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Proteomics tools

An experimental unified interface to query several protein identification tools accessible on the web.

Species conversion list.

In order to use species information with different programs CombSearch has to convert this species information to those the used by each of the programs.

• PeptIdent, MultiIdent and TagIdent.
  CombSearch uses SWISS-PROT OS/OC compatible species naming, so no conversion is necessary.
• MS-Fit.

CombSearch (OS/OC field)	MS-Fit (Taxonomic category)
all	All
EUKARYOTA	All
-METAZOA	All
--INSECTA	All
------DROSOPHILA MELANOGASTER (FRUIT FLY)	DROSOPHILA MELANOGASTER
--CHORDATA	All
---VERTEBRATA	All
----AMPHIBIA	All
----PISCES	All
----AVES	All
----MAMMALIA	MAMMALS
------HOMO SAPIENS (HUMAN)	HOMO SAPIENS
------BOS TAURUS (BOVINE)	BOS TAURUS
------ORYCTOLAGUS CUNICULUS (RABBIT)	MAMMALS
-----RODENTIA	RODENT
------MUS MUSCULUS (MOUSE)	MUS MUSCULUS
------RATTUS NORVEGICUS (RAT)	RATTUS NORVEGICUS
-VIRIDIPLANTAE	All
------ARABIDOPSIS THALIANA (MOUSE-EAR CRESS)	ARABIDOPSIS THALIANA
------ZEA MAYS (MAIZE)	All
-FUNGI	All
------SACCHAROMYCES CEREVISIAE (BAKER'S YEAST)	SACCHAROMYCES CEREVISIAE
------SCHIZOSACCHAROMYCES POMBE (FISSION YEAST)	MICROORGANISMS
BACTERIA	All
------ESCHERICHIA COLI	ESCHERICHIA COLI
-FIRMICUTES	MICROORGANISMS
------BACILLUS SUBTILIS	BACILLUS SUBTILIS
-GRACILICUTES	MICROORGANISMS
VIRUSES	All
-BACTERIOPHAGE	All
ARCHAEA	All

• ProFound.

CombSearch (OS/OC field)	ProFound (Taxonomic category)
all	All Kingdoms
EUKARYOTA	- Eucaryotes
-METAZOA	- Eukaryotes
--INSECTA	--- Animals
------DROSOPHILA MELANOGASTER (FRUIT FLY)	--- Drosophila
--CHORDATA	--- Chordates
---VERTEBRATA	--- Chordates
----AMPHIBIA	---- Other Chordates
----PISCES	---- Other Chordates
----AVES	---- Other Chordates
----MAMMALIA	---- Mammals
------HOMO SAPIENS (HUMAN)	----- Primates
------BOS TAURUS (BOVINE)	----- Other Mammals
------ORYCTOLAGUS CUNICULUS (RABBIT)	----- Other Mammals
-----RODENTIA	----- Rodents
------MUS MUSCULUS (MOUSE)	----- Rodents
------RATTUS NORVEGICUS (RAT)	----- Rodents
-VIRIDIPLANTAE	-- Green Plants
------ARABIDOPSIS THALIANA (MOUSE-EAR CRESS)	--- Arabidopsis Thaliana
------ZEA MAYS (MAIZE)	-- Other Green Plants
-FUNGI	-- Fungi
------SACCHAROMYCES CEREVISIAE (BAKER'S YEAST)	--- S. Cerevisiae
------SCHIZOSACCHAROMYCES POMBE (FISSION YEAST)	--- Other Fungi
BACTERIA	- Eubacteria
------ESCHERICHIA COLI	--- E. Coli
-FIRMICUTES	- Eubacteria
------BACILLUS SUBTILIS	--- Bacillus Subtilis
-GRACILICUTES	- Eubacteria
VIRUSES	- Viruses
-BACTERIOPHAGE	- Viruses
ARCHAEA	- Archaebacteria

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Proteomics tools