
                                 mwfilter 



Function

   Filter noisy molwts from mass spec output

Description

   mwfilter is designed to remove unwanted (noisy) data from mass
   spectrometry output in proteomics. Given a list of molecular weights
   this program removes those which are:

     * Contaminating trypsin or keratin
     * Modified oxy-methionine or oxy-threonine
     * Peaks associated with sodium ions.

   The last two operations can be done as most peaks are reported in both
   modified and unmodified forms. Removal of modified peaks aids in
   database searching for protein identification.

Usage

   Here is a sample session with mwfilter


% mwfilter 
Filter noisy molwts from mass spec output
Molecular weights file: molwts.dat
Ppm tolerance [50.0]: 
Molecular weights output file [molwts.mwfilter]: 

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

Command line arguments

   Standard (Mandatory) qualifiers:
  [-infile]            infile     Molecular weights file
   -tolerance          float      [50.0] Ppm tolerance (Any numeric value)
  [-outfile]           outfile    [*.mwfilter] Molecular weights output file

   Additional (Optional) qualifiers:
   -showdel            boolean    [N] Output deleted mwts

   Advanced (Unprompted) qualifiers:
   -datafile           datafile   [Emwfilter.dat] Molecular weight standards
                                  data file

   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: molwts.dat

874.364756
927.450380
1045.572
1068.397129
1121.431124
1163.584593
1305.660840
1428.596448
1479.748341
1502.549157
1554.591658
1567.686209
1576.708354
1639.868056
1748.611920
1753.745298
1880.841178
2383.99

   The input file is a simple list of the 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 with the unwanted
   (noisy) data removed.

  Output files for usage example

  File: molwts.mwfilter

874.364756
927.450380
1068.397129
1121.431124
1163.584593
1305.660840
1428.596448
1479.748341
1502.549157
1554.591658
1567.686209
1576.708354
1639.868056
1748.611920
1753.745298
1880.841178

Data files

   The program reads the data file Emwfilter.dat for the molecular
   weights of items to be deleted from the experimental data.

   EMBOSS data files are distributed with the application and stored in
   the standard EMBOSS data directory, which is defined by the EMBOSS
   environment variable EMBOSS_DATA.

   To see the available EMBOSS data files, run:

% embossdata -showall

   To fetch one of the data files (for example 'Exxx.dat') into your
   current directory for you to inspect or modify, run:

% embossdata -fetch -file Exxx.dat

   Users can provide their own data files in their own directories.
   Project specific files can be put in the current directory, or for
   tidier directory listings in a subdirectory called ".embossdata".
   Files for all EMBOSS runs can be put in the user's home directory, or
   again in a subdirectory called ".embossdata".

   The directories are searched in the following order:
     * . (your current directory)
     * .embossdata (under your current directory)
     * ~/ (your home directory)
     * ~/.embossdata

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
   mwcontam      Shows molwts that match across a set of files
   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 (Jan 2002) - Alan Bleasby.

Target users

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

Comments

   None
