
                                 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
Comma separated file list: ../data/mw2.dat,mw3.dat
Ppm tolerance [50.0]: 
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   Comma separated file list
   -tolerance          float      Ppm tolerance
  [-outfile]           outfile    Output file name

   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 deaths


   Standard (Mandatory) qualifiers Allowed values Default
   [-files]
   (Parameter 1) Comma separated file list Comma-separated file list
   comma-separated file list
   -tolerance Ppm tolerance Any numeric value 50.0
   [-outfile]
   (Parameter 2) Output file name Output file <sequence>.mwcontam
   Additional (Optional) qualifiers Allowed values Default
   (none)
   Advanced (Unprompted) qualifiers Allowed values Default
   (none)

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
   backtranseq  Back translate a protein sequence
   charge       Protein charge plot
   checktrans   Reports STOP codons and ORF statistics of a protein
   compseq      Counts the 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 (ableasby © rfcgr.mrc.ac.uk)
   MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust
   Genome Campus, Hinxton, Cambridge, CB10 1SB, 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
