM "transition".
MS/MS
Tandem Mass Spectrometry; a selected precursor ion of interest may be fragmented by collision induction, and their mass analyzed
NES
Nano-electrospray; a miniaturized version of ESI that allows for greater sensitivity

Interaction proteomics

Proteome wide study of the interactions between individual proteins and protein complexes
pI
Net charge of protein in aqueous solution
PMF
Peptide Mass Fingerprinting; generating a fingerprint or a group of characteristic peptide peaks by analyzing the mass of proteolyzed fragments.

ppm
Parts per million ("ppm") denotes one particle of a given substance for every 999,999 other particles. Generally used to measure and denote the concentration of chemical in very low quantity.
Protein Mapping
Identification of proteins according to their mass and isoelectric point. This term may also be used to indicate location of a protein on a gene.
Proteome
"The total protein complement of a genome"; complete set of proteins expressed by a cell, tissue or organism

Proteomics: The study of protein structure and function within a cell. For example, knowing the characteristics and shape of a key protein in a given disease could allow researchers to custom-design therapeutic agents. Researchers would be able to create a drug molecule that would bind securely to the protein. This could interrupt the protein's signal, thus stopping, starting or modifying a biological process. Proteomics works hand in hand with genomics.
PSD
Post Source Decay, an MS/MS mode in MALDI where fragment ions can be detected and their mass used to do sequence analysis

PTM
Post-translational Modification; Alteration of the protein's chemical nature after translation by covalent addition of other molecules, proteolytic cleavage etc.

QQQ

Triple quadrupole
Q-TOF
Quadrupole-Time of Flight, this combines the ion handling capacity of a quadrupole instrument with resolving power and duty cycle of a TOF analyzer

Reflectron Mode
A mode in MALDI where ions are reflected back in the flight tube, resulting in greater mass accuracy
Reverse-Phase
A chromatographic technique in which analytes bind non specifically through hydrophobic interaction to material such as C18 and are differentially eluted by increasing concentration of a non polar solvent such as acetonitrile
SELDI
Surface-Enhanced Laser Desorption and Ionization. A method of protein capture and enrichment on a chemically or bioaffinity active solid phase surface often followed by selective washing steps and then followed by laser "elution" of the proteins into a detector, usually a time-of-flight mass spectrometer. The whole method is often referred to as SELDI-TOF MS. With similarities to MALDI technology (in which the sample probe is not an active binding partner to protein analytes), an energy absorbing molecule or protein co-crystallization matrix is typically added on top of the captured proteins to assist ionization via laser excitation.
Sequence Tagging
Extraction of de novo sequence information from individual precursor ions

SILAC

Stable isotope labeling with amino acids in cell culture. Approach for in vivo incorporation of a label into proteins for mass spectrometry (MS)-based quantitative proteomics. SILAC relies on metabolic incorporation of a given 'light' or 'heavy' form of the amino acid into the proteins. The method relies on the incorporation of amino acids with substituted stable isotopic nuclei (e.g. deuterium, 13C, 15N). Thus in an experiment, two cell populations are grown in culture media that are identical except that one of them contains a 'light' and the other a 'heavy' form of a particular amino acid (e.g. 12C and 13C labeled L-lysine, respectively). When the labeled analog of an amino acid is supplied to cells in culture instead of the natural amino acid, it is incorporated into all newly synthesized proteins. After a number of cell divisions, this particular amino acid will be completely replaced by its isotope labeled analog. There is hardly any chemical difference between the labeled and natural amino acid isotopes. Incorporation of the isotope label is 100%.
Size-Exclusion Chromatography
A chromatography technique that separates proteins according to their hydrodynamic diameter by dynamic exclusion
Soft-ionization
Ionization that does not fragment a molecule or change its covalent structure
Sypro Ruby
Non-destructive fluorescent protein stain (sensitivity 1-2 ng)
TOF

(see Time of Flight)

Top-down (proteomics)

Method of protein identification and characterization that uses an ion trapping mass spectrometer to store an isolated intact protein ion for mass measurement followed by fragmentation of the protein and analysis by tandem mass spectrometry
Time-of-flight

detection Method for Mass Spectrometry based on correlation of mass of a molecule to its time of flight, often used with either MALDI or ESI ionization
Western blotting
Immunodetection of proteins blotted on to a solid support followed by proteolysis and affinity selection of peptides containing the selectively derivitized groups. The relative abundance of co-migrating peptides is determined by mass spectrometry.