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Understand the
definitions and usage of common scientific terms in proteomics by
browsing this Glossary from the Proteome Society®.
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D
Data
cleaning
A process whereby automated or semi-automated algorithms are used
to process experimental data, including noise, experimental errors
and other artifacts, in order to generate and store high-quality data
for use in subsequent analysis.
Data mining
The ability to query very large databases in order to satisfy a
hypothesis ("top down" data mining); or to interrogate
a database in order to generate new hypotheses based on rigorous
statistical correlations ("bottom-up" data mining).
Database
Collection of data in machine-readable form, which can be manipulated
by software to appear in varying arrangements and subsets.
Delayed Extraction
A technique that allows for greater unison in the take-off of ions
in MALDI mode.
Desalting
Removing salts from mixtures of peptides or other sample- this is
necessary for mass spec analysis.
DIGE
Differential in Gel Electrophoresis: 2D co-separation of protein
samples labeled with different fluorescent dyes (Amersham Pharmacia)
TOP
Distance
matrix
The method used to present the results of the calculation of an
optimal pairwise alignment score. The matrix field (i,j) is the
score assigned to the optimal alignment between two residues (up
to a total of i by j residues) from the input sequences. Each entry
is calculated from the top-left neighboring entries by way of a
recursive equation.
Distance
measure
A function that associates a non-negative numeric value with a pair
of biosequences. The shorter distance between the sequences (i.e.,
the lower the number), the greater the similarity. For example,
the distance between leusine and alanine is small while the distance
between leusine and argenine is large.
DNA
Deoxyribonucleic Acid; a polymer made of 4 types of nucleobases
attached to a sugar and phosphate linked backbone, that makes up
a gene.
Domain
A discrete portion of a protein with its own function. The combination
of domains in a single protein determines its overall function.
DTT
Dithiothreitol: a reducing agent for disulfide bonds
TOP
E
Edman
degradation
Chemical method for determining the amino acid sequence of a protein
starting from the N-terminus.
Electrophoresis
Separation of charged molecules in an electric field across a porous
medium.
Entrez
A WWW-based database retrieval program created by the National Center
for Biotechnology Information (NCBI), a division of the NIH.
ESI
Electrospray Ionization
EST
Expressed Sequence Tag; Small region of a deciphered gene
TOP
Eukaryotic
cell
A cell containing a nucleus, in which the genes or DNA is housed
E-value
For a given score, (eg BLAST) the number of hits in a database search
that we expect to see by chance with this score or better. The E-value
takes into account the size of the database. The lower the E-value,
the more significant the score.
Exon
Region of a gene containing DNA that codes for a protein
ExPASy
Expert Protein Analysis System - set of software tools, maintained
by the Swiss Institute of Bioinformatics
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