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<HTML>
<HEAD>
<TITLE>
EMBOSS: mwcontam
</TITLE>
</HEAD>
<BODY BGCOLOR="#FFFFFF" text="#000000">
<table align=center border=0 cellspacing=0 cellpadding=0>
<tr><td valign=top>
<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>
</td>
<td align=left valign=middle>
<b><font size="+6">
mwcontam
</font></b>
</td></tr>
</table>
<br>
<p>
<H2>
Function
</H2>
Shows molwts that match across a set of files
<H2>
Description
</H2>
<b>mwcontam</b> 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.
<p>
The output of <b>mwcontam</b>, with minimal editing, can be added to the
data file for the <a href="mwfilter.html"><b>mwfilter</b></a> program
('Emwfilter.dat').
<H2>
Usage
</H2>
<b>Here is a sample session with mwcontam</b>
<p>
<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
% <b>mwcontam </b>
Shows molwts that match across a set of files
Molecular weights file list: <b>../data/mw2.dat,mw3.dat</b>
Ppm tolerance [50.0]: <b></b>
Molecular weights output file [outfile.mwcontam]: <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:
[-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
</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>[-files]<br>(Parameter 1)</td>
<td>Molecular weights file list</td>
<td>Comma-separated file list</td>
<td><i>comma-separated file list</i></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><*></i>.mwcontam</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 colspan=4>(none)</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 colspan=4>(none)</td>
</tr>
</table>
<H2>
Input file format
</H2>
<a name="input.1"></a>
<h3>Input files for usage example </h3>
<p><h3>File: mw1.dat</h3>
<table width="90%"><tr><td bgcolor="#FFCCFF">
<pre>
20.0
33.0
67.0
128.0
415.0
999.0
</pre>
</td></tr></table><p>
<p><h3>File: mw2.dat</h3>
<table width="90%"><tr><td bgcolor="#FFCCFF">
<pre>
13.0
41.0
67.0
415.0
846.0
781.0
</pre>
</td></tr></table><p>
<p><h3>File: mw3.dat</h3>
<table width="90%"><tr><td bgcolor="#FFCCFF">
<pre>
3.0
18.0
67.0
124.0
197.0
236.0
415.0
587.0
632.0
</pre>
</td></tr></table><p>
<p>
The input is a comma-separated list of files containing simple list of
experimental molecular weights.
<p>
There should be one weight per line.
<p>
Comments in the data file start with a '#' character in the first
column.
<p>
Blank lines are ignored.
<H2>
Output file format
</H2>
The output is a list of the molecular weights common to all files.
<p>
<a name="output.1"></a>
<h3>Output files for usage example </h3>
<p><h3>File: outfile.mwcontam</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
67.000
415.000
</pre>
</td></tr></table><p>
<H2>
Data files
</H2>
<b>mwcontam</b> uses no data files.
<p>
The output of <b>mwcontam</b>, with minimal editing, can be added to the
data file for the <a href="mwfilter.html"><b>mwfilter</b></a> program
('Emwfilter.dat'). For example you might like to fetch 'Emwfilter.dat'
using <b>embossdata</b> (as described in the <b>mwfilter</b>
documentation) and edit it to include the lines:
<p>
<hr>
<pre>
# data produced from the program mwcontam
mwcontam 67.000
mwcontam 415.000
</pre>
<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="mwfilter.html">mwfilter</a></td>
<td>Filter noisy molwts from mass spec output</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 © ebi.ac.uk)
<br>
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
<H2>
History
</H2>
Written (July 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
</BODY>
</HTML>
|
