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<HTML>
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<TITLE>CompNovoIdentification Class Reference</TITLE>
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<li class="navelem"><a class="el" href="namespaceOpenMS.html">OpenMS</a></li><li class="navelem"><a class="el" href="classOpenMS_1_1CompNovoIdentification.html">CompNovoIdentification</a></li> </ul>
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<div class="header">
<div class="summary">
<a href="#pub-types">Public Types</a> |
<a href="#pub-methods">Public Member Functions</a> |
<a href="#pro-methods">Protected Member Functions</a> |
<a href="classOpenMS_1_1CompNovoIdentification-members.html">List of all members</a> </div>
<div class="headertitle">
<div class="title">CompNovoIdentification Class Reference<div class="ingroups"><a class="el" href="group__Analysis__ID.html">Identification</a></div></div> </div>
</div><!--header-->
<div class="contents">
<p>run with <a class="el" href="classOpenMS_1_1CompNovoIdentification.html" title="run with CompNovoIdentification ">CompNovoIdentification</a>
<a href="classOpenMS_1_1CompNovoIdentification.html#details">More...</a></p>
<p><code>#include <<a class="el" href="CompNovoIdentification_8h_source.html">OpenMS/ANALYSIS/DENOVO/CompNovoIdentification.h</a>></code></p>
<div class="dynheader">
Inheritance diagram for CompNovoIdentification:</div>
<div class="dyncontent">
<div class="center">
<img src="classOpenMS_1_1CompNovoIdentification.png" usemap="#CompNovoIdentification_map" alt=""/>
<map id="CompNovoIdentification_map" name="CompNovoIdentification_map">
<area href="classOpenMS_1_1CompNovoIdentificationBase.html" title="run with CompNovoIdentificationBase " alt="CompNovoIdentificationBase" shape="rect" coords="0,56,173,80"/>
<area href="classOpenMS_1_1DefaultParamHandler.html" title="A base class for all classes handling default parameters. " alt="DefaultParamHandler" shape="rect" coords="0,0,173,24"/>
</map>
</div></div>
<table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-types"></a>
Public Types</h2></td></tr>
<tr class="memitem:acc1a3401cf6077f8a9625b25b51e0731"><td class="memItemLeft" align="right" valign="top">typedef <br class="typebreak"/>
<a class="el" href="classOpenMS_1_1CompNovoIonScoringBase.html#af7e67702d51d0eff4c3db8ea8763a59f">CompNovoIonScoringBase::IsotopeType</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1CompNovoIdentification.html#acc1a3401cf6077f8a9625b25b51e0731">IsotopeType</a></td></tr>
<tr class="separator:acc1a3401cf6077f8a9625b25b51e0731"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a7b7c9d2595dd3328e664293d3fec5ef9"><td class="memItemLeft" align="right" valign="top">typedef <br class="typebreak"/>
<a class="el" href="structOpenMS_1_1CompNovoIonScoringBase_1_1IonScore.html">CompNovoIonScoringBase::IonScore</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1CompNovoIdentification.html#a7b7c9d2595dd3328e664293d3fec5ef9">IonScore</a></td></tr>
<tr class="separator:a7b7c9d2595dd3328e664293d3fec5ef9"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a6cb23966d9741fbd0d2e87a1668042df"><td class="memItemLeft" align="right" valign="top">typedef <br class="typebreak"/>
<a class="el" href="classOpenMS_1_1CompNovoIdentificationBase_1_1Permut.html">CompNovoIdentificationBase::Permut</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1CompNovoIdentification.html#a6cb23966d9741fbd0d2e87a1668042df">Permut</a></td></tr>
<tr class="separator:a6cb23966d9741fbd0d2e87a1668042df"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="inherit_header pub_types_classOpenMS_1_1CompNovoIdentificationBase"><td colspan="2" onclick="javascript:toggleInherit('pub_types_classOpenMS_1_1CompNovoIdentificationBase')"><img src="closed.png" alt="-"/> Public Types inherited from <a class="el" href="classOpenMS_1_1CompNovoIdentificationBase.html">CompNovoIdentificationBase</a></td></tr>
<tr class="memitem:a7b7c9d2595dd3328e664293d3fec5ef9 inherit pub_types_classOpenMS_1_1CompNovoIdentificationBase"><td class="memItemLeft" align="right" valign="top">typedef <br class="typebreak"/>
<a class="el" href="structOpenMS_1_1CompNovoIonScoringBase_1_1IonScore.html">CompNovoIonScoringBase::IonScore</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1CompNovoIdentificationBase.html#a7b7c9d2595dd3328e664293d3fec5ef9">IonScore</a></td></tr>
<tr class="separator:a7b7c9d2595dd3328e664293d3fec5ef9 inherit pub_types_classOpenMS_1_1CompNovoIdentificationBase"><td class="memSeparator" colspan="2"> </td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a>
Public Member Functions</h2></td></tr>
<tr class="memitem:afb1a8581f4e501807fd365232e5f0d3d"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1CompNovoIdentification.html">CompNovoIdentification</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1CompNovoIdentification.html#afb1a8581f4e501807fd365232e5f0d3d">operator=</a> (const <a class="el" href="classOpenMS_1_1CompNovoIdentification.html">CompNovoIdentification</a> &source)</td></tr>
<tr class="separator:afb1a8581f4e501807fd365232e5f0d3d"><td class="memSeparator" colspan="2"> </td></tr>
<tr><td colspan="2"><div class="groupHeader">constructors and destructors</div></td></tr>
<tr class="memitem:a8129bc56362a847658910193aeeabfc0"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1CompNovoIdentification.html#a8129bc56362a847658910193aeeabfc0">CompNovoIdentification</a> ()</td></tr>
<tr class="memdesc:a8129bc56362a847658910193aeeabfc0"><td class="mdescLeft"> </td><td class="mdescRight">default constructor <a href="#a8129bc56362a847658910193aeeabfc0">More...</a><br/></td></tr>
<tr class="separator:a8129bc56362a847658910193aeeabfc0"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:adcea6777982db4d1176671d8eadce15e"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1CompNovoIdentification.html#adcea6777982db4d1176671d8eadce15e">CompNovoIdentification</a> (const <a class="el" href="classOpenMS_1_1CompNovoIdentification.html">CompNovoIdentification</a> &source)</td></tr>
<tr class="memdesc:adcea6777982db4d1176671d8eadce15e"><td class="mdescLeft"> </td><td class="mdescRight">copy constructor <a href="#adcea6777982db4d1176671d8eadce15e">More...</a><br/></td></tr>
<tr class="separator:adcea6777982db4d1176671d8eadce15e"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a00660c31aeb6d55b4330c73d98b18530"><td class="memItemLeft" align="right" valign="top">virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1CompNovoIdentification.html#a00660c31aeb6d55b4330c73d98b18530">~CompNovoIdentification</a> ()</td></tr>
<tr class="memdesc:a00660c31aeb6d55b4330c73d98b18530"><td class="mdescLeft"> </td><td class="mdescRight">destructor <a href="#a00660c31aeb6d55b4330c73d98b18530">More...</a><br/></td></tr>
<tr class="separator:a00660c31aeb6d55b4330c73d98b18530"><td class="memSeparator" colspan="2"> </td></tr>
<tr><td colspan="2"><div class="groupHeader">Accessors</div></td></tr>
<tr class="memitem:a66985dceac27f10a05c23d68dd4094c0"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1CompNovoIdentification.html#a66985dceac27f10a05c23d68dd4094c0">getIdentifications</a> (std::vector< <a class="el" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a> > &ids, const <a class="el" href="group__Kernel.html#gac459ab9d68b68f31561c7763c7da61ef">PeakMap</a> &exp)</td></tr>
<tr class="memdesc:a66985dceac27f10a05c23d68dd4094c0"><td class="mdescLeft"> </td><td class="mdescRight">performs an <a class="el" href="classOpenMS_1_1ProteinIdentification.html" title="Representation of a protein identification run. ">ProteinIdentification</a> run on a PeakMap <a href="#a66985dceac27f10a05c23d68dd4094c0">More...</a><br/></td></tr>
<tr class="separator:a66985dceac27f10a05c23d68dd4094c0"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ac09c06c1068f5c752575bbac4c3f68a1"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1CompNovoIdentification.html#ac09c06c1068f5c752575bbac4c3f68a1">getIdentification</a> (<a class="el" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a> &id, const <a class="el" href="group__Kernel.html#ga3ba16951dc40c7a6c7457f3452e096ab">PeakSpectrum</a> &CID_spec, const <a class="el" href="group__Kernel.html#ga3ba16951dc40c7a6c7457f3452e096ab">PeakSpectrum</a> &ETD_spec)</td></tr>
<tr class="memdesc:ac09c06c1068f5c752575bbac4c3f68a1"><td class="mdescLeft"> </td><td class="mdescRight">performs an <a class="el" href="classOpenMS_1_1ProteinIdentification.html" title="Representation of a protein identification run. ">ProteinIdentification</a> run on a PeakSpectrum <a href="#ac09c06c1068f5c752575bbac4c3f68a1">More...</a><br/></td></tr>
<tr class="separator:ac09c06c1068f5c752575bbac4c3f68a1"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="inherit_header pub_methods_classOpenMS_1_1CompNovoIdentificationBase"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_classOpenMS_1_1CompNovoIdentificationBase')"><img src="closed.png" alt="-"/> Public Member Functions inherited from <a class="el" href="classOpenMS_1_1CompNovoIdentificationBase.html">CompNovoIdentificationBase</a></td></tr>
<tr class="memitem:a615baed6b8ce9260b7f230e97fb0bdc9 inherit pub_methods_classOpenMS_1_1CompNovoIdentificationBase"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1CompNovoIdentificationBase.html">CompNovoIdentificationBase</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1CompNovoIdentificationBase.html#a615baed6b8ce9260b7f230e97fb0bdc9">operator=</a> (const <a class="el" href="classOpenMS_1_1CompNovoIdentificationBase.html">CompNovoIdentificationBase</a> &source)</td></tr>
<tr class="memdesc:a615baed6b8ce9260b7f230e97fb0bdc9 inherit pub_methods_classOpenMS_1_1CompNovoIdentificationBase"><td class="mdescLeft"> </td><td class="mdescRight">assignment operator <a href="#a615baed6b8ce9260b7f230e97fb0bdc9">More...</a><br/></td></tr>
<tr class="separator:a615baed6b8ce9260b7f230e97fb0bdc9 inherit pub_methods_classOpenMS_1_1CompNovoIdentificationBase"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:abf7f47daa3ae6a785ef3bfcfde6e102b inherit pub_methods_classOpenMS_1_1CompNovoIdentificationBase"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1CompNovoIdentificationBase.html#abf7f47daa3ae6a785ef3bfcfde6e102b">CompNovoIdentificationBase</a> ()</td></tr>
<tr class="memdesc:abf7f47daa3ae6a785ef3bfcfde6e102b inherit pub_methods_classOpenMS_1_1CompNovoIdentificationBase"><td class="mdescLeft"> </td><td class="mdescRight">default constructor <a href="#abf7f47daa3ae6a785ef3bfcfde6e102b">More...</a><br/></td></tr>
<tr class="separator:abf7f47daa3ae6a785ef3bfcfde6e102b inherit pub_methods_classOpenMS_1_1CompNovoIdentificationBase"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a7ed8739eba71fe3e681d89626ee8eddb inherit pub_methods_classOpenMS_1_1CompNovoIdentificationBase"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1CompNovoIdentificationBase.html#a7ed8739eba71fe3e681d89626ee8eddb">CompNovoIdentificationBase</a> (const <a class="el" href="classOpenMS_1_1CompNovoIdentificationBase.html">CompNovoIdentificationBase</a> &source)</td></tr>
<tr class="memdesc:a7ed8739eba71fe3e681d89626ee8eddb inherit pub_methods_classOpenMS_1_1CompNovoIdentificationBase"><td class="mdescLeft"> </td><td class="mdescRight">copy constructor <a href="#a7ed8739eba71fe3e681d89626ee8eddb">More...</a><br/></td></tr>
<tr class="separator:a7ed8739eba71fe3e681d89626ee8eddb inherit pub_methods_classOpenMS_1_1CompNovoIdentificationBase"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a0273d70939fe8c4f6f60d049190e3a8e inherit pub_methods_classOpenMS_1_1CompNovoIdentificationBase"><td class="memItemLeft" align="right" valign="top">virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1CompNovoIdentificationBase.html#a0273d70939fe8c4f6f60d049190e3a8e">~CompNovoIdentificationBase</a> ()</td></tr>
<tr class="memdesc:a0273d70939fe8c4f6f60d049190e3a8e inherit pub_methods_classOpenMS_1_1CompNovoIdentificationBase"><td class="mdescLeft"> </td><td class="mdescRight">destructor <a href="#a0273d70939fe8c4f6f60d049190e3a8e">More...</a><br/></td></tr>
<tr class="separator:a0273d70939fe8c4f6f60d049190e3a8e inherit pub_methods_classOpenMS_1_1CompNovoIdentificationBase"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="inherit_header pub_methods_classOpenMS_1_1DefaultParamHandler"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_classOpenMS_1_1DefaultParamHandler')"><img src="closed.png" alt="-"/> Public Member Functions inherited from <a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a></td></tr>
<tr class="memitem:afb6802fda161cb0c1a4a05597f94aecc inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#afb6802fda161cb0c1a4a05597f94aecc">DefaultParamHandler</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &name)</td></tr>
<tr class="memdesc:afb6802fda161cb0c1a4a05597f94aecc inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Constructor with name that is displayed in error messages. <a href="#afb6802fda161cb0c1a4a05597f94aecc">More...</a><br/></td></tr>
<tr class="separator:afb6802fda161cb0c1a4a05597f94aecc inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a954da7eef3cfddda446574eaadd20abb inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a954da7eef3cfddda446574eaadd20abb">DefaultParamHandler</a> (const <a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a> &rhs)</td></tr>
<tr class="memdesc:a954da7eef3cfddda446574eaadd20abb inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Copy constructor. <a href="#a954da7eef3cfddda446574eaadd20abb">More...</a><br/></td></tr>
<tr class="separator:a954da7eef3cfddda446574eaadd20abb inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a11e9d6dd34fe8860874aa8abe0ec121b inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a11e9d6dd34fe8860874aa8abe0ec121b">~DefaultParamHandler</a> ()</td></tr>
<tr class="memdesc:a11e9d6dd34fe8860874aa8abe0ec121b inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Destructor. <a href="#a11e9d6dd34fe8860874aa8abe0ec121b">More...</a><br/></td></tr>
<tr class="separator:a11e9d6dd34fe8860874aa8abe0ec121b inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ae6b6d68036a573a44f6609460ba2dfb6 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">virtual <a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#ae6b6d68036a573a44f6609460ba2dfb6">operator=</a> (const <a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a> &rhs)</td></tr>
<tr class="memdesc:ae6b6d68036a573a44f6609460ba2dfb6 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Assignment operator. <a href="#ae6b6d68036a573a44f6609460ba2dfb6">More...</a><br/></td></tr>
<tr class="separator:ae6b6d68036a573a44f6609460ba2dfb6 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ac435f2dd4d9f9328db83af97129a8d7e inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">virtual bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#ac435f2dd4d9f9328db83af97129a8d7e">operator==</a> (const <a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a> &rhs) const </td></tr>
<tr class="memdesc:ac435f2dd4d9f9328db83af97129a8d7e inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Equality operator. <a href="#ac435f2dd4d9f9328db83af97129a8d7e">More...</a><br/></td></tr>
<tr class="separator:ac435f2dd4d9f9328db83af97129a8d7e inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:abc8067511cfc949ae942ea2b08588f81 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#abc8067511cfc949ae942ea2b08588f81">setParameters</a> (const <a class="el" href="classOpenMS_1_1Param.html">Param</a> &param)</td></tr>
<tr class="memdesc:abc8067511cfc949ae942ea2b08588f81 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Sets the parameters. <a href="#abc8067511cfc949ae942ea2b08588f81">More...</a><br/></td></tr>
<tr class="separator:abc8067511cfc949ae942ea2b08588f81 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a7f6aab5a7dfbdd1c062a4352a29361f3 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">const <a class="el" href="classOpenMS_1_1Param.html">Param</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a7f6aab5a7dfbdd1c062a4352a29361f3">getParameters</a> () const </td></tr>
<tr class="memdesc:a7f6aab5a7dfbdd1c062a4352a29361f3 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Non-mutable access to the parameters. <a href="#a7f6aab5a7dfbdd1c062a4352a29361f3">More...</a><br/></td></tr>
<tr class="separator:a7f6aab5a7dfbdd1c062a4352a29361f3 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a02f02fa9832ca3e8d47c575a39803a2a inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">const <a class="el" href="classOpenMS_1_1Param.html">Param</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a02f02fa9832ca3e8d47c575a39803a2a">getDefaults</a> () const </td></tr>
<tr class="memdesc:a02f02fa9832ca3e8d47c575a39803a2a inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Non-mutable access to the default parameters. <a href="#a02f02fa9832ca3e8d47c575a39803a2a">More...</a><br/></td></tr>
<tr class="separator:a02f02fa9832ca3e8d47c575a39803a2a inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aaee0f2845288173de9f6ad47e6ad31d5 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">const <a class="el" href="classOpenMS_1_1String.html">String</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#aaee0f2845288173de9f6ad47e6ad31d5">getName</a> () const </td></tr>
<tr class="memdesc:aaee0f2845288173de9f6ad47e6ad31d5 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Non-mutable access to the name. <a href="#aaee0f2845288173de9f6ad47e6ad31d5">More...</a><br/></td></tr>
<tr class="separator:aaee0f2845288173de9f6ad47e6ad31d5 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a77d37f2e1c12e8bd33ea0e660a89e927 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a77d37f2e1c12e8bd33ea0e660a89e927">setName</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &name)</td></tr>
<tr class="memdesc:a77d37f2e1c12e8bd33ea0e660a89e927 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Mutable access to the name. <a href="#a77d37f2e1c12e8bd33ea0e660a89e927">More...</a><br/></td></tr>
<tr class="separator:a77d37f2e1c12e8bd33ea0e660a89e927 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a768d4a2093627a2f34728656a9721bdf inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">const std::vector< <a class="el" href="classOpenMS_1_1String.html">String</a> > & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a768d4a2093627a2f34728656a9721bdf">getSubsections</a> () const </td></tr>
<tr class="memdesc:a768d4a2093627a2f34728656a9721bdf inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Non-mutable access to the registered subsections. <a href="#a768d4a2093627a2f34728656a9721bdf">More...</a><br/></td></tr>
<tr class="separator:a768d4a2093627a2f34728656a9721bdf inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pro-methods"></a>
Protected Member Functions</h2></td></tr>
<tr class="memitem:a498523428224f2456ba7c90aa5d67d91"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1CompNovoIdentification.html#a498523428224f2456ba7c90aa5d67d91">getDecompositionsDAC_</a> (std::set< <a class="el" href="classOpenMS_1_1String.html">String</a> > &sequences, <a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> left, <a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> right, <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> peptide_weight, const <a class="el" href="group__Kernel.html#ga3ba16951dc40c7a6c7457f3452e096ab">PeakSpectrum</a> &CID_orig_spec, const <a class="el" href="group__Kernel.html#ga3ba16951dc40c7a6c7457f3452e096ab">PeakSpectrum</a> &ETD_orig_spec, <a class="el" href="classOpenMS_1_1Map.html">Map</a>< <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a>, <a class="el" href="classOpenMS_1_1CompNovoIdentification.html#a7b7c9d2595dd3328e664293d3fec5ef9">IonScore</a> > &CID_nodes)</td></tr>
<tr class="memdesc:a498523428224f2456ba7c90aa5d67d91"><td class="mdescLeft"> </td><td class="mdescRight">call the DAC algorithm for the subspectrum defined via left and right peaks and fill the set with candidates sequences <a href="#a498523428224f2456ba7c90aa5d67d91">More...</a><br/></td></tr>
<tr class="separator:a498523428224f2456ba7c90aa5d67d91"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a7c8fe8f058261f294a5220f03e1300db"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1CompNovoIdentification.html#a7c8fe8f058261f294a5220f03e1300db">reducePermuts_</a> (std::set< <a class="el" href="classOpenMS_1_1String.html">String</a> > &permuts, const <a class="el" href="group__Kernel.html#ga3ba16951dc40c7a6c7457f3452e096ab">PeakSpectrum</a> &CID_orig_spec, const <a class="el" href="group__Kernel.html#ga3ba16951dc40c7a6c7457f3452e096ab">PeakSpectrum</a> &ETD_orig_spec, <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> prefix, <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> suffix)</td></tr>
<tr class="memdesc:a7c8fe8f058261f294a5220f03e1300db"><td class="mdescLeft"> </td><td class="mdescRight">reduces the given number of permuts by scoring the perumtations to the CID and ETD spec <a href="#a7c8fe8f058261f294a5220f03e1300db">More...</a><br/></td></tr>
<tr class="separator:a7c8fe8f058261f294a5220f03e1300db"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:adeb3341d290a37767ad698f303e382df"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1CompNovoIdentification.html#adeb3341d290a37767ad698f303e382df">getETDSpectrum_</a> (<a class="el" href="group__Kernel.html#ga3ba16951dc40c7a6c7457f3452e096ab">PeakSpectrum</a> &spec, const <a class="el" href="classOpenMS_1_1String.html">String</a> &sequence, <a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a>, <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> prefix=0.0, <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> suffix=0.0)</td></tr>
<tr class="memdesc:adeb3341d290a37767ad698f303e382df"><td class="mdescLeft"> </td><td class="mdescRight">fills the spectrum with c and z type ions <a href="#adeb3341d290a37767ad698f303e382df">More...</a><br/></td></tr>
<tr class="separator:adeb3341d290a37767ad698f303e382df"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a7c667a23f2582027b56a5ab08a05452b"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1CompNovoIdentification.html#a7c667a23f2582027b56a5ab08a05452b">estimatePrecursorWeight_</a> (const <a class="el" href="group__Kernel.html#ga3ba16951dc40c7a6c7457f3452e096ab">PeakSpectrum</a> &ETD_spec, <a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> &charge)</td></tr>
<tr class="memdesc:a7c667a23f2582027b56a5ab08a05452b"><td class="mdescLeft"> </td><td class="mdescRight">estimates an exact precursor weight of the ETD spectrum, because in most of the cases the precursor is found in the MS/MS spec <a href="#a7c667a23f2582027b56a5ab08a05452b">More...</a><br/></td></tr>
<tr class="separator:a7c667a23f2582027b56a5ab08a05452b"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="inherit_header pro_methods_classOpenMS_1_1CompNovoIdentificationBase"><td colspan="2" onclick="javascript:toggleInherit('pro_methods_classOpenMS_1_1CompNovoIdentificationBase')"><img src="closed.png" alt="-"/> Protected Member Functions inherited from <a class="el" href="classOpenMS_1_1CompNovoIdentificationBase.html">CompNovoIdentificationBase</a></td></tr>
<tr class="memitem:aaf258e1a9846d9b238ee4b3005ad3ee9 inherit pro_methods_classOpenMS_1_1CompNovoIdentificationBase"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1CompNovoIdentificationBase.html#aaf258e1a9846d9b238ee4b3005ad3ee9">updateMembers_</a> ()</td></tr>
<tr class="memdesc:aaf258e1a9846d9b238ee4b3005ad3ee9 inherit pro_methods_classOpenMS_1_1CompNovoIdentificationBase"><td class="mdescLeft"> </td><td class="mdescRight">update members method from <a class="el" href="classOpenMS_1_1DefaultParamHandler.html" title="A base class for all classes handling default parameters. ">DefaultParamHandler</a> to update the members <a href="#aaf258e1a9846d9b238ee4b3005ad3ee9">More...</a><br/></td></tr>
<tr class="separator:aaf258e1a9846d9b238ee4b3005ad3ee9 inherit pro_methods_classOpenMS_1_1CompNovoIdentificationBase"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a0de3150c54197aec0713c045ddecd495 inherit pro_methods_classOpenMS_1_1CompNovoIdentificationBase"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1CompNovoIdentificationBase.html#a0de3150c54197aec0713c045ddecd495">filterPermuts_</a> (std::set< <a class="el" href="classOpenMS_1_1String.html">String</a> > &permut)</td></tr>
<tr class="memdesc:a0de3150c54197aec0713c045ddecd495 inherit pro_methods_classOpenMS_1_1CompNovoIdentificationBase"><td class="mdescLeft"> </td><td class="mdescRight">filters the permutations <a href="#a0de3150c54197aec0713c045ddecd495">More...</a><br/></td></tr>
<tr class="separator:a0de3150c54197aec0713c045ddecd495 inherit pro_methods_classOpenMS_1_1CompNovoIdentificationBase"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a41eac7221a0bd2a75e451ee5192d7d0d inherit pro_methods_classOpenMS_1_1CompNovoIdentificationBase"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1CompNovoIdentificationBase.html#a41eac7221a0bd2a75e451ee5192d7d0d">selectPivotIons_</a> (std::vector< <a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> > &pivots, <a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> left, <a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> right, <a class="el" href="classOpenMS_1_1Map.html">Map</a>< <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a>, <a class="el" href="classOpenMS_1_1CompNovoIdentificationBase.html#a7b7c9d2595dd3328e664293d3fec5ef9">IonScore</a> > &CID_nodes, const <a class="el" href="group__Kernel.html#ga3ba16951dc40c7a6c7457f3452e096ab">PeakSpectrum</a> &CID_orig_spec, <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> precursor_weight, bool full_range=false)</td></tr>
<tr class="memdesc:a41eac7221a0bd2a75e451ee5192d7d0d inherit pro_methods_classOpenMS_1_1CompNovoIdentificationBase"><td class="mdescLeft"> </td><td class="mdescRight">selects pivot ion of the given range using the scores given in CID_nodes <a href="#a41eac7221a0bd2a75e451ee5192d7d0d">More...</a><br/></td></tr>
<tr class="separator:a41eac7221a0bd2a75e451ee5192d7d0d inherit pro_methods_classOpenMS_1_1CompNovoIdentificationBase"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a74e50effd6fb4d93e3384065118df15b inherit pro_methods_classOpenMS_1_1CompNovoIdentificationBase"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1CompNovoIdentificationBase.html#a74e50effd6fb4d93e3384065118df15b">filterDecomps_</a> (std::vector< <a class="el" href="classOpenMS_1_1MassDecomposition.html">MassDecomposition</a> > &decomps)</td></tr>
<tr class="memdesc:a74e50effd6fb4d93e3384065118df15b inherit pro_methods_classOpenMS_1_1CompNovoIdentificationBase"><td class="mdescLeft"> </td><td class="mdescRight">filters the decomps by the amino acid frequencies <a href="#a74e50effd6fb4d93e3384065118df15b">More...</a><br/></td></tr>
<tr class="separator:a74e50effd6fb4d93e3384065118df15b inherit pro_methods_classOpenMS_1_1CompNovoIdentificationBase"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a2079f6f37ba3d2b31a3832bb7f27751a inherit pro_methods_classOpenMS_1_1CompNovoIdentificationBase"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1CompNovoIdentificationBase.html#a2079f6f37ba3d2b31a3832bb7f27751a">getDecompositions_</a> (std::vector< <a class="el" href="classOpenMS_1_1MassDecomposition.html">MassDecomposition</a> > &decomps, <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> mass, bool no_caching=false)</td></tr>
<tr class="memdesc:a2079f6f37ba3d2b31a3832bb7f27751a inherit pro_methods_classOpenMS_1_1CompNovoIdentificationBase"><td class="mdescLeft"> </td><td class="mdescRight">produces mass decompositions using the given mass <a href="#a2079f6f37ba3d2b31a3832bb7f27751a">More...</a><br/></td></tr>
<tr class="separator:a2079f6f37ba3d2b31a3832bb7f27751a inherit pro_methods_classOpenMS_1_1CompNovoIdentificationBase"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a6c4e9f2bd8d2f8ee5d253e579571b72e inherit pro_methods_classOpenMS_1_1CompNovoIdentificationBase"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1CompNovoIdentificationBase.html#a6c4e9f2bd8d2f8ee5d253e579571b72e">permute_</a> (<a class="el" href="classOpenMS_1_1String.html">String</a> prefix, <a class="el" href="classOpenMS_1_1String.html">String</a> s, std::set< <a class="el" href="classOpenMS_1_1String.html">String</a> > &permutations)</td></tr>
<tr class="memdesc:a6c4e9f2bd8d2f8ee5d253e579571b72e inherit pro_methods_classOpenMS_1_1CompNovoIdentificationBase"><td class="mdescLeft"> </td><td class="mdescRight">permuts the <a class="el" href="classOpenMS_1_1String.html" title="A more convenient string class. ">String</a> s adds the prefix and stores the results in permutations <a href="#a6c4e9f2bd8d2f8ee5d253e579571b72e">More...</a><br/></td></tr>
<tr class="separator:a6c4e9f2bd8d2f8ee5d253e579571b72e inherit pro_methods_classOpenMS_1_1CompNovoIdentificationBase"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aaa25c86b47d7c7126c67861df50b5d7a inherit pro_methods_classOpenMS_1_1CompNovoIdentificationBase"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1CompNovoIdentificationBase.html#aaa25c86b47d7c7126c67861df50b5d7a">countMissedCleavagesTryptic_</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &peptide) const </td></tr>
<tr class="separator:aaa25c86b47d7c7126c67861df50b5d7a inherit pro_methods_classOpenMS_1_1CompNovoIdentificationBase"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a202e48c66d303fc512ce0a5a4e847371 inherit pro_methods_classOpenMS_1_1CompNovoIdentificationBase"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1CompNovoIdentificationBase.html#a202e48c66d303fc512ce0a5a4e847371">getCIDSpectrumLight_</a> (<a class="el" href="group__Kernel.html#ga3ba16951dc40c7a6c7457f3452e096ab">PeakSpectrum</a> &spec, const <a class="el" href="classOpenMS_1_1String.html">String</a> &sequence, <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> prefix, <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> suffix)</td></tr>
<tr class="memdesc:a202e48c66d303fc512ce0a5a4e847371 inherit pro_methods_classOpenMS_1_1CompNovoIdentificationBase"><td class="mdescLeft"> </td><td class="mdescRight">fills the spec with b and y ions, no other ion types or doubly charged variants are used <a href="#a202e48c66d303fc512ce0a5a4e847371">More...</a><br/></td></tr>
<tr class="separator:a202e48c66d303fc512ce0a5a4e847371 inherit pro_methods_classOpenMS_1_1CompNovoIdentificationBase"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a534a7779c702c4db69a34e8374c8c568 inherit pro_methods_classOpenMS_1_1CompNovoIdentificationBase"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1CompNovoIdentificationBase.html#a534a7779c702c4db69a34e8374c8c568">getCIDSpectrum_</a> (<a class="el" href="group__Kernel.html#ga3ba16951dc40c7a6c7457f3452e096ab">PeakSpectrum</a> &spec, const <a class="el" href="classOpenMS_1_1String.html">String</a> &sequence, <a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> charge, <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> prefix=0.0, <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> suffix=0.0)</td></tr>
<tr class="memdesc:a534a7779c702c4db69a34e8374c8c568 inherit pro_methods_classOpenMS_1_1CompNovoIdentificationBase"><td class="mdescLeft"> </td><td class="mdescRight">fills the spectrum with b,y ions, multiple charged variants; if prefix and suffix weights are given, the sequence is treated as tag <a href="#a534a7779c702c4db69a34e8374c8c568">More...</a><br/></td></tr>
<tr class="separator:a534a7779c702c4db69a34e8374c8c568 inherit pro_methods_classOpenMS_1_1CompNovoIdentificationBase"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a65b27e7219c985ac0f9e97a493266131 inherit pro_methods_classOpenMS_1_1CompNovoIdentificationBase"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1CompNovoIdentificationBase.html#a65b27e7219c985ac0f9e97a493266131">initIsotopeDistributions_</a> ()</td></tr>
<tr class="memdesc:a65b27e7219c985ac0f9e97a493266131 inherit pro_methods_classOpenMS_1_1CompNovoIdentificationBase"><td class="mdescLeft"> </td><td class="mdescRight">initializes the score distribution precalculated for the use in spectrum generation <a href="#a65b27e7219c985ac0f9e97a493266131">More...</a><br/></td></tr>
<tr class="separator:a65b27e7219c985ac0f9e97a493266131 inherit pro_methods_classOpenMS_1_1CompNovoIdentificationBase"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a7c667a23f2582027b56a5ab08a05452b inherit pro_methods_classOpenMS_1_1CompNovoIdentificationBase"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1CompNovoIdentificationBase.html#a7c667a23f2582027b56a5ab08a05452b">estimatePrecursorWeight_</a> (const <a class="el" href="group__Kernel.html#ga3ba16951dc40c7a6c7457f3452e096ab">PeakSpectrum</a> &ETD_spec, <a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> &charge)</td></tr>
<tr class="memdesc:a7c667a23f2582027b56a5ab08a05452b inherit pro_methods_classOpenMS_1_1CompNovoIdentificationBase"><td class="mdescLeft"> </td><td class="mdescRight">estimates an exact precursor weight of the ETD spectrum, because in most of the cases the precursor is found in the MS/MS spec <a href="#a7c667a23f2582027b56a5ab08a05452b">More...</a><br/></td></tr>
<tr class="separator:a7c667a23f2582027b56a5ab08a05452b inherit pro_methods_classOpenMS_1_1CompNovoIdentificationBase"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:abafd16ae1c148cfc77e288766af3dbdc inherit pro_methods_classOpenMS_1_1CompNovoIdentificationBase"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1CompNovoIdentificationBase.html#abafd16ae1c148cfc77e288766af3dbdc">windowMower_</a> (<a class="el" href="group__Kernel.html#ga3ba16951dc40c7a6c7457f3452e096ab">PeakSpectrum</a> &spec, <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> windowsize, <a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> no_peaks)</td></tr>
<tr class="memdesc:abafd16ae1c148cfc77e288766af3dbdc inherit pro_methods_classOpenMS_1_1CompNovoIdentificationBase"><td class="mdescLeft"> </td><td class="mdescRight">keep for each window of size windowsize in the m/z range of the spectrum exactly no_peaks <a href="#abafd16ae1c148cfc77e288766af3dbdc">More...</a><br/></td></tr>
<tr class="separator:abafd16ae1c148cfc77e288766af3dbdc inherit pro_methods_classOpenMS_1_1CompNovoIdentificationBase"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a03573d18ed22e1e4531427cc2ae02f7e inherit pro_methods_classOpenMS_1_1CompNovoIdentificationBase"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1CompNovoIdentificationBase.html#a03573d18ed22e1e4531427cc2ae02f7e">compareSpectra_</a> (const <a class="el" href="group__Kernel.html#ga3ba16951dc40c7a6c7457f3452e096ab">PeakSpectrum</a> &s1, const <a class="el" href="group__Kernel.html#ga3ba16951dc40c7a6c7457f3452e096ab">PeakSpectrum</a> &s2)</td></tr>
<tr class="memdesc:a03573d18ed22e1e4531427cc2ae02f7e inherit pro_methods_classOpenMS_1_1CompNovoIdentificationBase"><td class="mdescLeft"> </td><td class="mdescRight">compares two spectra <a href="#a03573d18ed22e1e4531427cc2ae02f7e">More...</a><br/></td></tr>
<tr class="separator:a03573d18ed22e1e4531427cc2ae02f7e inherit pro_methods_classOpenMS_1_1CompNovoIdentificationBase"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a8dede5d573722ed26d933e3bb072d601 inherit pro_methods_classOpenMS_1_1CompNovoIdentificationBase"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1AASequence.html">AASequence</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1CompNovoIdentificationBase.html#a8dede5d573722ed26d933e3bb072d601">getModifiedAASequence_</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &sequence)</td></tr>
<tr class="memdesc:a8dede5d573722ed26d933e3bb072d601 inherit pro_methods_classOpenMS_1_1CompNovoIdentificationBase"><td class="mdescLeft"> </td><td class="mdescRight">returns a modified <a class="el" href="classOpenMS_1_1AASequence.html" title="Representation of a peptide/protein sequence. ">AASequence</a> from a given internal representation <a href="#a8dede5d573722ed26d933e3bb072d601">More...</a><br/></td></tr>
<tr class="separator:a8dede5d573722ed26d933e3bb072d601 inherit pro_methods_classOpenMS_1_1CompNovoIdentificationBase"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a62e2deacbe2df393642370527ec373aa inherit pro_methods_classOpenMS_1_1CompNovoIdentificationBase"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1String.html">String</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1CompNovoIdentificationBase.html#a62e2deacbe2df393642370527ec373aa">getModifiedStringFromAASequence_</a> (const <a class="el" href="classOpenMS_1_1AASequence.html">AASequence</a> &sequence)</td></tr>
<tr class="memdesc:a62e2deacbe2df393642370527ec373aa inherit pro_methods_classOpenMS_1_1CompNovoIdentificationBase"><td class="mdescLeft"> </td><td class="mdescRight">returns the internal representation of a given <a class="el" href="classOpenMS_1_1AASequence.html" title="Representation of a peptide/protein sequence. ">AASequence</a> <a href="#a62e2deacbe2df393642370527ec373aa">More...</a><br/></td></tr>
<tr class="separator:a62e2deacbe2df393642370527ec373aa inherit pro_methods_classOpenMS_1_1CompNovoIdentificationBase"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="inherit_header pro_methods_classOpenMS_1_1DefaultParamHandler"><td colspan="2" onclick="javascript:toggleInherit('pro_methods_classOpenMS_1_1DefaultParamHandler')"><img src="closed.png" alt="-"/> Protected Member Functions inherited from <a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a></td></tr>
<tr class="memitem:a2802c591e6d7fd3fd9cc35f5e875d0ba inherit pro_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a2802c591e6d7fd3fd9cc35f5e875d0ba">defaultsToParam_</a> ()</td></tr>
<tr class="memdesc:a2802c591e6d7fd3fd9cc35f5e875d0ba inherit pro_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Updates the parameters after the defaults have been set in the constructor. <a href="#a2802c591e6d7fd3fd9cc35f5e875d0ba">More...</a><br/></td></tr>
<tr class="separator:a2802c591e6d7fd3fd9cc35f5e875d0ba inherit pro_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="inherited"></a>
Additional Inherited Members</h2></td></tr>
<tr class="inherit_header pro_attribs_classOpenMS_1_1CompNovoIdentificationBase"><td colspan="2" onclick="javascript:toggleInherit('pro_attribs_classOpenMS_1_1CompNovoIdentificationBase')"><img src="closed.png" alt="-"/> Protected Attributes inherited from <a class="el" href="classOpenMS_1_1CompNovoIdentificationBase.html">CompNovoIdentificationBase</a></td></tr>
<tr class="memitem:adc6ddd4883b749e4fc2cb7600c41103b inherit pro_attribs_classOpenMS_1_1CompNovoIdentificationBase"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1Map.html">Map</a>< char, const <a class="el" href="classOpenMS_1_1Residue.html">Residue</a> * > </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1CompNovoIdentificationBase.html#adc6ddd4883b749e4fc2cb7600c41103b">name_to_residue_</a></td></tr>
<tr class="memdesc:adc6ddd4883b749e4fc2cb7600c41103b inherit pro_attribs_classOpenMS_1_1CompNovoIdentificationBase"><td class="mdescLeft"> </td><td class="mdescRight">mapping for the internal representation character to the actual residue <a href="#adc6ddd4883b749e4fc2cb7600c41103b">More...</a><br/></td></tr>
<tr class="separator:adc6ddd4883b749e4fc2cb7600c41103b inherit pro_attribs_classOpenMS_1_1CompNovoIdentificationBase"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ab935c51dfc71c9f00e6bdd21a1932c6f inherit pro_attribs_classOpenMS_1_1CompNovoIdentificationBase"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1Map.html">Map</a>< const <a class="el" href="classOpenMS_1_1Residue.html">Residue</a> *, char > </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1CompNovoIdentificationBase.html#ab935c51dfc71c9f00e6bdd21a1932c6f">residue_to_name_</a></td></tr>
<tr class="memdesc:ab935c51dfc71c9f00e6bdd21a1932c6f inherit pro_attribs_classOpenMS_1_1CompNovoIdentificationBase"><td class="mdescLeft"> </td><td class="mdescRight">mapping of the actual residue to the internal representing character <a href="#ab935c51dfc71c9f00e6bdd21a1932c6f">More...</a><br/></td></tr>
<tr class="separator:ab935c51dfc71c9f00e6bdd21a1932c6f inherit pro_attribs_classOpenMS_1_1CompNovoIdentificationBase"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a478012ec394ab8b0d4d4ea97ba16e37f inherit pro_attribs_classOpenMS_1_1CompNovoIdentificationBase"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1Map.html">Map</a>< <a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a>, std::vector<br class="typebreak"/>
< <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> > > </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1CompNovoIdentificationBase.html#a478012ec394ab8b0d4d4ea97ba16e37f">isotope_distributions_</a></td></tr>
<tr class="separator:a478012ec394ab8b0d4d4ea97ba16e37f inherit pro_attribs_classOpenMS_1_1CompNovoIdentificationBase"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aa8c6a0786e4331831d8e6f3729594207 inherit pro_attribs_classOpenMS_1_1CompNovoIdentificationBase"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1Map.html">Map</a>< char, <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1CompNovoIdentificationBase.html#aa8c6a0786e4331831d8e6f3729594207">aa_to_weight_</a></td></tr>
<tr class="memdesc:aa8c6a0786e4331831d8e6f3729594207 inherit pro_attribs_classOpenMS_1_1CompNovoIdentificationBase"><td class="mdescLeft"> </td><td class="mdescRight">masses of the amino acids <a href="#aa8c6a0786e4331831d8e6f3729594207">More...</a><br/></td></tr>
<tr class="separator:aa8c6a0786e4331831d8e6f3729594207 inherit pro_attribs_classOpenMS_1_1CompNovoIdentificationBase"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a43ef3d7b1af3fddb3c210d380b3e534f inherit pro_attribs_classOpenMS_1_1CompNovoIdentificationBase"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1MassDecompositionAlgorithm.html">MassDecompositionAlgorithm</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1CompNovoIdentificationBase.html#a43ef3d7b1af3fddb3c210d380b3e534f">mass_decomp_algorithm_</a></td></tr>
<tr class="separator:a43ef3d7b1af3fddb3c210d380b3e534f inherit pro_attribs_classOpenMS_1_1CompNovoIdentificationBase"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:abb2ee242a9ea3383ede3b04f3c581e5c inherit pro_attribs_classOpenMS_1_1CompNovoIdentificationBase"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1CompNovoIdentificationBase.html#abb2ee242a9ea3383ede3b04f3c581e5c">min_aa_weight_</a></td></tr>
<tr class="separator:abb2ee242a9ea3383ede3b04f3c581e5c inherit pro_attribs_classOpenMS_1_1CompNovoIdentificationBase"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:acbe94f316242ea59d88b8a42421f0a8f inherit pro_attribs_classOpenMS_1_1CompNovoIdentificationBase"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1ZhangSimilarityScore.html">ZhangSimilarityScore</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1CompNovoIdentificationBase.html#acbe94f316242ea59d88b8a42421f0a8f">zhang_</a></td></tr>
<tr class="separator:acbe94f316242ea59d88b8a42421f0a8f inherit pro_attribs_classOpenMS_1_1CompNovoIdentificationBase"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aa34c4934ed81b76bd18a61b2ae05a008 inherit pro_attribs_classOpenMS_1_1CompNovoIdentificationBase"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1Map.html">Map</a>< <a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a>, <a class="el" href="classOpenMS_1_1Map.html">Map</a>< <a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a>, std::set<br class="typebreak"/>
< <a class="el" href="classOpenMS_1_1String.html">String</a> > > > </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1CompNovoIdentificationBase.html#aa34c4934ed81b76bd18a61b2ae05a008">subspec_to_sequences_</a></td></tr>
<tr class="separator:aa34c4934ed81b76bd18a61b2ae05a008 inherit pro_attribs_classOpenMS_1_1CompNovoIdentificationBase"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a185649daf5577a9a653481339ad31050 inherit pro_attribs_classOpenMS_1_1CompNovoIdentificationBase"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1CompNovoIdentificationBase.html#a185649daf5577a9a653481339ad31050">max_number_aa_per_decomp_</a></td></tr>
<tr class="separator:a185649daf5577a9a653481339ad31050 inherit pro_attribs_classOpenMS_1_1CompNovoIdentificationBase"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a269e179e59449e35188ff860d9b17cc2 inherit pro_attribs_classOpenMS_1_1CompNovoIdentificationBase"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1CompNovoIdentificationBase.html#a269e179e59449e35188ff860d9b17cc2">tryptic_only_</a></td></tr>
<tr class="separator:a269e179e59449e35188ff860d9b17cc2 inherit pro_attribs_classOpenMS_1_1CompNovoIdentificationBase"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a03d038e2ce9f971ebd73bcb86f417dc8 inherit pro_attribs_classOpenMS_1_1CompNovoIdentificationBase"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1CompNovoIdentificationBase.html#a03d038e2ce9f971ebd73bcb86f417dc8">fragment_mass_tolerance_</a></td></tr>
<tr class="separator:a03d038e2ce9f971ebd73bcb86f417dc8 inherit pro_attribs_classOpenMS_1_1CompNovoIdentificationBase"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a56e61563cf61e1757a66f9575e2b0ff9 inherit pro_attribs_classOpenMS_1_1CompNovoIdentificationBase"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1CompNovoIdentificationBase.html#a56e61563cf61e1757a66f9575e2b0ff9">max_number_pivot_</a></td></tr>
<tr class="separator:a56e61563cf61e1757a66f9575e2b0ff9 inherit pro_attribs_classOpenMS_1_1CompNovoIdentificationBase"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a13a6f47c92acba9ea98495e4fb4c4830 inherit pro_attribs_classOpenMS_1_1CompNovoIdentificationBase"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1CompNovoIdentificationBase.html#a13a6f47c92acba9ea98495e4fb4c4830">decomp_weights_precision_</a></td></tr>
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< <a class="el" href="classOpenMS_1_1MassDecomposition.html">MassDecomposition</a> > > </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1CompNovoIdentificationBase.html#a899270a4fe96f27b6955a953491b3b5c">decomp_cache_</a></td></tr>
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<tr class="inherit_header pro_attribs_classOpenMS_1_1DefaultParamHandler"><td colspan="2" onclick="javascript:toggleInherit('pro_attribs_classOpenMS_1_1DefaultParamHandler')"><img src="closed.png" alt="-"/> Protected Attributes inherited from <a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a></td></tr>
<tr class="memitem:a28c73e623c63a4fe3bfceb1ae8274f39 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1Param.html">Param</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a28c73e623c63a4fe3bfceb1ae8274f39">param_</a></td></tr>
<tr class="memdesc:a28c73e623c63a4fe3bfceb1ae8274f39 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Container for current parameters. <a href="#a28c73e623c63a4fe3bfceb1ae8274f39">More...</a><br/></td></tr>
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<tr class="memdesc:a761b1937850c141d0c6fff0e4d633a04 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Container for default parameters. This member should be filled in the constructor of derived classes! <a href="#a761b1937850c141d0c6fff0e4d633a04">More...</a><br/></td></tr>
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<tr class="memitem:ac4b0e20bc59c7a5afe016c69067e428c inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">std::vector< <a class="el" href="classOpenMS_1_1String.html">String</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#ac4b0e20bc59c7a5afe016c69067e428c">subsections_</a></td></tr>
<tr class="memdesc:ac4b0e20bc59c7a5afe016c69067e428c inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Container for registered subsections. This member should be filled in the constructor of derived classes! <a href="#ac4b0e20bc59c7a5afe016c69067e428c">More...</a><br/></td></tr>
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<tr class="memdesc:a5a51f3f150b09068256195e934339a19 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Name that is displayed in error messages during the parameter checking. <a href="#a5a51f3f150b09068256195e934339a19">More...</a><br/></td></tr>
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<tr class="memitem:a7c3b265b697a57615da5cd3274780efd inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a7c3b265b697a57615da5cd3274780efd">check_defaults_</a></td></tr>
<tr class="memdesc:a7c3b265b697a57615da5cd3274780efd inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">If this member is set to false no checking if parameters in done;. <a href="#a7c3b265b697a57615da5cd3274780efd">More...</a><br/></td></tr>
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<tr class="memitem:aba444910e4fccb93f91bf7ab135f508a inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#aba444910e4fccb93f91bf7ab135f508a">warn_empty_defaults_</a></td></tr>
<tr class="memdesc:aba444910e4fccb93f91bf7ab135f508a inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">If this member is set to false no warning is emitted when defaults are empty;. <a href="#aba444910e4fccb93f91bf7ab135f508a">More...</a><br/></td></tr>
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</table>
<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
<div class="textblock"><p>run with <a class="el" href="classOpenMS_1_1CompNovoIdentification.html" title="run with CompNovoIdentification ">CompNovoIdentification</a> </p>
<B>Parameters of this class are:</B><BR><BR>
<table border="1" style="border-style:solid; border-collapse:collapse; border-color:#c0c0c0;" width="100%" cellpadding="4">
<tr style="border-bottom:1px solid black; background:#fffff0"><th>Name</th><th>Type</th><th>Default</th><th>Restrictions</th><th>Description</th></tr>
<tr>
<td style="vertical-align:top"><i>max_number_aa_per_decomp</i></td>
<td style="vertical-align:top">int</td><td style="vertical-align:top">4</td>
<td style="vertical-align:top"> </td><td style="vertical-align:top">maximal amino acid frequency per decomposition</td>
</tr>
<tr>
<td style="vertical-align:top"><b>tryptic_only</b></td>
<td style="vertical-align:top">string</td><td style="vertical-align:top">true</td>
<td style="vertical-align:top"> </td><td style="vertical-align:top">if set to true only tryptic peptides are reported</td>
</tr>
<tr>
<td style="vertical-align:top"><b>precursor_mass_tolerance</b></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">1.5</td>
<td style="vertical-align:top"> </td><td style="vertical-align:top">precursor mass tolerance</td>
</tr>
<tr>
<td style="vertical-align:top"><b>fragment_mass_tolerance</b></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">0.3</td>
<td style="vertical-align:top"> </td><td style="vertical-align:top">fragment mass tolerance</td>
</tr>
<tr>
<td style="vertical-align:top"><i>max_number_pivot</i></td>
<td style="vertical-align:top">int</td><td style="vertical-align:top">9</td>
<td style="vertical-align:top"> </td><td style="vertical-align:top">maximal number of pivot ions to be used</td>
</tr>
<tr>
<td style="vertical-align:top"><i>max_subscore_number</i></td>
<td style="vertical-align:top">int</td><td style="vertical-align:top">40</td>
<td style="vertical-align:top"> </td><td style="vertical-align:top">maximal number of solutions of a subsegment that are kept</td>
</tr>
<tr>
<td style="vertical-align:top"><i>decomp_weights_precision</i></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">0.01</td>
<td style="vertical-align:top"> </td><td style="vertical-align:top">precision used to calculate the decompositions, this only affects cache usage!</td>
</tr>
<tr>
<td style="vertical-align:top"><i>double_charged_iso_threshold</i></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">0.6</td>
<td style="vertical-align:top"> </td><td style="vertical-align:top">minimal isotope intensity correlation of doubly charged ions to be used to score the single scored ions</td>
</tr>
<tr>
<td style="vertical-align:top"><b>max_mz</b></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">2000</td>
<td style="vertical-align:top"> </td><td style="vertical-align:top">maximal m/z value used to calculate isotope distributions</td>
</tr>
<tr>
<td style="vertical-align:top"><b>min_mz</b></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">200</td>
<td style="vertical-align:top"> </td><td style="vertical-align:top">minimal m/z value used to calculate the isotope distributions</td>
</tr>
<tr>
<td style="vertical-align:top"><i>max_isotope_to_score</i></td>
<td style="vertical-align:top">int</td><td style="vertical-align:top">3</td>
<td style="vertical-align:top"> </td><td style="vertical-align:top">max isotope peak to be considered in the scoring</td>
</tr>
<tr>
<td style="vertical-align:top"><i>max_decomp_weight</i></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">450</td>
<td style="vertical-align:top"> </td><td style="vertical-align:top">maximal m/z difference used to calculate the decompositions</td>
</tr>
<tr>
<td style="vertical-align:top"><i>max_isotope</i></td>
<td style="vertical-align:top">int</td><td style="vertical-align:top">3</td>
<td style="vertical-align:top"> </td><td style="vertical-align:top">max isotope used in the theoretical spectra to score</td>
</tr>
<tr>
<td style="vertical-align:top"><b>missed_cleavages</b></td>
<td style="vertical-align:top">int</td><td style="vertical-align:top">1</td>
<td style="vertical-align:top"> </td><td style="vertical-align:top">maximal number of missed cleavages allowed per peptide</td>
</tr>
<tr>
<td style="vertical-align:top"><b>number_of_hits</b></td>
<td style="vertical-align:top">int</td><td style="vertical-align:top">100</td>
<td style="vertical-align:top"> </td><td style="vertical-align:top">maximal number of hits which are reported per spectrum</td>
</tr>
<tr>
<td style="vertical-align:top"><b>estimate_precursor_mz</b></td>
<td style="vertical-align:top">string</td><td style="vertical-align:top">true</td>
<td style="vertical-align:top">true, false</td><td style="vertical-align:top">If set to true, the precursor charge will be estimated, e.g. from the precursor peaks of the ETD spectrum.<BR>The input is believed otherwise.</td>
</tr>
<tr>
<td style="vertical-align:top"><i>number_of_prescoring_hits</i></td>
<td style="vertical-align:top">int</td><td style="vertical-align:top">250</td>
<td style="vertical-align:top"> </td><td style="vertical-align:top">how many sequences are kept after first rough scoring for better scoring</td>
</tr>
<tr>
<td style="vertical-align:top"><b>fixed_modifications</b></td>
<td style="vertical-align:top">string list</td><td style="vertical-align:top">[]</td>
<td style="vertical-align:top">15dB-biotin (C), 2-succinyl (C), 2HPG (R), 3-deoxyglucosone (R), 3sulfo (N-term), 4-ONE (C), 4-ONE (H), 4-ONE (K), 4-ONE+Delta:H(-2)O(-1) (C), 4-ONE+Delta:H(-2)O(-1) (H), 4-ONE+Delta:H(-2)O(-1) (K), 4AcAllylGal (C), ADP-Ribosyl (C), ADP-Ribosyl (E), ADP-Ribosyl (N), ADP-Ribosyl (R), ADP-Ribosyl (S), AEBS (H), AEBS (K), AEBS (S), AEBS (Y), AEC-MAEC (S), AEC-MAEC (T), AEC-MAEC:2H(4) (S), AEC-MAEC:2H(4) (T), AROD (C), AccQTag (K), AccQTag (N-term), Acetyl (C), Acetyl (H), Acetyl (K), Acetyl (N-term), Acetyl (S), Acetyl (T), Acetyl (Y), Acetyl:2H(3) (K), Acetyl:2H(3) (N-term), Ala->Asp (A), Ala->Glu (A), Ala->Gly (A), Ala->Pro (A), Ala->Ser (A), Ala->Thr (A), Ala->Val (A), Amidated (C-term), Amidine (K), Amidine (N-term), Amidino (C), Amino (Y), Ammonia-loss (N), Ammonia-loss (N-term C), Ammonium (C-term), Ammonium (D), Ammonium (E), Archaeol (C), Arg->Cys (R), Arg->Gln (R), Arg->GluSA (R), Arg->Gly (R), Arg->His (R), Arg->Ile (R), Arg->Lys (R), Arg->Met (R), Arg->Npo (R), Arg->Orn (R), Arg->Pro (R), Arg->Ser (R), Arg->Thr (R), Arg->Trp (R), Arg2PG (R), Argbiotinhydrazide (R), Asn->Asp (N), Asn->His (N), Asn->Ile (N), Asn->Lys (N), Asn->Ser (N), Asn->Thr (N), Asn->Tyr (N), Asp->Ala (D), Asp->Asn (D), Asp->Glu (D), Asp->Gly (D), Asp->His (D), Asp->Tyr (D), Asp->Val (D), Atto495Maleimide (C), BADGE (C), BDMAPP (H), BDMAPP (K), BDMAPP (W), BDMAPP (Y), BHAc (K), BHT (C), BHT (H), BHT (K), BHTOH (C), BHTOH (H), BHTOH (K), BITC (C), BITC (K), BITC (N-term), BMOE (C), Bacillosamine (N), Benzoyl (K), Benzoyl (N-term), Biotin (K), Biotin (N-term), Biotin-HPDP (C), Biotin-PEG-PRA (M), Biotin-PEO-Amine (D), Biotin-PEO-Amine (E), Biotin-PEO4-hydrazide (C-term), Biotin-maleimide (C), Biotin-phenacyl (C), Biotin-phenacyl (H), Biotin-phenacyl (S), BisANS (K), Bodipy (C), Bromo (F), Bromo (H), Bromo (W), Bromobimane (C), C8-QAT (K), C8-QAT (N-term), CAF (N-term), CAMthiopropanoyl (K), CHDH (D), CLIP_TRAQ_1 (K), CLIP_TRAQ_1 (N-term), CLIP_TRAQ_1 (Y), CLIP_TRAQ_2 (K), CLIP_TRAQ_2 (N-term), CLIP_TRAQ_2 (Y), CLIP_TRAQ_3 (K), CLIP_TRAQ_3 (N-term), CLIP_TRAQ_3 (Y), CLIP_TRAQ_4 (K), CLIP_TRAQ_4 (N-term), CLIP_TRAQ_4 (Y), Can-FP-biotin (S), Can-FP-biotin (T), Can-FP-biotin (Y), Carbamidomethyl (C), Carbamidomethyl (D), Carbamidomethyl (E), Carbamidomethyl (H), Carbamidomethyl (K), Carbamidomethyl (N-term), CarbamidomethylDTT (C), Carbamyl (C), Carbamyl (K), Carbamyl (M), Carbamyl (N-term), Carbamyl (R), Carbamyl (S), Carbamyl (T), Carbamyl (Y), Carbofuran (S), Carboxy (D), Carboxy (E), Carboxy (K), Carboxy (W), Carboxyethyl (K), Carboxymethyl (C), Carboxymethyl (K), Carboxymethyl (N-term), Carboxymethyl (W), Carboxymethyl:13C(2) (C), CarboxymethylDTT (C), Cation:Ag (C-term), Cation:Ag (D), Cation:Ag (E), Cation:Ca[II] (C-term), Cation:Ca[II] (D), Cation:Ca[II] (E), Cation:Cu[I] (C-term), Cation:Cu[I] (D), Cation:Cu[I] (E), Cation:Fe[II] (C-term), Cation:Fe[II] (D), Cation:Fe[II] (E), Cation:K (C-term), Cation:K (D), Cation:K (E), Cation:Li (C-term), Cation:Li (D), Cation:Li (E), Cation:Mg[II] (C-term), Cation:Mg[II] (D), Cation:Mg[II] (E), Cation:Na (C-term), Cation:Na (D), Cation:Na (E), Cation:Ni[II] (C-term), Cation:Ni[II] (D), Cation:Ni[II] (E), Cation:Zn[II] (C-term), Cation:Zn[II] (D), Cation:Zn[II] (E), Chlorination (Y), Chlorpyrifos (S), Chlorpyrifos (T), Chlorpyrifos (Y), ChromoBiotin (K), CoenzymeA (C), Crotonaldehyde (C), Crotonaldehyde (H), Crotonaldehyde (K), CuSMo (C), Cy3b-maleimide (C), CyDye-Cy3 (C), CyDye-Cy5 (C), Cyano (C), Cys->Arg (C), Cys->Dha (C), Cys->Gly (C), Cys->Oxoalanine (C), Cys->Phe (C), Cys->Ser (C), Cys->Trp (C), Cys->Tyr (C), Cys->ethylaminoAla (C), Cys->methylaminoAla (C), Cysteinyl (C), Cytopiloyne (C), Cytopiloyne (K), Cytopiloyne (N-term), Cytopiloyne (P), Cytopiloyne (R), Cytopiloyne (S), Cytopiloyne (Y), Cytopiloyne+water (C), Cytopiloyne+water (K), Cytopiloyne+water (N-term), Cytopiloyne+water (R), Cytopiloyne+water (S), Cytopiloyne+water (T), Cytopiloyne+water (Y), DAET (S), DAET (T), DFDNB (K), DFDNB (N), DFDNB (Q), DFDNB (R), DHP (C), DNPS (C), DNPS (W), DTBP (K), DTBP (N), DTBP (Q), DTBP (R), DTT_C (C), DTT_C:2H(6) (C), DTT_ST (S), DTT_ST (T), DTT_ST:2H(6) (S), DTT_ST:2H(6) (T), Dansyl (K), Dansyl (N-term), DeStreak (C), Deamidated (N), Deamidated (Q), Deamidated (R), Deamidated:18O(1) (N), Deamidated:18O(1) (Q), Decanoyl (S), Decanoyl (T), Dehydrated (D), Dehydrated (N-term C), Dehydrated (S), Dehydrated (T), Dehydrated (Y), Dehydro (C), Delta:H(1)O(-1)18O(1) (N), Delta:H(2)C(2) (H), Delta:H(2)C(2) (K), Delta:H(2)C(3) (K), Delta:H(2)C(3)O(1) (K), Delta:H(2)C(3)O(1) (R), Delta:H(2)C(5) (K), Delta:H(4)C(2) (H), Delta:H(4)C(2) (K), Delta:H(4)C(2)O(-1)S(1) (S), Delta:H(4)C(3) (H), Delta:H(4)C(3) (K), Delta:H(4)C(3)O(1) (C), Delta:H(4)C(3)O(1) (H), Delta:H(4)C(3)O(1) (K), Delta:H(4)C(6) (K), Delta:H(5)C(2) (P), Delta:H(6)C(6)O(1) (K), Delta:H(8)C(6)O(2) (K), Delta:Hg(1) (C), Delta:S(-1)Se(1) (C), Delta:S(-1)Se(1) (M), Delta:Se(1) (C), Deoxy (D), Deoxy (S), Deoxy (T), Dethiomethyl (M), Diacylglycerol (C), Dibromo (Y), Didehydro (C-term K), Didehydro (S), Didehydro (T), Didehydro (Y), Didehydroretinylidene (K), Diethyl (K), Diethyl (N-term), Dihydroxyimidazolidine (R), Diiodo (Y), Diironsubcluster (C), Diisopropylphosphate (K), Diisopropylphosphate (S), Diisopropylphosphate (T), Diisopropylphosphate (Y), Dimethyl (K), Dimethyl (N), Dimethyl (N-term), Dimethyl (R), Dimethyl:2H(4) (K), Dimethyl:2H(4) (N-term), Dimethyl:2H(4)13C(2) (K), Dimethyl:2H(4)13C(2) (N-term), Dimethyl:2H(6)13C(2) (K), Dimethyl:2H(6)13C(2) (N-term), Dimethyl:2H(6)13C(2) (R), DimethylArsino (C), DimethylamineGMBS (C), DimethylpyrroleAdduct (K), Dioxidation (C), Dioxidation (F), Dioxidation (K), Dioxidation (M), Dioxidation (P), Dioxidation (R), Dioxidation (W), Dioxidation (Y), Diphthamide (H), Dipyrrolylmethanemethyl (C), DyLight-maleimide (C), EDT-iodoacetyl-PEO-biotin (S), EDT-iodoacetyl-PEO-biotin (T), EDT-maleimide-PEO-biotin (S), EDT-maleimide-PEO-biotin (T), EQAT (C), EQAT:2H(5) (C), EQIGG (K), ESP (K), ESP (N-term), ESP:2H(10) (K), ESP:2H(10) (N-term), Ethanedithiol (S), Ethanedithiol (T), Ethanolamine (C-term), Ethanolamine (D), Ethanolamine (E), Ethanolyl (C), Ethanolyl (K), Ethanolyl (R), Ethoxyformyl (H), Ethyl (C-term), Ethyl (D), Ethyl (E), Ethyl (K), Ethyl (N-term), EthylAmide (N), EthylAmide (Q), ExacTagAmine (K), ExacTagThiol (C), FAD (C), FAD (H), FAD (Y), FMN (S), FMN (T), FMNC (C), FMNH (C), FMNH (H), FNEM (C), FP-Biotin (K), FP-Biotin (S), FP-Biotin (T), FP-Biotin (Y), FTC (C), FTC (K), FTC (P), FTC (R), FTC (S), Farnesyl (C), Fluorescein (C), Fluoro (F), Fluoro (W), Fluoro (Y), Formyl (K), Formyl (N-term), Formyl (S), Formyl (T), G-H1 (R), GIST-Quat (K), GIST-Quat (N-term), GIST-Quat:2H(3) (K), GIST-Quat:2H(3) (N-term), GIST-Quat:2H(6) (K), GIST-Quat:2H(6) (N-term), GIST-Quat:2H(9) (K), GIST-Quat:2H(9) (N-term), GalNAzBiotin (N), GalNAzBiotin (S), GalNAzBiotin (T), Galactosyl (K), GeranylGeranyl (C), Gln->Arg (Q), Gln->Glu (Q), Gln->His (Q), Gln->Leu (Q), Gln->Lys (Q), Gln->Pro (Q), Gln->pyro-Glu (N-term Q), Glu (E), Glu->Ala (E), Glu->Asp (E), Glu->Gln (E), Glu->Gly (E), Glu->Lys (E), Glu->Val (E), Glu->pyro-Glu (N-term E), GluGlu (E), GluGluGlu (E), GluGluGluGlu (E), Glucosylgalactosyl (K), Glucuronyl (S), Glutathione (C), Gly->Ala (G), Gly->Arg (G), Gly->Asp (G), Gly->Cys (G), Gly->Glu (G), Gly->Ser (G), Gly->Trp (G), Gly->Val (G), Gly-loss+Amide (C-term G), GlyGly (C), GlyGly (K), GlyGly (S), GlyGly (T), Glycerophospho (S), GlycerylPE (E), Glycosyl (P), Guanidinyl (K), HMVK (C), HNE (C), HNE (H), HNE (K), HNE+Delta:H(2) (C), HNE+Delta:H(2) (H), HNE+Delta:H(2) (K), HNE-BAHAH (C), HNE-BAHAH (H), HNE-BAHAH (K), HNE-Delta:H(2)O (C), HNE-Delta:H(2)O (H), HNE-Delta:H(2)O (K), HPG (R), Heme (C), Heme (H), Hep (K), Hep (N), Hep (Q), Hep (R), Hep (S), Hep (T), Hex (C), Hex (K), Hex (N), Hex (N-term), Hex (R), Hex (T), Hex (W), Hex (Y), Hex(1)HexNAc(1)NeuAc(1) (N), Hex(1)HexNAc(1)NeuAc(1) (S), Hex(1)HexNAc(1)NeuAc(1) (T), Hex(1)HexNAc(1)NeuAc(2) (N), Hex(1)HexNAc(1)NeuAc(2) (S), Hex(1)HexNAc(1)NeuAc(2) (T), Hex(1)HexNAc(1)dHex(1) (N), Hex(1)HexNAc(2) (N), Hex(1)HexNAc(2)Pent(1) (N), Hex(1)HexNAc(2)dHex(1) (N), Hex(1)HexNAc(2)dHex(1)Pent(1) (N), Hex(1)HexNAc(2)dHex(2) (N), Hex(2) (K), Hex(2) (R), Hex(2)HexNAc(2) (N), Hex(2)HexNAc(2)Pent(1) (N), Hex(2)HexNAc(2)dHex(1) (N), Hex(3) (N), Hex(3)HexNAc(1)Pent(1) (N), Hex(3)HexNAc(2) (N), Hex(3)HexNAc(2)P(1) (N), Hex(3)HexNAc(4) (N), Hex(4)HexNAc(4) (N), Hex(5)HexNAc(2) (N), Hex(5)HexNAc(4) (N), Hex1HexNAc1 (S), Hex1HexNAc1 (T), HexN (K), HexN (N), HexN (T), HexN (W), HexNAc (N), HexNAc (S), HexNAc (T), HexNAc(1)dHex(1) (N), HexNAc(1)dHex(2) (N), HexNAc(2) (N), HexNAc(2)dHex(1) (N), HexNAc(2)dHex(2) (N), His->Arg (H), His->Asn (H), His->Asp (H), His->Gln (H), His->Leu (H), His->Pro (H), His->Tyr (H), Hydroxycinnamyl (C), Hydroxyfarnesyl (C), Hydroxyheme (E), Hydroxymethyl (N), HydroxymethylOP (K), Hydroxytrimethyl (K), Hypusine (K), IBTP (C), ICAT-C (C), ICAT-C:13C(9) (C), ICAT-D (C), ICAT-D:2H(8) (C), ICAT-G (C), ICAT-G:2H(8) (C), ICAT-H (C), ICAT-H:13C(6) (C), ICPL (K), ICPL (N-term), ICPL:13C(6) (K), ICPL:13C(6) (N-term), ICPL:13C(6)2H(4) (K), ICPL:13C(6)2H(4) (N-term), ICPL:2H(4) (K), ICPL:2H(4) (N-term), IDEnT (C), IED-Biotin (C), IGBP (C), IGBP:13C(2) (C), IMID (K), IMID:2H(4) (K), ISD_z+2_ion (N-term), Ile->Arg (I), Ile->Asn (I), Ile->Lys (I), Ile->Met (I), Ile->Phe (I), Ile->Ser (I), Ile->Thr (I), Ile->Val (I), Iminobiotin (K), Iminobiotin (N-term), Iodo (H), Iodo (Y), IodoU-AMP (F), IodoU-AMP (W), IodoU-AMP (Y), Isopropylphospho (S), Isopropylphospho (T), Isopropylphospho (Y), LG-Hlactam-K (K), LG-Hlactam-R (R), LG-anhydrolactam (K), LG-anhydrolactam (N-term), LG-anhyropyrrole (K), LG-anhyropyrrole (N-term), LG-lactam-K (K), LG-lactam-R (R), LG-pyrrole (K), LG-pyrrole (N-term), Label:13C(1)2H(3) (M), Label:13C(1)2H(3)+Oxidation (M), Label:13C(4)15N(2)+GlyGly (K), Label:13C(5) (P), Label:13C(5)15N(1) (M), Label:13C(5)15N(1) (P), Label:13C(5)15N(1) (V), Label:13C(6) (I), Label:13C(6) (K), Label:13C(6) (L), Label:13C(6) (R), Label:13C(6)+Acetyl (K), Label:13C(6)+Dimethyl (K), Label:13C(6)+GlyGly (K), Label:13C(6)15N(1) (I), Label:13C(6)15N(1) (L), Label:13C(6)15N(2) (K), Label:13C(6)15N(2)+Acetyl (K), Label:13C(6)15N(2)+Dimethyl (K), Label:13C(6)15N(2)+GlyGly (K), Label:13C(6)15N(4) (R), Label:13C(8)15N(2) (R), Label:13C(9) (F), Label:13C(9) (Y), Label:13C(9)+Phospho (Y), Label:13C(9)15N(1) (F), Label:15N(1) (A), Label:15N(1) (C), Label:15N(1) (D), Label:15N(1) (E), Label:15N(1) (F), Label:15N(1) (G), Label:15N(1) (I), Label:15N(1) (L), Label:15N(1) (M), Label:15N(1) (P), Label:15N(1) (S), Label:15N(1) (T), Label:15N(1) (V), Label:15N(1) (Y), Label:15N(2) (K), Label:15N(2) (N), Label:15N(2) (Q), Label:15N(2) (W), Label:15N(2)2H(9) (K), Label:15N(3) (H), Label:15N(4) (R), Label:18O(1) (C-term), Label:18O(1) (S), Label:18O(1) (T), Label:18O(1) (Y), Label:18O(2) (C-term), Label:2H(3) (L), Label:2H(4) (F), Label:2H(4) (K), Label:2H(4) (Y), Label:2H(4)+Acetyl (K), Label:2H(4)+GlyGly (K), Label:2H(9)13C(6)15N(2) (K), Leu->Arg (L), Leu->Gln (L), Leu->His (L), Leu->Met (L), Leu->MetOx (L), Leu->Phe (L), Leu->Pro (L), Leu->Ser (L), Leu->Trp (L), Leu->Val (L), LeuArgGlyGly (K), Lipoyl (K), Lys->Allysine (K), Lys->AminoadipicAcid (K), Lys->Arg (K), Lys->Asn (K), Lys->CamCys (K), Lys->Gln (K), Lys->Glu (K), Lys->Ile (K), Lys->Met (K), Lys->MetOx (K), Lys->Thr (K), Lysbiotinhydrazide (K), MDCC (C), MG-H1 (R), MTSL (C), Maleimide-PEO2-Biotin (C), Malonyl (C), Malonyl (S), Menadione (C), Menadione (K), Menadione-HQ (C), Menadione-HQ (K), MercaptoEthanol (S), MercaptoEthanol (T), Met->Aha (M), Met->Arg (M), Met->Hpg (M), Met->Hse (C-term M), Met->Hsl (C-term M), Met->Ile (M), Met->Leu (M), Met->Lys (M), Met->Thr (M), Met->Val (M), Methyl (C), Methyl (C-term), Methyl (D), Methyl (E), Methyl (H), Methyl (I), Methyl (K), Methyl (L), Methyl (N), Methyl (N-term), Methyl (Q), Methyl (R), Methyl (S), Methyl (T), Methyl+Acetyl:2H(3) (K), Methyl+Deamidated (N), Methyl+Deamidated (Q), Methyl-PEO12-Maleimide (C), Methyl:2H(2) (K), Methyl:2H(3) (C-term), Methyl:2H(3) (D), Methyl:2H(3) (E), Methyl:2H(3)13C(1) (R), Methylamine (S), Methylamine (T), Methylmalonylation (S), Methylphosphonate (S), Methylphosphonate (T), Methylphosphonate (Y), Methylpyrroline (K), Methylthio (C), Methylthio (D), Methylthio (N), Molybdopterin (C), MolybdopterinGD (C), MolybdopterinGD (D), MolybdopterinGD+Delta:S(-1)Se(1) (C), Myristoyl (C), Myristoyl (K), Myristoyl (N-term G), NA-LNO2 (C), NA-LNO2 (H), NA-OA-NO2 (C), NA-OA-NO2 (H), NBS (W), NBS:13C(6) (W), NDA (K), NDA (N-term), NEIAA (C), NEIAA (Y), NEIAA:2H(5) (C), NEIAA:2H(5) (Y), NEM:2H(5) (C), NHS-LC-Biotin (K), NHS-LC-Biotin (N-term), NIC (N-term), NIPCAM (C), NO_SMX_SEMD (C), NO_SMX_SIMD (C), NO_SMX_SMCT (C), Nethylmaleimide (C), Nethylmaleimide+water (C), Nethylmaleimide+water (K), Nitro (W), Nitro (Y), Nitrosyl (C), Nmethylmaleimide (C), Nmethylmaleimide (K), Nmethylmaleimide+water (C), O-Diethylphosphate (C), O-Diethylphosphate (H), O-Diethylphosphate (K), O-Diethylphosphate (S), O-Diethylphosphate (T), O-Diethylphosphate (Y), O-Dimethylphosphate (S), O-Dimethylphosphate (T), O-Dimethylphosphate (Y), O-Ethylphosphate (S), O-Ethylphosphate (T), O-Ethylphosphate (Y), O-Isopropylmethylphosphonate (S), O-Isopropylmethylphosphonate (T), O-Isopropylmethylphosphonate (Y), O-Methylphosphate (S), O-Methylphosphate (T), O-Methylphosphate (Y), O-pinacolylmethylphosphonate (H), O-pinacolylmethylphosphonate (K), O-pinacolylmethylphosphonate (S), O-pinacolylmethylphosphonate (T), O-pinacolylmethylphosphonate (Y), Octanoyl (S), Octanoyl (T), OxArgBiotin (R), OxArgBiotinRed (R), OxLysBiotin (K), OxLysBiotinRed (K), OxProBiotin (P), OxProBiotinRed (P), Oxidation (C), Oxidation (C-term G), Oxidation (D), Oxidation (F), Oxidation (H), Oxidation (K), Oxidation (M), Oxidation (N), Oxidation (P), Oxidation (R), Oxidation (W), Oxidation (Y), PEITC (C), PEITC (K), PEITC (N-term), PEO-Iodoacetyl-LC-Biotin (C), PET (S), PET (T), PGA1-biotin (C), Palmitoleyl (C), Palmitoleyl (S), Palmitoleyl (T), Palmitoyl (C), Palmitoyl (K), Palmitoyl (S), Palmitoyl (T), Pentylamine (Q), PentylamineBiotin (Q), Phe->CamCys (F), Phe->Cys (F), Phe->Ile (F), Phe->Ser (F), Phe->Tyr (F), Phe->Val (F), Phenylisocyanate (N-term), Phenylisocyanate:2H(5) (N-term), Phospho (C), Phospho (D), Phospho (H), Phospho (R), Phospho (S), Phospho (T), Phospho (Y), PhosphoHex (S), PhosphoHexNAc (S), PhosphoUridine (H), PhosphoUridine (Y), Phosphoadenosine (H), Phosphoadenosine (K), Phosphoadenosine (T), Phosphoadenosine (Y), Phosphoguanosine (H), Phosphoguanosine (K), Phosphopantetheine (S), Phosphopropargyl (S), Phosphopropargyl (T), Phosphopropargyl (Y), PhosphoribosyldephosphoCoA (S), Phycocyanobilin (C), Phycoerythrobilin (C), Phytochromobilin (C), Piperidine (K), Piperidine (N-term), Pro->Ala (P), Pro->Arg (P), Pro->Gln (P), Pro->His (P), Pro->Leu (P), Pro->Pyrrolidinone (P), Pro->Pyrrolidone (P), Pro->Ser (P), Pro->Thr (P), Pro->pyro-Glu (P), Propargylamine (C-term), Propargylamine (D), Propargylamine (E), Propionamide (C), Propionamide:2H(3) (C), Propionyl (K), Propionyl (N-term), Propionyl (S), Propionyl:13C(3) (K), Propionyl:13C(3) (N-term), PropylNAGthiazoline (C), Puromycin (C-term), PyMIC (N-term), PyridoxalPhosphate (K), Pyridylacetyl (K), Pyridylacetyl (N-term), Pyridylethyl (C), Pyro-carbamidomethyl (N-term C), PyruvicAcidIminyl (K), QAT (C), QAT:2H(3) (C), QEQTGG (K), QQQTGG (K), Quinone (W), Quinone (Y), RNPXlink1 (C), RNPXlink2 (F), RNPXlink2 (K), RNPXlink2 (L), RNPXlink3 (C), RNPXlink3 (F), RNPXlink4 (C), RNPXlink5 (F), RNPXlink5 (Y), Retinylidene (K), SMA (K), SMA (N-term), SMCC-maleimide (C), SPITC (K), SPITC (N-term), SPITC:13C(6) (K), SPITC:13C(6) (N-term), SUMO2135 (K), SUMO3549 (K), Ser->Ala (S), Ser->Arg (S), Ser->Asn (S), Ser->Cys (S), Ser->Gly (S), Ser->Ile (S), Ser->Phe (S), Ser->Pro (S), Ser->Thr (S), Ser->Trp (S), Ser->Tyr (S), Succinyl (K), Succinyl (N-term), Succinyl:13C(4) (K), Succinyl:13C(4) (N-term), Succinyl:2H(4) (K), Succinyl:2H(4) (N-term), SulfanilicAcid (C-term), SulfanilicAcid (D), SulfanilicAcid (E), SulfanilicAcid:13C(6) (C-term), SulfanilicAcid:13C(6) (D), SulfanilicAcid:13C(6) (E), Sulfide (C), Sulfide (D), Sulfo (C), Sulfo (S), Sulfo (T), Sulfo (Y), Sulfo-NHS-LC-LC-Biotin (K), Sulfo-NHS-LC-LC-Biotin (N-term), SulfoGMBS (C), TMAB (K), TMAB (N-term), TMAB:2H(9) (K), TMAB:2H(9) (N-term), TMPP-Ac (N-term), TMT (K), TMT (N-term), TMT2plex (K), TMT2plex (N-term), TMT6plex (K), TMT6plex (N-term), TNBS (K), TNBS (N-term), Thioacyl (K), Thioacyl (N-term), Thiophos-S-S-biotin (S), Thiophos-S-S-biotin (T), Thiophos-S-S-biotin (Y), Thiophospho (S), Thiophospho (T), Thiophospho (Y), Thr->Ala (T), Thr->Arg (T), Thr->Asn (T), Thr->Ile (T), Thr->Lys (T), Thr->Met (T), Thr->Pro (T), Thr->Ser (T), Thrbiotinhydrazide (T), Thyroxine (Y), Triiodo (Y), Triiodothyronine (Y), Trimethyl (K), Trimethyl (R), Trioxidation (C), Trp->Arg (W), Trp->Cys (W), Trp->Gly (W), Trp->Hydroxykynurenin (W), Trp->Kynurenin (W), Trp->Leu (W), Trp->Oxolactone (W), Trp->Ser (W), Tyr->Asn (Y), Tyr->Asp (Y), Tyr->Cys (Y), Tyr->Dha (Y), Tyr->His (Y), Tyr->Phe (Y), Tyr->Ser (Y), VFQQQTGG (K), VIEVYQEQTGG (K), Val->Ala (V), Val->Asp (V), Val->Glu (V), Val->Gly (V), Val->Ile (V), Val->Met (V), Val->Phe (V), Xlink:B10621 (C), Xlink:DMP (K), Xlink:DMP-s (K), Xlink:SSD (K), ZGB (K), ZGB (N-term), a-type-ion (C-term), cGMP (C), cGMP (S), cGMP+RMP-loss (C), cGMP+RMP-loss (S), cysTMT (C), cysTMT6plex (C), dHex (S), dHex (T), dHex(1)Hex(3)HexNAc(4) (N), dHex(1)Hex(4)HexNAc(4) (N), dHex(1)Hex(5)HexNAc(4) (N), dNIC (N-term), dichlorination (Y), ethylamino (S), ethylamino (T), glucosone (R), iTRAQ4plex (K), iTRAQ4plex (N-term), iTRAQ4plex (Y), iTRAQ4plex114 (K), iTRAQ4plex114 (N-term), iTRAQ4plex114 (Y), iTRAQ4plex115 (K), iTRAQ4plex115 (N-term), iTRAQ4plex115 (Y), iTRAQ8plex (K), iTRAQ8plex (N-term), iTRAQ8plex (Y), iTRAQ8plex:13C(6)15N(2) (K), iTRAQ8plex:13C(6)15N(2) (N-term), iTRAQ8plex:13C(6)15N(2) (Y), lapachenole (C), mTRAQ (K), mTRAQ (N-term), mTRAQ (Y), mTRAQ:13C(3)15N(1) (K), mTRAQ:13C(3)15N(1) (N-term), mTRAQ:13C(3)15N(1) (Y), maleimide (C), maleimide (K), maleimide3 (C), maleimide3 (K), maleimide5 (C), maleimide5 (K), probiotinhydrazide (P), pyrophospho (S), pyrophospho (T), sulfo+amino (Y), thioacylPA (K), trifluoro (L)</td><td style="vertical-align:top">fixed modifications, specified using UniMod (www.unimod.org) terms, e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'</td>
</tr>
<tr>
<td style="vertical-align:top"><b>variable_modifications</b></td>
<td style="vertical-align:top">string list</td><td style="vertical-align:top">[]</td>
<td style="vertical-align:top">15dB-biotin (C), 2-succinyl (C), 2HPG (R), 3-deoxyglucosone (R), 3sulfo (N-term), 4-ONE (C), 4-ONE (H), 4-ONE (K), 4-ONE+Delta:H(-2)O(-1) (C), 4-ONE+Delta:H(-2)O(-1) (H), 4-ONE+Delta:H(-2)O(-1) (K), 4AcAllylGal (C), ADP-Ribosyl (C), ADP-Ribosyl (E), ADP-Ribosyl (N), ADP-Ribosyl (R), ADP-Ribosyl (S), AEBS (H), AEBS (K), AEBS (S), AEBS (Y), AEC-MAEC (S), AEC-MAEC (T), AEC-MAEC:2H(4) (S), AEC-MAEC:2H(4) (T), AROD (C), AccQTag (K), AccQTag (N-term), Acetyl (C), Acetyl (H), Acetyl (K), Acetyl (N-term), Acetyl (S), Acetyl (T), Acetyl (Y), Acetyl:2H(3) (K), Acetyl:2H(3) (N-term), Ala->Asp (A), Ala->Glu (A), Ala->Gly (A), Ala->Pro (A), Ala->Ser (A), Ala->Thr (A), Ala->Val (A), Amidated (C-term), Amidine (K), Amidine (N-term), Amidino (C), Amino (Y), Ammonia-loss (N), Ammonia-loss (N-term C), Ammonium (C-term), Ammonium (D), Ammonium (E), Archaeol (C), Arg->Cys (R), Arg->Gln (R), Arg->GluSA (R), Arg->Gly (R), Arg->His (R), Arg->Ile (R), Arg->Lys (R), Arg->Met (R), Arg->Npo (R), Arg->Orn (R), Arg->Pro (R), Arg->Ser (R), Arg->Thr (R), Arg->Trp (R), Arg2PG (R), Argbiotinhydrazide (R), Asn->Asp (N), Asn->His (N), Asn->Ile (N), Asn->Lys (N), Asn->Ser (N), Asn->Thr (N), Asn->Tyr (N), Asp->Ala (D), Asp->Asn (D), Asp->Glu (D), Asp->Gly (D), Asp->His (D), Asp->Tyr (D), Asp->Val (D), Atto495Maleimide (C), BADGE (C), BDMAPP (H), BDMAPP (K), BDMAPP (W), BDMAPP (Y), BHAc (K), BHT (C), BHT (H), BHT (K), BHTOH (C), BHTOH (H), BHTOH (K), BITC (C), BITC (K), BITC (N-term), BMOE (C), Bacillosamine (N), Benzoyl (K), Benzoyl (N-term), Biotin (K), Biotin (N-term), Biotin-HPDP (C), Biotin-PEG-PRA (M), Biotin-PEO-Amine (D), Biotin-PEO-Amine (E), Biotin-PEO4-hydrazide (C-term), Biotin-maleimide (C), Biotin-phenacyl (C), Biotin-phenacyl (H), Biotin-phenacyl (S), BisANS (K), Bodipy (C), Bromo (F), Bromo (H), Bromo (W), Bromobimane (C), C8-QAT (K), C8-QAT (N-term), CAF (N-term), CAMthiopropanoyl (K), CHDH (D), CLIP_TRAQ_1 (K), CLIP_TRAQ_1 (N-term), CLIP_TRAQ_1 (Y), CLIP_TRAQ_2 (K), CLIP_TRAQ_2 (N-term), CLIP_TRAQ_2 (Y), CLIP_TRAQ_3 (K), CLIP_TRAQ_3 (N-term), CLIP_TRAQ_3 (Y), CLIP_TRAQ_4 (K), CLIP_TRAQ_4 (N-term), CLIP_TRAQ_4 (Y), Can-FP-biotin (S), Can-FP-biotin (T), Can-FP-biotin (Y), Carbamidomethyl (C), Carbamidomethyl (D), Carbamidomethyl (E), Carbamidomethyl (H), Carbamidomethyl (K), Carbamidomethyl (N-term), CarbamidomethylDTT (C), Carbamyl (C), Carbamyl (K), Carbamyl (M), Carbamyl (N-term), Carbamyl (R), Carbamyl (S), Carbamyl (T), Carbamyl (Y), Carbofuran (S), Carboxy (D), Carboxy (E), Carboxy (K), Carboxy (W), Carboxyethyl (K), Carboxymethyl (C), Carboxymethyl (K), Carboxymethyl (N-term), Carboxymethyl (W), Carboxymethyl:13C(2) (C), CarboxymethylDTT (C), Cation:Ag (C-term), Cation:Ag (D), Cation:Ag (E), Cation:Ca[II] (C-term), Cation:Ca[II] (D), Cation:Ca[II] (E), Cation:Cu[I] (C-term), Cation:Cu[I] (D), Cation:Cu[I] (E), Cation:Fe[II] (C-term), Cation:Fe[II] (D), Cation:Fe[II] (E), Cation:K (C-term), Cation:K (D), Cation:K (E), Cation:Li (C-term), Cation:Li (D), Cation:Li (E), Cation:Mg[II] (C-term), Cation:Mg[II] (D), Cation:Mg[II] (E), Cation:Na (C-term), Cation:Na (D), Cation:Na (E), Cation:Ni[II] (C-term), Cation:Ni[II] (D), Cation:Ni[II] (E), Cation:Zn[II] (C-term), Cation:Zn[II] (D), Cation:Zn[II] (E), Chlorination (Y), Chlorpyrifos (S), Chlorpyrifos (T), Chlorpyrifos (Y), ChromoBiotin (K), CoenzymeA (C), Crotonaldehyde (C), Crotonaldehyde (H), Crotonaldehyde (K), CuSMo (C), Cy3b-maleimide (C), CyDye-Cy3 (C), CyDye-Cy5 (C), Cyano (C), Cys->Arg (C), Cys->Dha (C), Cys->Gly (C), Cys->Oxoalanine (C), Cys->Phe (C), Cys->Ser (C), Cys->Trp (C), Cys->Tyr (C), Cys->ethylaminoAla (C), Cys->methylaminoAla (C), Cysteinyl (C), Cytopiloyne (C), Cytopiloyne (K), Cytopiloyne (N-term), Cytopiloyne (P), Cytopiloyne (R), Cytopiloyne (S), Cytopiloyne (Y), Cytopiloyne+water (C), Cytopiloyne+water (K), Cytopiloyne+water (N-term), Cytopiloyne+water (R), Cytopiloyne+water (S), Cytopiloyne+water (T), Cytopiloyne+water (Y), DAET (S), DAET (T), DFDNB (K), DFDNB (N), DFDNB (Q), DFDNB (R), DHP (C), DNPS (C), DNPS (W), DTBP (K), DTBP (N), DTBP (Q), DTBP (R), DTT_C (C), DTT_C:2H(6) (C), DTT_ST (S), DTT_ST (T), DTT_ST:2H(6) (S), DTT_ST:2H(6) (T), Dansyl (K), Dansyl (N-term), DeStreak (C), Deamidated (N), Deamidated (Q), Deamidated (R), Deamidated:18O(1) (N), Deamidated:18O(1) (Q), Decanoyl (S), Decanoyl (T), Dehydrated (D), Dehydrated (N-term C), Dehydrated (S), Dehydrated (T), Dehydrated (Y), Dehydro (C), Delta:H(1)O(-1)18O(1) (N), Delta:H(2)C(2) (H), Delta:H(2)C(2) (K), Delta:H(2)C(3) (K), Delta:H(2)C(3)O(1) (K), Delta:H(2)C(3)O(1) (R), Delta:H(2)C(5) (K), Delta:H(4)C(2) (H), Delta:H(4)C(2) (K), Delta:H(4)C(2)O(-1)S(1) (S), Delta:H(4)C(3) (H), Delta:H(4)C(3) (K), Delta:H(4)C(3)O(1) (C), Delta:H(4)C(3)O(1) (H), Delta:H(4)C(3)O(1) (K), Delta:H(4)C(6) (K), Delta:H(5)C(2) (P), Delta:H(6)C(6)O(1) (K), Delta:H(8)C(6)O(2) (K), Delta:Hg(1) (C), Delta:S(-1)Se(1) (C), Delta:S(-1)Se(1) (M), Delta:Se(1) (C), Deoxy (D), Deoxy (S), Deoxy (T), Dethiomethyl (M), Diacylglycerol (C), Dibromo (Y), Didehydro (C-term K), Didehydro (S), Didehydro (T), Didehydro (Y), Didehydroretinylidene (K), Diethyl (K), Diethyl (N-term), Dihydroxyimidazolidine (R), Diiodo (Y), Diironsubcluster (C), Diisopropylphosphate (K), Diisopropylphosphate (S), Diisopropylphosphate (T), Diisopropylphosphate (Y), Dimethyl (K), Dimethyl (N), Dimethyl (N-term), Dimethyl (R), Dimethyl:2H(4) (K), Dimethyl:2H(4) (N-term), Dimethyl:2H(4)13C(2) (K), Dimethyl:2H(4)13C(2) (N-term), Dimethyl:2H(6)13C(2) (K), Dimethyl:2H(6)13C(2) (N-term), Dimethyl:2H(6)13C(2) (R), DimethylArsino (C), DimethylamineGMBS (C), DimethylpyrroleAdduct (K), Dioxidation (C), Dioxidation (F), Dioxidation (K), Dioxidation (M), Dioxidation (P), Dioxidation (R), Dioxidation (W), Dioxidation (Y), Diphthamide (H), Dipyrrolylmethanemethyl (C), DyLight-maleimide (C), EDT-iodoacetyl-PEO-biotin (S), EDT-iodoacetyl-PEO-biotin (T), EDT-maleimide-PEO-biotin (S), EDT-maleimide-PEO-biotin (T), EQAT (C), EQAT:2H(5) (C), EQIGG (K), ESP (K), ESP (N-term), ESP:2H(10) (K), ESP:2H(10) (N-term), Ethanedithiol (S), Ethanedithiol (T), Ethanolamine (C-term), Ethanolamine (D), Ethanolamine (E), Ethanolyl (C), Ethanolyl (K), Ethanolyl (R), Ethoxyformyl (H), Ethyl (C-term), Ethyl (D), Ethyl (E), Ethyl (K), Ethyl (N-term), EthylAmide (N), EthylAmide (Q), ExacTagAmine (K), ExacTagThiol (C), FAD (C), FAD (H), FAD (Y), FMN (S), FMN (T), FMNC (C), FMNH (C), FMNH (H), FNEM (C), FP-Biotin (K), FP-Biotin (S), FP-Biotin (T), FP-Biotin (Y), FTC (C), FTC (K), FTC (P), FTC (R), FTC (S), Farnesyl (C), Fluorescein (C), Fluoro (F), Fluoro (W), Fluoro (Y), Formyl (K), Formyl (N-term), Formyl (S), Formyl (T), G-H1 (R), GIST-Quat (K), GIST-Quat (N-term), GIST-Quat:2H(3) (K), GIST-Quat:2H(3) (N-term), GIST-Quat:2H(6) (K), GIST-Quat:2H(6) (N-term), GIST-Quat:2H(9) (K), GIST-Quat:2H(9) (N-term), GalNAzBiotin (N), GalNAzBiotin (S), GalNAzBiotin (T), Galactosyl (K), GeranylGeranyl (C), Gln->Arg (Q), Gln->Glu (Q), Gln->His (Q), Gln->Leu (Q), Gln->Lys (Q), Gln->Pro (Q), Gln->pyro-Glu (N-term Q), Glu (E), Glu->Ala (E), Glu->Asp (E), Glu->Gln (E), Glu->Gly (E), Glu->Lys (E), Glu->Val (E), Glu->pyro-Glu (N-term E), GluGlu (E), GluGluGlu (E), GluGluGluGlu (E), Glucosylgalactosyl (K), Glucuronyl (S), Glutathione (C), Gly->Ala (G), Gly->Arg (G), Gly->Asp (G), Gly->Cys (G), Gly->Glu (G), Gly->Ser (G), Gly->Trp (G), Gly->Val (G), Gly-loss+Amide (C-term G), GlyGly (C), GlyGly (K), GlyGly (S), GlyGly (T), Glycerophospho (S), GlycerylPE (E), Glycosyl (P), Guanidinyl (K), HMVK (C), HNE (C), HNE (H), HNE (K), HNE+Delta:H(2) (C), HNE+Delta:H(2) (H), HNE+Delta:H(2) (K), HNE-BAHAH (C), HNE-BAHAH (H), HNE-BAHAH (K), HNE-Delta:H(2)O (C), HNE-Delta:H(2)O (H), HNE-Delta:H(2)O (K), HPG (R), Heme (C), Heme (H), Hep (K), Hep (N), Hep (Q), Hep (R), Hep (S), Hep (T), Hex (C), Hex (K), Hex (N), Hex (N-term), Hex (R), Hex (T), Hex (W), Hex (Y), Hex(1)HexNAc(1)NeuAc(1) (N), Hex(1)HexNAc(1)NeuAc(1) (S), Hex(1)HexNAc(1)NeuAc(1) (T), Hex(1)HexNAc(1)NeuAc(2) (N), Hex(1)HexNAc(1)NeuAc(2) (S), Hex(1)HexNAc(1)NeuAc(2) (T), Hex(1)HexNAc(1)dHex(1) (N), Hex(1)HexNAc(2) (N), Hex(1)HexNAc(2)Pent(1) (N), Hex(1)HexNAc(2)dHex(1) (N), Hex(1)HexNAc(2)dHex(1)Pent(1) (N), Hex(1)HexNAc(2)dHex(2) (N), Hex(2) (K), Hex(2) (R), Hex(2)HexNAc(2) (N), Hex(2)HexNAc(2)Pent(1) (N), Hex(2)HexNAc(2)dHex(1) (N), Hex(3) (N), Hex(3)HexNAc(1)Pent(1) (N), Hex(3)HexNAc(2) (N), Hex(3)HexNAc(2)P(1) (N), Hex(3)HexNAc(4) (N), Hex(4)HexNAc(4) (N), Hex(5)HexNAc(2) (N), Hex(5)HexNAc(4) (N), Hex1HexNAc1 (S), Hex1HexNAc1 (T), HexN (K), HexN (N), HexN (T), HexN (W), HexNAc (N), HexNAc (S), HexNAc (T), HexNAc(1)dHex(1) (N), HexNAc(1)dHex(2) (N), HexNAc(2) (N), HexNAc(2)dHex(1) (N), HexNAc(2)dHex(2) (N), His->Arg (H), His->Asn (H), His->Asp (H), His->Gln (H), His->Leu (H), His->Pro (H), His->Tyr (H), Hydroxycinnamyl (C), Hydroxyfarnesyl (C), Hydroxyheme (E), Hydroxymethyl (N), HydroxymethylOP (K), Hydroxytrimethyl (K), Hypusine (K), IBTP (C), ICAT-C (C), ICAT-C:13C(9) (C), ICAT-D (C), ICAT-D:2H(8) (C), ICAT-G (C), ICAT-G:2H(8) (C), ICAT-H (C), ICAT-H:13C(6) (C), ICPL (K), ICPL (N-term), ICPL:13C(6) (K), ICPL:13C(6) (N-term), ICPL:13C(6)2H(4) (K), ICPL:13C(6)2H(4) (N-term), ICPL:2H(4) (K), ICPL:2H(4) (N-term), IDEnT (C), IED-Biotin (C), IGBP (C), IGBP:13C(2) (C), IMID (K), IMID:2H(4) (K), ISD_z+2_ion (N-term), Ile->Arg (I), Ile->Asn (I), Ile->Lys (I), Ile->Met (I), Ile->Phe (I), Ile->Ser (I), Ile->Thr (I), Ile->Val (I), Iminobiotin (K), Iminobiotin (N-term), Iodo (H), Iodo (Y), IodoU-AMP (F), IodoU-AMP (W), IodoU-AMP (Y), Isopropylphospho (S), Isopropylphospho (T), Isopropylphospho (Y), LG-Hlactam-K (K), LG-Hlactam-R (R), LG-anhydrolactam (K), LG-anhydrolactam (N-term), LG-anhyropyrrole (K), LG-anhyropyrrole (N-term), LG-lactam-K (K), LG-lactam-R (R), LG-pyrrole (K), LG-pyrrole (N-term), Label:13C(1)2H(3) (M), Label:13C(1)2H(3)+Oxidation (M), Label:13C(4)15N(2)+GlyGly (K), Label:13C(5) (P), Label:13C(5)15N(1) (M), Label:13C(5)15N(1) (P), Label:13C(5)15N(1) (V), Label:13C(6) (I), Label:13C(6) (K), Label:13C(6) (L), Label:13C(6) (R), Label:13C(6)+Acetyl (K), Label:13C(6)+Dimethyl (K), Label:13C(6)+GlyGly (K), Label:13C(6)15N(1) (I), Label:13C(6)15N(1) (L), Label:13C(6)15N(2) (K), Label:13C(6)15N(2)+Acetyl (K), Label:13C(6)15N(2)+Dimethyl (K), Label:13C(6)15N(2)+GlyGly (K), Label:13C(6)15N(4) (R), Label:13C(8)15N(2) (R), Label:13C(9) (F), Label:13C(9) (Y), Label:13C(9)+Phospho (Y), Label:13C(9)15N(1) (F), Label:15N(1) (A), Label:15N(1) (C), Label:15N(1) (D), Label:15N(1) (E), Label:15N(1) (F), Label:15N(1) (G), Label:15N(1) (I), Label:15N(1) (L), Label:15N(1) (M), Label:15N(1) (P), Label:15N(1) (S), Label:15N(1) (T), Label:15N(1) (V), Label:15N(1) (Y), Label:15N(2) (K), Label:15N(2) (N), Label:15N(2) (Q), Label:15N(2) (W), Label:15N(2)2H(9) (K), Label:15N(3) (H), Label:15N(4) (R), Label:18O(1) (C-term), Label:18O(1) (S), Label:18O(1) (T), Label:18O(1) (Y), Label:18O(2) (C-term), Label:2H(3) (L), Label:2H(4) (F), Label:2H(4) (K), Label:2H(4) (Y), Label:2H(4)+Acetyl (K), Label:2H(4)+GlyGly (K), Label:2H(9)13C(6)15N(2) (K), Leu->Arg (L), Leu->Gln (L), Leu->His (L), Leu->Met (L), Leu->MetOx (L), Leu->Phe (L), Leu->Pro (L), Leu->Ser (L), Leu->Trp (L), Leu->Val (L), LeuArgGlyGly (K), Lipoyl (K), Lys->Allysine (K), Lys->AminoadipicAcid (K), Lys->Arg (K), Lys->Asn (K), Lys->CamCys (K), Lys->Gln (K), Lys->Glu (K), Lys->Ile (K), Lys->Met (K), Lys->MetOx (K), Lys->Thr (K), Lysbiotinhydrazide (K), MDCC (C), MG-H1 (R), MTSL (C), Maleimide-PEO2-Biotin (C), Malonyl (C), Malonyl (S), Menadione (C), Menadione (K), Menadione-HQ (C), Menadione-HQ (K), MercaptoEthanol (S), MercaptoEthanol (T), Met->Aha (M), Met->Arg (M), Met->Hpg (M), Met->Hse (C-term M), Met->Hsl (C-term M), Met->Ile (M), Met->Leu (M), Met->Lys (M), Met->Thr (M), Met->Val (M), Methyl (C), Methyl (C-term), Methyl (D), Methyl (E), Methyl (H), Methyl (I), Methyl (K), Methyl (L), Methyl (N), Methyl (N-term), Methyl (Q), Methyl (R), Methyl (S), Methyl (T), Methyl+Acetyl:2H(3) (K), Methyl+Deamidated (N), Methyl+Deamidated (Q), Methyl-PEO12-Maleimide (C), Methyl:2H(2) (K), Methyl:2H(3) (C-term), Methyl:2H(3) (D), Methyl:2H(3) (E), Methyl:2H(3)13C(1) (R), Methylamine (S), Methylamine (T), Methylmalonylation (S), Methylphosphonate (S), Methylphosphonate (T), Methylphosphonate (Y), Methylpyrroline (K), Methylthio (C), Methylthio (D), Methylthio (N), Molybdopterin (C), MolybdopterinGD (C), MolybdopterinGD (D), MolybdopterinGD+Delta:S(-1)Se(1) (C), Myristoyl (C), Myristoyl (K), Myristoyl (N-term G), NA-LNO2 (C), NA-LNO2 (H), NA-OA-NO2 (C), NA-OA-NO2 (H), NBS (W), NBS:13C(6) (W), NDA (K), NDA (N-term), NEIAA (C), NEIAA (Y), NEIAA:2H(5) (C), NEIAA:2H(5) (Y), NEM:2H(5) (C), NHS-LC-Biotin (K), NHS-LC-Biotin (N-term), NIC (N-term), NIPCAM (C), NO_SMX_SEMD (C), NO_SMX_SIMD (C), NO_SMX_SMCT (C), Nethylmaleimide (C), Nethylmaleimide+water (C), Nethylmaleimide+water (K), Nitro (W), Nitro (Y), Nitrosyl (C), Nmethylmaleimide (C), Nmethylmaleimide (K), Nmethylmaleimide+water (C), O-Diethylphosphate (C), O-Diethylphosphate (H), O-Diethylphosphate (K), O-Diethylphosphate (S), O-Diethylphosphate (T), O-Diethylphosphate (Y), O-Dimethylphosphate (S), O-Dimethylphosphate (T), O-Dimethylphosphate (Y), O-Ethylphosphate (S), O-Ethylphosphate (T), O-Ethylphosphate (Y), O-Isopropylmethylphosphonate (S), O-Isopropylmethylphosphonate (T), O-Isopropylmethylphosphonate (Y), O-Methylphosphate (S), O-Methylphosphate (T), O-Methylphosphate (Y), O-pinacolylmethylphosphonate (H), O-pinacolylmethylphosphonate (K), O-pinacolylmethylphosphonate (S), O-pinacolylmethylphosphonate (T), O-pinacolylmethylphosphonate (Y), Octanoyl (S), Octanoyl (T), OxArgBiotin (R), OxArgBiotinRed (R), OxLysBiotin (K), OxLysBiotinRed (K), OxProBiotin (P), OxProBiotinRed (P), Oxidation (C), Oxidation (C-term G), Oxidation (D), Oxidation (F), Oxidation (H), Oxidation (K), Oxidation (M), Oxidation (N), Oxidation (P), Oxidation (R), Oxidation (W), Oxidation (Y), PEITC (C), PEITC (K), PEITC (N-term), PEO-Iodoacetyl-LC-Biotin (C), PET (S), PET (T), PGA1-biotin (C), Palmitoleyl (C), Palmitoleyl (S), Palmitoleyl (T), Palmitoyl (C), Palmitoyl (K), Palmitoyl (S), Palmitoyl (T), Pentylamine (Q), PentylamineBiotin (Q), Phe->CamCys (F), Phe->Cys (F), Phe->Ile (F), Phe->Ser (F), Phe->Tyr (F), Phe->Val (F), Phenylisocyanate (N-term), Phenylisocyanate:2H(5) (N-term), Phospho (C), Phospho (D), Phospho (H), Phospho (R), Phospho (S), Phospho (T), Phospho (Y), PhosphoHex (S), PhosphoHexNAc (S), PhosphoUridine (H), PhosphoUridine (Y), Phosphoadenosine (H), Phosphoadenosine (K), Phosphoadenosine (T), Phosphoadenosine (Y), Phosphoguanosine (H), Phosphoguanosine (K), Phosphopantetheine (S), Phosphopropargyl (S), Phosphopropargyl (T), Phosphopropargyl (Y), PhosphoribosyldephosphoCoA (S), Phycocyanobilin (C), Phycoerythrobilin (C), Phytochromobilin (C), Piperidine (K), Piperidine (N-term), Pro->Ala (P), Pro->Arg (P), Pro->Gln (P), Pro->His (P), Pro->Leu (P), Pro->Pyrrolidinone (P), Pro->Pyrrolidone (P), Pro->Ser (P), Pro->Thr (P), Pro->pyro-Glu (P), Propargylamine (C-term), Propargylamine (D), Propargylamine (E), Propionamide (C), Propionamide:2H(3) (C), Propionyl (K), Propionyl (N-term), Propionyl (S), Propionyl:13C(3) (K), Propionyl:13C(3) (N-term), PropylNAGthiazoline (C), Puromycin (C-term), PyMIC (N-term), PyridoxalPhosphate (K), Pyridylacetyl (K), Pyridylacetyl (N-term), Pyridylethyl (C), Pyro-carbamidomethyl (N-term C), PyruvicAcidIminyl (K), QAT (C), QAT:2H(3) (C), QEQTGG (K), QQQTGG (K), Quinone (W), Quinone (Y), RNPXlink1 (C), RNPXlink2 (F), RNPXlink2 (K), RNPXlink2 (L), RNPXlink3 (C), RNPXlink3 (F), RNPXlink4 (C), RNPXlink5 (F), RNPXlink5 (Y), Retinylidene (K), SMA (K), SMA (N-term), SMCC-maleimide (C), SPITC (K), SPITC (N-term), SPITC:13C(6) (K), SPITC:13C(6) (N-term), SUMO2135 (K), SUMO3549 (K), Ser->Ala (S), Ser->Arg (S), Ser->Asn (S), Ser->Cys (S), Ser->Gly (S), Ser->Ile (S), Ser->Phe (S), Ser->Pro (S), Ser->Thr (S), Ser->Trp (S), Ser->Tyr (S), Succinyl (K), Succinyl (N-term), Succinyl:13C(4) (K), Succinyl:13C(4) (N-term), Succinyl:2H(4) (K), Succinyl:2H(4) (N-term), SulfanilicAcid (C-term), SulfanilicAcid (D), SulfanilicAcid (E), SulfanilicAcid:13C(6) (C-term), SulfanilicAcid:13C(6) (D), SulfanilicAcid:13C(6) (E), Sulfide (C), Sulfide (D), Sulfo (C), Sulfo (S), Sulfo (T), Sulfo (Y), Sulfo-NHS-LC-LC-Biotin (K), Sulfo-NHS-LC-LC-Biotin (N-term), SulfoGMBS (C), TMAB (K), TMAB (N-term), TMAB:2H(9) (K), TMAB:2H(9) (N-term), TMPP-Ac (N-term), TMT (K), TMT (N-term), TMT2plex (K), TMT2plex (N-term), TMT6plex (K), TMT6plex (N-term), TNBS (K), TNBS (N-term), Thioacyl (K), Thioacyl (N-term), Thiophos-S-S-biotin (S), Thiophos-S-S-biotin (T), Thiophos-S-S-biotin (Y), Thiophospho (S), Thiophospho (T), Thiophospho (Y), Thr->Ala (T), Thr->Arg (T), Thr->Asn (T), Thr->Ile (T), Thr->Lys (T), Thr->Met (T), Thr->Pro (T), Thr->Ser (T), Thrbiotinhydrazide (T), Thyroxine (Y), Triiodo (Y), Triiodothyronine (Y), Trimethyl (K), Trimethyl (R), Trioxidation (C), Trp->Arg (W), Trp->Cys (W), Trp->Gly (W), Trp->Hydroxykynurenin (W), Trp->Kynurenin (W), Trp->Leu (W), Trp->Oxolactone (W), Trp->Ser (W), Tyr->Asn (Y), Tyr->Asp (Y), Tyr->Cys (Y), Tyr->Dha (Y), Tyr->His (Y), Tyr->Phe (Y), Tyr->Ser (Y), VFQQQTGG (K), VIEVYQEQTGG (K), Val->Ala (V), Val->Asp (V), Val->Glu (V), Val->Gly (V), Val->Ile (V), Val->Met (V), Val->Phe (V), Xlink:B10621 (C), Xlink:DMP (K), Xlink:DMP-s (K), Xlink:SSD (K), ZGB (K), ZGB (N-term), a-type-ion (C-term), cGMP (C), cGMP (S), cGMP+RMP-loss (C), cGMP+RMP-loss (S), cysTMT (C), cysTMT6plex (C), dHex (S), dHex (T), dHex(1)Hex(3)HexNAc(4) (N), dHex(1)Hex(4)HexNAc(4) (N), dHex(1)Hex(5)HexNAc(4) (N), dNIC (N-term), dichlorination (Y), ethylamino (S), ethylamino (T), glucosone (R), iTRAQ4plex (K), iTRAQ4plex (N-term), iTRAQ4plex (Y), iTRAQ4plex114 (K), iTRAQ4plex114 (N-term), iTRAQ4plex114 (Y), iTRAQ4plex115 (K), iTRAQ4plex115 (N-term), iTRAQ4plex115 (Y), iTRAQ8plex (K), iTRAQ8plex (N-term), iTRAQ8plex (Y), iTRAQ8plex:13C(6)15N(2) (K), iTRAQ8plex:13C(6)15N(2) (N-term), iTRAQ8plex:13C(6)15N(2) (Y), lapachenole (C), mTRAQ (K), mTRAQ (N-term), mTRAQ (Y), mTRAQ:13C(3)15N(1) (K), mTRAQ:13C(3)15N(1) (N-term), mTRAQ:13C(3)15N(1) (Y), maleimide (C), maleimide (K), maleimide3 (C), maleimide3 (K), maleimide5 (C), maleimide5 (K), probiotinhydrazide (P), pyrophospho (S), pyrophospho (T), sulfo+amino (Y), thioacylPA (K), trifluoro (L)</td><td style="vertical-align:top">variable modifications, specified using UniMod (www.unimod.org) terms, e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'</td>
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<td style="vertical-align:top"><i>residue_set</i></td>
<td style="vertical-align:top">string</td><td style="vertical-align:top">Natural19WithoutI</td>
<td style="vertical-align:top"> </td><td style="vertical-align:top">The predefined amino acid set that should be used, see doc of ResidueDB for possible residue sets</td>
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<LI> If a section name is documented, the documentation is displayed as tooltip.
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<td class="memname">typedef <a class="el" href="structOpenMS_1_1CompNovoIonScoringBase_1_1IonScore.html">CompNovoIonScoringBase::IonScore</a> <a class="el" href="classOpenMS_1_1CompNovoIdentification.html#a7b7c9d2595dd3328e664293d3fec5ef9">IonScore</a></td>
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<td class="memname">typedef <a class="el" href="classOpenMS_1_1CompNovoIonScoringBase.html#af7e67702d51d0eff4c3db8ea8763a59f">CompNovoIonScoringBase::IsotopeType</a> <a class="el" href="classOpenMS_1_1CompNovoIonScoringBase.html#af7e67702d51d0eff4c3db8ea8763a59f">IsotopeType</a></td>
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<td class="memname">typedef <a class="el" href="classOpenMS_1_1CompNovoIdentificationBase_1_1Permut.html">CompNovoIdentificationBase::Permut</a> <a class="el" href="classOpenMS_1_1CompNovoIdentification.html#a6cb23966d9741fbd0d2e87a1668042df">Permut</a></td>
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<h2 class="groupheader">Constructor & Destructor Documentation</h2>
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<td class="memname"><a class="el" href="classOpenMS_1_1CompNovoIdentification.html">CompNovoIdentification</a> </td>
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<p>default constructor </p>
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<td class="paramtype">const <a class="el" href="classOpenMS_1_1CompNovoIdentification.html">CompNovoIdentification</a> & </td>
<td class="paramname"><em>source</em></td><td>)</td>
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<p>copy constructor </p>
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<td class="memname">virtual ~<a class="el" href="classOpenMS_1_1CompNovoIdentification.html">CompNovoIdentification</a> </td>
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<p>destructor </p>
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<td class="memname"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> estimatePrecursorWeight_ </td>
<td>(</td>
<td class="paramtype">const <a class="el" href="group__Kernel.html#ga3ba16951dc40c7a6c7457f3452e096ab">PeakSpectrum</a> & </td>
<td class="paramname"><em>ETD_spec</em>, </td>
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<td class="paramtype"><a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> & </td>
<td class="paramname"><em>charge</em> </td>
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<p>estimates an exact precursor weight of the ETD spectrum, because in most of the cases the precursor is found in the MS/MS spec </p>
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<td class="paramtype"><a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> </td>
<td class="paramname"><em>left</em>, </td>
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<td class="paramtype"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> </td>
<td class="paramname"><em>peptide_weight</em>, </td>
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<td class="paramname"><em>CID_orig_spec</em>, </td>
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<td class="paramname"><em>ETD_orig_spec</em>, </td>
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<td class="paramtype"><a class="el" href="classOpenMS_1_1Map.html">Map</a>< <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a>, <a class="el" href="classOpenMS_1_1CompNovoIdentification.html#a7b7c9d2595dd3328e664293d3fec5ef9">IonScore</a> > & </td>
<td class="paramname"><em>CID_nodes</em> </td>
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<p>call the DAC algorithm for the subspectrum defined via left and right peaks and fill the set with candidates sequences </p>
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<td class="memname">void getETDSpectrum_ </td>
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<td class="paramname"><em>spec</em>, </td>
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<td class="paramname">, </td>
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<td class="paramname"><em>prefix</em> = <code>0.0</code>, </td>
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<p>fills the spectrum with c and z type ions </p>
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<td class="memname">void getIdentification </td>
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<td class="paramtype">const <a class="el" href="group__Kernel.html#ga3ba16951dc40c7a6c7457f3452e096ab">PeakSpectrum</a> & </td>
<td class="paramname"><em>CID_spec</em>, </td>
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<td class="paramname"><em>ETD_spec</em> </td>
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<p>performs an <a class="el" href="classOpenMS_1_1ProteinIdentification.html" title="Representation of a protein identification run. ">ProteinIdentification</a> run on a PeakSpectrum </p>
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<td class="paramname"><em>ids</em>, </td>
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<td class="paramtype">const <a class="el" href="group__Kernel.html#gac459ab9d68b68f31561c7763c7da61ef">PeakMap</a> & </td>
<td class="paramname"><em>exp</em> </td>
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<p>performs an <a class="el" href="classOpenMS_1_1ProteinIdentification.html" title="Representation of a protein identification run. ">ProteinIdentification</a> run on a PeakMap </p>
<p>Implements <a class="el" href="classOpenMS_1_1CompNovoIdentificationBase.html#a803a9d92440a270074aefe1dced49504">CompNovoIdentificationBase</a>.</p>
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<td class="memname"><a class="el" href="classOpenMS_1_1CompNovoIdentification.html">CompNovoIdentification</a>& operator= </td>
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<td class="memname">void reducePermuts_ </td>
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<td class="paramname"><em>permuts</em>, </td>
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<td class="paramtype">const <a class="el" href="group__Kernel.html#ga3ba16951dc40c7a6c7457f3452e096ab">PeakSpectrum</a> & </td>
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<td class="paramtype">const <a class="el" href="group__Kernel.html#ga3ba16951dc40c7a6c7457f3452e096ab">PeakSpectrum</a> & </td>
<td class="paramname"><em>ETD_orig_spec</em>, </td>
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<p>reduces the given number of permuts by scoring the perumtations to the CID and ETD spec </p>
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