1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
|
<HTML>
<HEAD>
<TITLE>SeedListGenerator</TITLE>
<LINK HREF="doxygen.css" REL="stylesheet" TYPE="text/css">
<LINK HREF="style_ini.css" REL="stylesheet" TYPE="text/css">
</HEAD>
<BODY BGCOLOR="#FFFFFF">
<A href="index.html">Home</A> ·
<A href="classes.html">Classes</A> ·
<A href="annotated.html">Annotated Classes</A> ·
<A href="modules.html">Modules</A> ·
<A href="functions_func.html">Members</A> ·
<A href="namespaces.html">Namespaces</A> ·
<A href="pages.html">Related Pages</A>
<HR style="height:1px; border:none; border-top:1px solid #c0c0c0;">
<!-- Generated by Doxygen 1.8.5 -->
</div><!-- top -->
<div class="header">
<div class="headertitle">
<div class="title">SeedListGenerator </div> </div>
</div><!--header-->
<div class="contents">
<div class="textblock"><p>Application to generate seed lists for feature detection.</p>
<center> <table class="doxtable">
<tr>
<td align="center" bgcolor="#EBEBEB">potential predecessor tools </td><td valign="middle" rowspan="4"><img class="formulaInl" alt="$ \longrightarrow $" src="form_91.png"/> SeedListGenerator <img class="formulaInl" alt="$ \longrightarrow $" src="form_91.png"/> </td><td align="center" bgcolor="#EBEBEB">potential successor tools </td></tr>
<tr>
<td valign="middle" align="center" rowspan="1"><a class="el" href="TOPP_IDFilter.html">IDFilter</a> </td><td valign="middle" align="center" rowspan="3"><a class="el" href="TOPP_FeatureFinderCentroided.html">FeatureFinderCentroided</a> </td></tr>
<tr>
<td valign="middle" align="center" rowspan="1"><a class="el" href="TOPP_IDMapper.html">IDMapper</a> </td></tr>
<tr>
<td valign="middle" align="center" rowspan="1"><a class="el" href="TOPP_FeatureLinkerUnlabeled.html">FeatureLinkerUnlabeled</a> <br/>
(or another feature grouping algorithm) </td></tr>
</table>
</center><p>Reference:<br/>
Weisser <em>et al.</em>: <a href="http://dx.doi.org/10.1021/pr300992u">An automated pipeline for high-throughput label-free quantitative proteomics</a> (J. Proteome Res., 2013, PMID: 23391308).</p>
<p>In feature detection algorithms, an early step is generally to identify points of interest in the LC-MS map (so-called seeds) that may later be extended to features. If supported by the feature detection algorithm (currently only the "centroided" algorithm), user-supplied seed lists allow greater control over this process.</p>
<p>The SeedListGenerator can automatically create seed lists from a variety of sources. The lists are exported in featureXML format - suitable as input to FeatureFinder -, but can be converted to or from text formats using the <a class="el" href="TOPP_TextExporter.html">TextExporter</a> (with "-minimal" option to convert to CSV) and <a class="el" href="TOPP_FileConverter.html">FileConverter</a> (to convert from CSV) tools.</p>
<p>Seed lists can be generated from the file types below. The seeds are created at the indicated positions (RT/MZ): </p>
<ul>
<li>
mzML: locations of MS2 precursors </li>
<li>
idXML: locations of peptide identifications </li>
<li>
featureXML: locations of unassigned peptide identifications </li>
<li>
consensusXML: locations of consensus features that do not contain sub-features from the respective map </li>
</ul>
<p>If input is consensusXML, one output file per constituent map is required (same order as in the consensusXML). Otherwise, exactly one output file.</p>
<p>What are possible use cases for custom seed lists?</p>
<ul>
<li>In analyses that can take into account only features with peptide annotations, it may be useful to focus directly on certain locations in the LC-MS map - on all MS2 precursors (mzML input), or on precursors whose fragment spectra could be matched to a peptide sequence (idXML input).</li>
<li>When additional information becomes available during an analysis, one might want to perform a second, targeted round of feature detection on the experimental data. For example, once a feature map is annotated with peptide identifications, it is possible to go back to the LC-MS map and look for features near unassigned peptides, potentially with a lower score threshold (featureXML input).</li>
<li>Similarly, when features from different experiments are aligned and grouped, the consensus map may reveal where features were missed in the initial detection round in some experiments. The locations of these "holes" in the consensus map can be compiled into seed lists for the individual experiments (consensusXML input). (Note that the resulting seed lists use the retention time scale of the consensus map, which might be different from the original time scales of the experiments if e.g. one of the MapAligner tools was used to perform retention time correction as part of the alignment process. In this case, the RT transformations from the alignment must be applied to the LC-MS maps prior to the seed list-based feature detection runs.)</li>
</ul>
<p><b>The command line parameters of this tool are:</b> </p>
<pre class="fragment">
SeedListGenerator -- Generates seed lists for feature detection.
Version: 1.11.1 Nov 14 2013, 11:18:15, Revision: 11976
Usage:
SeedListGenerator <options>
Options (mandatory options marked with '*'):
-in <file>* Input file (see below for details) (valid formats: 'mzML', 'idXML', 'featureXML', 'cons
ensusXML')
-out <file(s)>* Output file(s) (valid formats: 'featureXML')
-use_peptide_mass [idXML input only] Use the monoisotopic mass of the best peptide hit for the m/z positi
on (default: use precursor m/z)
Common TOPP 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">+SeedListGenerator</span><span class="node_description">Generates seed lists for feature detection.</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 'SeedListGenerator'</span></div>
<div class="item"><span class="item_name item_required" style="padding-left:24px;">in</span><span class="item_value"></span>
<span class="item_description">Input file (see below for details)</span><span class="item_tags">input file</span><span class="item_restrictions">*.mzML,*.idXML,*.featureXML,*.consensusXML</span></div> <div class="item"><span class="item_name item_required" style="padding-left:24px;">out</span><span class="item_value">[]</span>
<span class="item_description">Output file(s)</span><span class="item_tags">output file</span><span class="item_restrictions">*.featureXML</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">use_peptide_mass</span><span class="item_value">false</span>
<span class="item_description">[idXML input only] Use the monoisotopic mass of the best peptide hit for the m/z position (default: use precursor m/z)</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;">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>
</div></div><!-- contents -->
<HR style="height:1px; border:none; border-top:1px solid #c0c0c0;">
<TABLE width="100%" border="0">
<TR>
<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>
</TR>
</TABLE>
</BODY>
</HTML>
|
