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<div class="title">MassCalculator </div> </div>
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<div class="textblock"><p>Calculates masses and mass-to-charge ratios of peptide sequences.</p>
<p>Given a peptide sequence and a charge state, the charged mass (including H+ adducts) and the mass-to-charge ratio are computed. The peptide sequence can include modifications (for information on valid notation see the <a class="el" href="classOpenMS_1_1AASequence.html">AASequence</a> class documentation). Neutral masses can be computed by using "0" as charge state.</p>
<p>Input can be given directly as values of the parameters: <code>in_seq</code> for peptide sequences and <code>charge</code> for charge states. Alternatively, it can be read from a file (see parameter <code>in</code>) with the following format: A peptide sequence at the beginning of each line, optionally followed by any number of charge states. Whitespace, commas or semicolons can de used to delimit the different items. Parts of the input that cannot be understood will be skipped. If charge states are given in the input file as well as via the <code>charge</code> parameter, results are returned for the union of both sets of charge states.</p>
<p>Output can be written to a file or to the screen (see parameter <code>out</code>). Results for different charge states are always ordered from lowest to highest charge. A number of different output formats are available via the parameter <code>format:</code> </p>
<ul>
<li><code>list</code> writes a human-readable list of the form "ABCDEF: z=1 m=566.192 m/z=566.192, z=2 m=567.199 m/z=283.599";</li>
<li><code>table</code> produces a CSV-like table (using parameter <code>separator</code> to delimit fields) with the columns "peptide", "charge", "mass", and "mass-to-charge", and with one row per peptide and charge state;</li>
<li><code>mass_only</code> writes only mass values (one line per peptide, values for different charge states separated by spaces);</li>
<li><code>mz_only</code> writes only mass-to-charge ratios (one line per peptide, values for different charge states separated by spaces).</li>
</ul>
<p><b>The command line parameters of this tool are:</b> </p>
<pre class="fragment">
MassCalculator -- Calculates masses and mass-to-charge ratios of peptide sequences
Version: 1.11.1 Nov 14 2013, 11:18:15, Revision: 11976
Usage:
MassCalculator <options>
Options (mandatory options marked with '*'):
-in <file> Input file with peptide sequences and optionally charge numbers (mutually excl
usive to 'in_seq') (valid formats: 'txt')
-in_seq <peptide_sequences> List of peptide sequences (mutually exclusive to 'in')
-out <file> Output file; if empty, output is written to the screen (valid formats: 'txt')
-charge <numbers> List of charge states; required if 'in_seq' is given (default: '[0]')
-format <choice> Output format ('list': human-readable list, 'table': CSV-like table, 'mass_onl
y': mass values only, 'mz_only': m/z values only)
(default: 'list' valid: 'list', 'table', 'mass_only', 'mz_only')
-average_mass Compute average (instead of monoisotopic) peptide masses
-fragment_type <choice> For what type of sequence/fragment the mass should be computed
(default: 'full' valid: 'full', 'internal', 'N-terminal', 'C-terminal', 'a-i
on', 'b-ion', 'c-ion', 'x-ion', 'y-ion', 'z-ion')
-separator <sep> Field separator for 'table' output format; by default, the 'tab' character is
used
Common UTIL options:
-ini <file> Use the given TOPP INI file
-threads <n> Sets the number of threads allowed to be used by the TOPP tool (default: '1')
-write_ini <file> Writes the default configuration file
--help Shows options
--helphelp Shows all options (including advanced)
</pre><p> <b>INI file documentation of this tool:</b> <div class="ini_global">
<div class="legend">
<b>Legend:</b><br>
<div class="item item_required">required parameter</div>
<div class="item item_advanced">advanced parameter</div>
</div>
<div class="node"><span class="node_name">+MassCalculator</span><span class="node_description">Calculates masses and mass-to-charge ratios of peptide sequences</span></div>
<div class="item item_advanced"><span class="item_name" style="padding-left:16px;">version</span><span class="item_value">1.11.1</span>
<span class="item_description">Version of the tool that generated this parameters file.</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="node"><span class="node_name">++1</span><span class="node_description">Instance '1' section for 'MassCalculator'</span></div>
<div class="item"><span class="item_name" style="padding-left:24px;">in</span><span class="item_value"></span>
<span class="item_description">Input file with peptide sequences and optionally charge numbers (mutually exclusive to 'in_seq')</span><span class="item_tags">input file</span><span class="item_restrictions">*.txt</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">in_seq</span><span class="item_value">[]</span>
<span class="item_description">List of peptide sequences (mutually exclusive to 'in')</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:24px;">out</span><span class="item_value"></span>
<span class="item_description">Output file; if empty, output is written to the screen</span><span class="item_tags">output file</span><span class="item_restrictions">*.txt</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">charge</span><span class="item_value">[0]</span>
<span class="item_description">List of charge states; required if 'in_seq' is given</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:24px;">format</span><span class="item_value">list</span>
<span class="item_description">Output format ('list': human-readable list, 'table': CSV-like table, 'mass_only': mass values only, 'mz_only': m/z values only)<br></span><span class="item_tags"></span><span class="item_restrictions">list,table,mass_only,mz_only</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">average_mass</span><span class="item_value">false</span>
<span class="item_description">Compute average (instead of monoisotopic) peptide masses</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">fragment_type</span><span class="item_value">full</span>
<span class="item_description">For what type of sequence/fragment the mass should be computed<br></span><span class="item_tags"></span><span class="item_restrictions">full,internal,N-terminal,C-terminal,a-ion,b-ion,c-ion,x-ion,y-ion,z-ion</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">separator</span><span class="item_value"></span>
<span class="item_description">Field separator for 'table' output format; by default, the 'tab' character is used</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:24px;">log</span><span class="item_value"></span>
<span class="item_description">Name of log file (created only when specified)</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:24px;">debug</span><span class="item_value">0</span>
<span class="item_description">Sets the debug level</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:24px;">threads</span><span class="item_value">1</span>
<span class="item_description">Sets the number of threads allowed to be used by the TOPP tool</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:24px;">no_progress</span><span class="item_value">false</span>
<span class="item_description">Disables progress logging to command line</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:24px;">test</span><span class="item_value">false</span>
<span class="item_description">Enables the test mode (needed for internal use only)</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div></div>
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<TD><font color="#c0c0c0">OpenMS / TOPP release 1.11.1</font></TD>
<TD align="right"><font color="#c0c0c0">Documentation generated on Thu Nov 14 2013 11:19:24 using doxygen 1.8.5</font></TD>
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