A glossary of the technical terms and abbreviations used on this site.
amino acid
A molecule with both an amino and a carboxylic acid group. There are 20 common
natural amino acids found in proteins.
CID
Collision induced dissociation. The process in which gaseous ions are broken into smaller
fragments by collision with gas atoms. The energy of the collisions influences
which chemical bonds are broken.
code 128
A type of barcode that may contain upper and lower case letters, numbers, symbols
and control codes. It also includes error checking.
combinatorial chemistry
Preparation of collections of compounds by joining molecular building blocks in different
combinations. Also known as combichem.
DLL
Dynamic link library. A type of program file used on Windows computers. Not a
stand-alone software package, but intended to be run from other programs.
Edman degradation
A chemical method of determining the amino acid sequence of a peptide or protein.
The amino acids are removed one by one and analysed to determine their
identity, and hence the sequence.
encoding
A technique used with split-and-pool combinatorial synthesis for identification
of library compounds. In addition to a library compound, each resin bead
carries an encoding compound(s). This is synthesized in parallel to the library
compound and designed to be easy to analyse. The structure of the library
compound can be deduced by analysis of the encoding compound.
ESI
Electrospray ionization. A method of forming gas ions from a solution of molecules. The
solution is sprayed in to a vacuum through a sharp needle to which a high
voltage is applied.
ion
An atom or molecule with an electrical charge.
library
A collection of chemical compounds prepared by combinatorial chemistry.
m/z
The mass to charge ratio of an ion.
mass spectrometer
Equipment for performing mass spectrometry.
mass spectrometry
Measurement of the mass of atoms or molecules. The molecules are first converted to ions,
which are separated using electric or magnetic fields according to the ratio of
their mass to electric charge. The measured masses are used to infer the
identity of the molecules.
mass spectrum
A plot of the count of the number of ions against their mass/charge ratio. The
output of a mass spectrometer.
MOPAC
A program for theoretical studies of molecules. It performs molecular orbital
calculations to determine molecular properties, such as geometry. While older
versions are available free, the latest version is sold by Fujitsu.
MS
Mass spectrometry/spectrometer/spectrum.
MSn
Ions are sorted according to their mass/charge ratio, then fragmented (see CID) and
a mass spectrum of the fragments is measured. This is known as MS/MS or MS2.
These fragments may themselves be sorted, and fragmented again, and so on, in n
sequential steps of mass spectrometry, hence the terminology MSn.
orbital
A mathematical description of the behaviour of an electron(s) in an atom or
molecule. The orbital describes the probable location of the electron, and can
be used to calculate other properties such as its energy.
peptide
A short chain of amino acids joined through their amino and carboxyl groups. In a
cyclic peptide, the ends are also joined together to give a circular
molecule. Proteins are longer chains,
typically of >50 amino acids.
POV-Ray
A free program for generating images of three dimensional objects. Uses the
technique of ray tracing.
PSD
Post source decay. Fragmentation of energized ions in a mass spectrometer after they
leave the ion source.
QSAR
Quantitative structure activity relationship. A mathematical relationship between biological
activity of a compound and computed (or measured) properties that depend on the
molecular structure.
residue
Part of a chemical structure that originates from a building block. In the case of
peptides and proteins, this refers to amino acids.
resin
An insoluble polymer, on which chemical reactions can be performed by addition of
reagent solutions. Usually supplied as spherical beads <1 mm diameter.
sequencing
Determination of the order of residues within a molecular chain of building blocks. Usually
refers to peptides/proteins with amino acid building blocks, or DNA with
nucleotide building blocks.
split-and-pool
A method of library synthesis using resin beads. Portions of beads are reacted
with different building blocks, then the beads are mixed, split into separate
portions again, which are reacted with the building blocks, and so on. The
result is a single compound identity per resin bead, although analysis is
required to find out what the compound is. Also known as split-and-mix.
VBA
Visual Basic for Applications. A programming language which is built in to many
popular software packages, including Microsoft Office, that allows automation
of tasks and creation of new features.