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)