NAME

       lutefisk - software for the de novo interpretation of peptide CID spectra

SYNOPSIS

       lutefisk [-q ] [ -m ] [ -d] [ -p ] [ -r ] [ -s ] [ -v] [ -h]  [-o ] <infile>

DESCRIPTION

       lutefisk  is  a software for the de novo interpretation of peptide CID spectra. It takes peptide CID data
       and some ancillary data files (of which the location is specified on the  command  line)  and  outputs  a
       results file containing all the sequences hypothetically matching the CID data.

       When  you  invoke lutefisk with the -h option, the program lists to the command line all the options that
       are available.

OPTIONS

       -h     Print a list of options

       -q     Run in quiet mode

       -m     Precursor ion mass

       -d     Pathname to the details file

       -p     Pathname to the params file

       -r     Pathname to the residues file

       -s     Pathname to the file with database sequences to score

       -v     Run in verbose mode

       -o     Output file

       <infile>
              CID data file

PROGRAM DATA

       The data required to run the program are located in /usr/share/lutefisk.

EXAMPLE DATA

       Example data are located in /usr/share/doc/lutefisk/examples.

BIBLIOGRAPHICAL REFERENCES TO BE CITED

       R. S. Johnson and J. A. Taylor (2002) "Searching sequence databases via de  novo  peptide  sequencing  by
       tandem mass spectrometry", Mol. Biotechnology Vol. 22, No. 3. (November 2002), pp. 301-315.

       J. A. Taylor and R. S. Johnson (2000) "Implementation and uses of automated de novo peptide sequencing by
       tandem mass spectrometry". Anal. Chem. 73:2594-2604.

       R. S. Johnson and J. A. Taylor (2000) "Searching sequence databases via de  novo  peptide  sequencing  by
       tandem  mass  spectrometry",  "Protein  and  Peptide Analysis: Advances in the Use of Mass Spectrometry",
       146:41-61 (Methods in Molecular Biology series, Humana Press).

       J. A. Taylor and R. S. Johnson (1997) "Sequence database searches  via  de  novo  peptide  sequencing  by
       tandem mass spectrometry". Rapid Comm. Mass Spec. 11:1067-1075.

SEE ALSO

       lutefisk-doc(7).

AUTHORS

        Richard S. Johnson <jsrichar@alum.mit.edu>.
           Program author.

       Filippo Rusconi <rusconi-debian@laposte.net>.
           Man-page author for the Debian distribution.

COPYRIGHT

       Copyright © 1995-1999 Richard S. Johnson

       Copyright © 2009 Filippo Rusconi

       This manual page was written for the Debian system (but may be used by others).

       Permission  is granted to copy, distribute and/or modify this document under the terms of the GNU General
       Public License, Version 3 or  (at  your  option)  any  later  version  published  by  the  Free  Software
       Foundation.

        On  a  Debian  system  the complete text of the GNU General Public License version 3 can be found in the
       file `/usr/share/common-licenses/GPL-3'.

                                                   2009/04/29                                        LUTEFISK(1)