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  <TITLE>
  EMBOSS: mwfilter
  </TITLE>
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<table align=center border=0 cellspacing=0 cellpadding=0>
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<A HREF="/" ONMOUSEOVER="self.status='Go to the EMBOSS home page';return true"><img border=0 src="emboss_icon.jpg" alt="" width=150 height=48></a>
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<td align=left valign=middle>
<b><font size="+6">
mwfilter
</font></b>
</td></tr>
</table>
<br>&nbsp;
<p>


<H2>
    Function
</H2>
Filter noisy molwts from mass spec output
<H2>
    Description
</H2>

<b>mwfilter</b> 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:

<p>
<ul>
  <li>Contaminating trypsin or keratin
  <li>Modified oxy-methionine or oxy-threonine
  <li>Peaks associated with sodium ions.
</ul>
<p>
 
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.

<H2>
    Usage
</H2>
<b>Here is a sample session with mwfilter</b>
<p>

<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>

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

</pre></td></tr></table><p>
<p>
<a href="#input.1">Go to the input files for this example</a><br><a href="#output.1">Go to the output files for this example</a><p><p>

<H2>
    Command line arguments
</H2>
<table CELLSPACING=0 CELLPADDING=3 BGCOLOR="#f5f5ff" ><tr><td>
<pre>
   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

</pre>
</td></tr></table>
<P>
<table border cellspacing=0 cellpadding=3 bgcolor="#ccccff">
<tr bgcolor="#FFFFCC">
<th align="left" colspan=2>Standard (Mandatory) qualifiers</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>

<tr>
<td>[-infile]<br>(Parameter 1)</td>
<td>Molecular weights file</td>
<td>Input file</td>
<td><b>Required</b></td>
</tr>

<tr>
<td>-tolerance</td>
<td>Ppm tolerance</td>
<td>Any numeric value</td>
<td>50.0</td>
</tr>

<tr>
<td>[-outfile]<br>(Parameter 2)</td>
<td>Molecular weights output file</td>
<td>Output file</td>
<td><i>&lt;*&gt;</i>.mwfilter</td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=2>Additional (Optional) qualifiers</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>

<tr>
<td>-showdel</td>
<td>Output deleted mwts</td>
<td>Boolean value Yes/No</td>
<td>No</td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=2>Advanced (Unprompted) qualifiers</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>

<tr>
<td>-datafile</td>
<td>Molecular weight standards data file</td>
<td>Data file</td>
<td>Emwfilter.dat</td>
</tr>

</table>

<H2>
    Input file format
</H2>


<a name="input.1"></a>
<h3>Input files for usage example </h3>
<p><h3>File: molwts.dat</h3>
<table width="90%"><tr><td bgcolor="#FFCCFF">
<pre>
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
</pre>
</td></tr></table><p>

<p>

The input file is a simple list of the experimental molecular weights.
<br>
There should be one weight per line.

<p>

Comments in the data file start with a '#' character in the first column.
<br>
Blank lines are ignored.


<H2>
    Output file format
</H2>

The output is a list of the molecular weights with the unwanted (noisy)
data removed. 

<p>


<a name="output.1"></a>
<h3>Output files for usage example </h3>
<p><h3>File: molwts.mwfilter</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
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
</pre>
</td></tr></table><p>

<H2>
    Data files
</H2>

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

<p>

<p>
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.

<p>

To see the available EMBOSS data files, run:
<p>
<pre>
% embossdata -showall
</pre>
<p>
To fetch one of the data files (for example 'Exxx.dat') into your
current directory for you to inspect or modify, run:

<pre>

% embossdata -fetch -file Exxx.dat

</pre>
<p>

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".

<p>
The directories are searched in the following order:

<ul>
   <li> . (your current directory)
   <li> .embossdata (under your current directory)
   <li> ~/ (your home directory)
   <li> ~/.embossdata
</ul>
<p>

<H2>
    Notes
</H2>

None.

<H2>
    References
</H2>

None.

<H2>
    Warnings
</H2>

None.

<H2>
    Diagnostic Error Messages
</H2>

None.

<H2>
    Exit status
</H2>

It always exits with status 0.


<H2>
    Known bugs
</H2>

None.

<h2><a name="See also">See also</a></h2>
<table border cellpadding=4 bgcolor="#FFFFF0">
<tr><th>Program name</th><th>Description</th></tr>
<tr>
<td><a href="backtranambig.html">backtranambig</a></td>
<td>Back translate a protein sequence to ambiguous codons</td>
</tr>

<tr>
<td><a href="backtranseq.html">backtranseq</a></td>
<td>Back translate a protein sequence</td>
</tr>

<tr>
<td><a href="charge.html">charge</a></td>
<td>Protein charge plot</td>
</tr>

<tr>
<td><a href="checktrans.html">checktrans</a></td>
<td>Reports STOP codons and ORF statistics of a protein</td>
</tr>

<tr>
<td><a href="compseq.html">compseq</a></td>
<td>Count composition of dimer/trimer/etc words in a sequence</td>
</tr>

<tr>
<td><a href="emowse.html">emowse</a></td>
<td>Protein identification by mass spectrometry</td>
</tr>

<tr>
<td><a href="freak.html">freak</a></td>
<td>Residue/base frequency table or plot</td>
</tr>

<tr>
<td><a href="iep.html">iep</a></td>
<td>Calculates the isoelectric point of a protein</td>
</tr>

<tr>
<td><a href="mwcontam.html">mwcontam</a></td>
<td>Shows molwts that match across a set of files</td>
</tr>

<tr>
<td><a href="octanol.html">octanol</a></td>
<td>Displays protein hydropathy</td>
</tr>

<tr>
<td><a href="pepinfo.html">pepinfo</a></td>
<td>Plots simple amino acid properties in parallel</td>
</tr>

<tr>
<td><a href="pepstats.html">pepstats</a></td>
<td>Protein statistics</td>
</tr>

<tr>
<td><a href="pepwindow.html">pepwindow</a></td>
<td>Displays protein hydropathy</td>
</tr>

<tr>
<td><a href="pepwindowall.html">pepwindowall</a></td>
<td>Displays protein hydropathy of a set of sequences</td>
</tr>

</table>

<H2>
    Author(s)
</H2>

Alan Bleasby (ajb&nbsp;&copy;&nbsp;ebi.ac.uk)
<br>
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK


<H2>
    History
</H2>

Written (Jan 2002) - Alan Bleasby.

<H2>
    Target users
</H2>
This program is intended to be used by everyone and everything, from naive users to embedded scripts.

<H2>
    Comments
</H2>
None


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