Software:Mascot2XML
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Getting the software
This software is included in the current TPP distribution.
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In a nutshell
Converts Mascot search results in .dat files to pepXML (.xml) format.
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More detail
pepXML is the open format we use for representing search-engine results. Mascot2XML coverts Mascot-specific search results to pepXML.
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Usage
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GUI
This program can be accessed from the web interface, under the Mascot mode --> Analysis Pipeline --> pepXML
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Command Line
(This documentation applies to TPP v3.1.0)
Mascot2XML(TPP v3.1 SQUALL rev.0, Build 200705311046)
usage: Mascot2XML <file.dat> (-D<database>) (-E<sample_enzyme>) (-html) (-pI) (-notgz) (-desc) (-shortid) (-verbose) (-t(!)<regression test>)
-html : generate html output (default output is pepXML)
-pI : calculate pI for the peptide
-notgz : do not generate (compressed) archive of .dta and .out
-desc : generate protein description in pepXML output
-shortid : use short protein id as per Mascot result (default uses full protein ids in fasta file)
-verbose : tell me more about what is going on
For developers:
use -t!foo.test to create a regression test basis file named foo.test
use -tfoo.test to check against a regression test basis file named foo.test
use -t! or -t to learn/use an automatically named test
Recognised <sample_enyzme> (semi-cleavage specification: semi<sample_enyzme>)
trypsin : cut(KR) nocuts(P) sense(C)
argc : cut(R) nocuts(P) sense(C)
aspn : cut(D) sense(N)
chymotrypsin : cut(YWFM) nocuts(P) sense(C)
clostripain : cut(R) nocuts(-) sense(C)
cnbr : cut(M) nocuts(P) sense(C)
elastase : cut(GVLIA) nocuts(P) sense(C)
formicacid : cut(D) nocuts(P) sense(C)
gluc : cut(DE) nocuts(P) sense(C)
gluc_bicarb : cut(E) nocuts(P) sense(C)
iodosobenzoate : cut(W) nocuts(-) sense(C)
lysc : cut(K) nocuts(P) sense(C)
lysc-p : cut(K) sense(C)
lysn : cut(K) sense(N)
lysn_promisc : cut(KASR) sense(N)
nonspecific : cut() sense(C)
pepsina : cut(FL) nocuts(-) sense(C)
protein_endopeptidase : cut(P) nocuts(-) sense(C)
staph_protease : cut(E) nocuts(-) sense(C)
tca : cut(KR) nocuts(P) sense(C)
: cut(YWFM) nocuts(P) sense(C)
: cut(D) sense(N)
trypsin/cnbr : cut(KR) nocuts(P) sense(C)
: cut(M) nocuts(P) sense(C)
trypsin_gluc : cut(DEKR) nocuts(P) sense(C)
trypsin_k : cut(K) nocuts(P) sense(C)
trypsin_r : cut(R) nocuts(P) sense(C)
Semi-cleavage can be specified as semi<sample_enyzme>,
e.g. semitrypsin, semiargc
** Please contact spctools-discuss@googlegroups.com
if you wish to add an enzyme missing from the list.
