mwcontam



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Function

   Find weights common to multiple molecular weights files

Description

   mwcontam finds molecular weights that are common between a set of mass
   spectrometry result files at a specified ppm tolerance. 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 input is a comma-separated list of files each
   containing a list of experimental molecular weights. The output is a
   file with a list of the molecular weights common to all files.

Usage

   Here is a sample session with mwcontam


% mwcontam
Find weights common to multiple molecular weights 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

Find weights common to multiple molecular weights files
Version: EMBOSS:6.4.0.0

   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 first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to 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 and exit. 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
   -version            boolean    Report version number and exit


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

   The output of mwcontam, with minimal editing, can be added to the data
   file for the mwfilter program (Emwfilter.dat), which will then remove
   these weights from its input file of molecular weights. 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

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 nucleotide
                    sequence
   backtranseq      Back-translate a protein sequence to a nucleotide sequence
   compseq          Calculate the composition of unique words in sequences
   emowse           Search protein sequences by digest fragment molecular weight
   freak            Generate residue/base frequency table or plot
   mwfilter         Filter noisy data from molecular weights file
   oddcomp          Identify proteins with specified sequence word composition
   pepdigest        Reports on protein proteolytic enzyme or reagent cleavage
                    sites
   pepinfo          Plot amino acid properties of a protein sequence in parallel
   pepstats         Calculates statistics of protein properties
   wordcount        Count and extract unique words in molecular sequence(s)

Author(s)

   Alan Bleasby
   European Bioinformatics Institute, Wellcome Trust Genome Campus,
   Hinxton, Cambridge CB10 1SD, UK

   Please report all bugs to the EMBOSS bug team
   (emboss-bug (c) emboss.open-bio.org) not to the original author.

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