
                                 mwcontam 



Function

   Shows molwts that match across a set of files

Description

   mwcontam finds molecular weights that are common between a set of mass
   spectrometry result files. Such molecular weights are usually a form
   of contamination resulting from autolysis of a protease, degradation
   of the matrix or presence of keratin from the sample preparer.

   The output of mwcontam, with minimal editing, can be added to the data
   file for the mwfilter program ('Emwfilter.dat').

Usage

   Here is a sample session with mwcontam


% mwcontam 
Shows molwts that match across a set of files
Molecular weights file list: ../data/mw2.dat,mw3.dat
Ppm tolerance [50.0]: 
Molecular weights output file [outfile.mwcontam]: 

   Go to the input files for this example
   Go to the output files for this example

Command line arguments

   Standard (Mandatory) qualifiers:
  [-files]             filelist   Molecular weights file list
   -tolerance          float      [50.0] Ppm tolerance (Any numeric value)
  [-outfile]           outfile    [*.mwcontam] Molecular weights output file

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers:

   "-outfile" associated qualifiers
   -odirectory2        string     Output directory

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write standard output
   -filter             boolean    Read standard input, write standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report dying program messages

Input file format

  Input files for usage example

  File: mw1.dat

20.0
33.0
67.0
128.0
415.0
999.0

  File: mw2.dat

13.0
41.0
67.0
415.0
846.0
781.0

  File: mw3.dat

3.0
18.0
67.0
124.0
197.0
236.0
415.0
587.0
632.0

   The input is a comma-separated list of files containing simple list of
   experimental molecular weights.

   There should be one weight per line.

   Comments in the data file start with a '#' character in the first
   column.

   Blank lines are ignored.

Output file format

   The output is a list of the molecular weights common to all files.

  Output files for usage example

  File: outfile.mwcontam

67.000
415.000

Data files

   mwcontam uses no data files.

   The output of mwcontam, with minimal editing, can be added to the data
   file for the mwfilter program ('Emwfilter.dat'). For example you might
   like to fetch 'Emwfilter.dat' using embossdata (as described in the
   mwfilter documentation) and edit it to include the lines:
     _________________________________________________________________

# data produced from the program mwcontam
mwcontam        67.000
mwcontam        415.000

Notes

   None.

References

   None.

Warnings

   None.

Diagnostic Error Messages

   None.

Exit status

   It always exits with status 0.

Known bugs

   None.

See also

   Program name                         Description
   backtranambig Back translate a protein sequence to ambiguous codons
   backtranseq   Back translate a protein sequence
   charge        Protein charge plot
   checktrans    Reports STOP codons and ORF statistics of a protein
   compseq       Count composition of dimer/trimer/etc words in a sequence
   emowse        Protein identification by mass spectrometry
   freak         Residue/base frequency table or plot
   iep           Calculates the isoelectric point of a protein
   mwfilter      Filter noisy molwts from mass spec output
   octanol       Displays protein hydropathy
   pepinfo       Plots simple amino acid properties in parallel
   pepstats      Protein statistics
   pepwindow     Displays protein hydropathy
   pepwindowall  Displays protein hydropathy of a set of sequences

Author(s)

   Alan Bleasby (ajb © ebi.ac.uk)
   European Bioinformatics Institute, Wellcome Trust Genome Campus,
   Hinxton, Cambridge CB10 1SD, UK

History

   Written (July 2002) - Alan Bleasby.

Target users

   This program is intended to be used by everyone and everything, from
   naive users to embedded scripts.

Comments

   None
