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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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P
Pairwise alignment
In the first step, two sequences are padded by gaps so that they are
the same length and so that they display the maximum similarity on
a residue to residue basis. An optimal pairwise alignment is an alignment
which has the maximum amount of similarity with the minimum number
of residue 'substitutions'.
PAM
matrix
Percent-accepted mutation - see "scoring matrix"
Paralogous
Two homologous sequences (e.g., sequences that share a common evolutionary
ancestor) that diverged by gene duplication, as opposed to orthologs,
which diverged by speciation.
Parameter
Parameters are user-selectable values, typically experimentally
determined, that govern the boundaries of an algorithm or program.
For instance, selection of the appropriate input parameters governs
the success of a search algorithm. Some of the most common search
parameters in bioinformatics tools include the stringency of an
alignment search tool, and the weights (penalties) provided for
mismatches and gaps.
Pathway
Network of interacting proteins used to carry out biological functions
such as metabolism and signal transduction.
PCR
Polymerase Chain Reaction; a technique for amplifying DNA, making
it easier to isolate, clone and sequence.
TOP
PDB
Brookhaven Protein Data Bank; a database and format of files, which
describe the 3D structure of a protein or nucleic acid, as determined
by X-ray crystallography or nuclear magnetic resonance (NMR) imaging.
The molecules described by the files are usually viewed locally
by dedicated software, or can be visualized on the World Wide Web.
PepFrag
PROWL tool for searching known protein sequences with peptide fragment
mass information
PeptideMass
ExPASy tool that computes a theoretical mass fingerprint for a SWISS-PROT
or TrEMBL entry, or a userdefined protein sequence.
Peptide-mass
searching
A method to identify proteins contained within a sequence database
using an algorithm to match a set of peptide-masses generated from
the protein of interest with MS using specific cleavage reagents
(either enzymatic or chemical), with theoretical peptide masses
calculated from each sequence entry in the database if the database
sequences had been cleaved with the same specificity as the reagent
in the experiment.
PeptIdent
ExPASy tool that compares experimentally determined mass fingerprints
with theoretically calculated mass fingerprints for proteins in
SWISS-PROT.
PeptideSearch
Tool at EMBL Heidelberg for protein database searching by mass spectrometric
data, such as peptide mass maps or (partial) amino acid sequences
PERL
Scripting language particularly well suited for sequence analysis
due to its string manipulation abilities.
TOP
Pfam
Database of protein domains with associated search tools based on
multiple alignments and hidden Markov models.
Physical
map
A map of the locations of identifiable landmarks on DNA (e.g., restriction
enzyme cutting sites, genes), regardless of inheritance. Distance
is measured in base pairs. For the human genome, the lowest- resolution
physical map is the banding patterns on the 24 different chromosomes;
the highest- resolution map would be the complete nucleotide sequence
of the chromosomes.
pI
Net charge of protein in aqueous solution
Picomole
10-12 mole
PIR
A redundant database of translated GenBank nucleotide sequences;
maintained at Georgetown University.
Platform
The operating system running software on a computer (e.g. Unix or
Windows95). Often used to refer to the type of computer, such as
a Macintosh or PC compatible.
TOP
PMF
Peptide Mass Fingerprinting; generating a fingerprint or a group
of characteristic peptide peaks by analyzing the mass of proteolyzed
fragments.
Ponceau S
Reversible stain for electroblotted proteins
Portability
The ability of a program to be run in various environments, operating
systems etc.
Post-translational
modifications
Protein modifications occurring after protein expression - includes
phosphorylation, glycosylation, acetylation.
Primary Structure
The amino acid sequence of a protein.
TOP
PRINTS
The protein motif fingerprint database created by Attwood and Beck.
Profile
A linear model of the consensus of a multiple alignment.
ProfileScan
A software tool that finds similarities between a query sequence
and a profile library - uses PROSITE, Pfam, and the Gribskov collection;
maintained at Swiss Institute for Experimental Cancer Research
ProFound
PROWL tool for searching known protein sequences with peptide mass
information.
Prokaryotic
Cell
A cell without a nucleus, in which genes are found without a housing.
PROPSEARCH
A software tool similar to AACompSin at EMBL Heidelberg that uses
the amino acid composition of proteins to detect relationships
TOP
PROSITE
A database of protein families and domains which is maintained at
the EMBL. It is based on the observation that, while there is a
huge number of different proteins, most of them can be grouped,
on the basis of similarities in their sequences, into a limited
number of families.
Protein
A polymer made of any combination of 20 natural amino acids that
is encoded by a gene and is the basis of biological function
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.
ProteinChip®
Array
A specific form of a protein biochip incorporating SELDI (see SELDI
definition) technology. ProteinChip Arrays are used in conjunction
with a time-of-flight mass spectrometer detector thus enabling protocols
of protein capture and detection from complex samples without additional
detection labels. ProteinChip Arrays can be designed with broad
capture affinities based on chromatographic interactions or more
specific affinities based on protein-protein, DNA-protein or receptor
ligand interactions. ProteinChip is a registered trademark of Ciphergen
Biosystems, Inc. (Fremont, CA).
ProteinProspector
Tools for mining sequence databases w/ mass spectrometry data; such
as MS Seq, MS-Pattern, MS-Tag, MS-Fit, MS-Digest, MS-Isotope; at
UCSF
Proteolysis
Process of cleavage of the polypeptide backbone- this may be specific
or non specific
TOP
Proteome
"The total protein complement of a genome"; complete set
of proteins expressed by a cell, tissue or organism
PROWL
Proteomics database at Rockefeller that provides tools for searching
a protein database with peptide fingerprints or partial sequence
information, as well as for mass spectrometry data analysis
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 covalent
structure fater translation
P-value
Like an E-value, but a P-value is the probability of a hit occurring
by chance with this score or better, as opposed to the expected
number of hits; a P-value has a maximum of 1.0.
PVDF
Polyvinyldifluoride membrane for Westerns
TOP
Q
QTOF
Quadrupole-Time of Flight, this combines the ion handling capacity
of a quadrupole instrument with resolving powere and duty cycle of
a TOF analyzer
Quaternary
Structure
The assembled structure of two or more polypeptide chains that function
as that assembled unit
Query (sequence)
Typically, a DNA, RNA or protein sequence used to search a database.
TOP
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