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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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R
Reflectron Mode
A mode in MALDI where ions are reflected back in the flight tube,
resulting in greater mass accuracy
Relational
database
A database that stores data in a structure consisting of one or
more tables of rows and columns, which may be interconnected. A
row corresponds to a record (tuple); columns correspond to attributes
(fields) in the record. Typically use Structured Query Language
(SQL) for data definition, data management, and data access and
retrieval.
Resolution
Degree of molecular detail on a physical map of DNA, ranging from
low to high.
Retentate
Chromatography™
A method of sample preparation on chromatographic interaction ProteinChip®
Arrays. In Retentate Chromatography, analytes that stay bound to
the chromatography media are detected as opposed to most common
forms of column chromatography that incorporate analyte detection
in the eluate stream. As incorporated in SELDI technology, retentate
chromatography is usually followed by laser desorption and ionization
time-of-flight mass spectrometry to detect proteins that bind to
a chromatographic surface. Advantages of this method over other
forms of protein chromatography include rapid optimization of chromatographic
conditions and minimization of protein loss prior to detection.
Retentate
Chromatography is a trademark of Ciphergen Biosystems, Inc. (Fremont,
CA).
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
RNA
Ribonucleic Acid; may be of many kinds, ribosomal, messenger or
transfer
Rosetta stone method A way of looking at the correlation of protein
domains across species. Some proteins have homologs that are fused
in other species, yielding clues as to the proteins with which they
might interact. In addition, proteins that have been identified
in particular complexes and pathways hint at the location and function
of their homologs in other species.
Rotofor
Large-scale liquid phase isoelctric focusing apparatus (Biorad)
TOP
S
Sample clean-up
Generally refers to removal of known impurities such as acrylamide
or salt from a sample
SAPS
Statistical analysis of protein sequences - a software tool / algorithm
at Institut Pasteur that provides extensive physicochemical information
that can be inferred from its sequence
Schema /
schemata
A description of the data represented within a database. The format
of the description varies but includes a table layout for a relational
database or an entity- relationship diagram.
Scoring
Function (also cost function or weight function)
The score of an alignment of two sequences (a and b) is the sum
of the score of all the replacement operations that lead from a
to b.
Scoring
matrix / substitution matrix
A matrix that defines scores for amino acid substitutions, reflecting
the similarity of physicochemical properties, and observed substitution
frequencies.
TOP
SDS
Sodium dodecyl sulfate; negatively charged detergent
SDS-PAGE
gel electrophoresis
Molecular weight polyacrylamide-gel separation of SDS coated proteins
Secondary
Structure
Structures that sections of the protein may fold on themselves to
form, such as • sheets or •-helices
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
Silver Stain
Silver-based protein stain
TOP
Size-Exclusion
A chromatography technique that separates proteins according to
their size by dynamic exclusion
Soft-ionization
Ionization that does not fragment a molecule or change its covalent
structure
Structural
Proteomics
Structural Characterization of the proteome, involves solving protein
structures by x-ray crystallography in high throughput mode
SWISS-PROT
An annotated protein sequence database established in 1986 and maintained
collaboratively, since 1987, by the Department of Medical Biochemistry
of the University of Geneva and the EMBL Data Library (now the EMBL
Outstation - The European Bioinformatics Institute (EBI)). The SWISS-PROT
protein sequence data bank consists of sequence entries. Sequence
entries are composed of different line-types, each with their own
format. For standardization purposes the format of SWISS-PROT follows
as closely as possible that of the EMBL Nucleotide Sequence Database.
Sypro
Ruby
Non-destructive
fluorescent protein stain (sensitivity 1-2 ng)
TOP
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