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Getting the software

This software is included in the current TPP distribution.

In a nutshell

Converts Mascot search results in .dat files to pepXML (.xml) format.

More detail

pepXML is the open format we use for representing search-engine results. Mascot2XML coverts Mascot-specific search results to pepXML.



This program can be accessed from the web interface, under the Mascot mode --> Analysis Pipeline --> pepXML

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
    if you wish to add an enzyme missing from the list.

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