← Back to branch summary

~ubuntu-branches/ubuntu/wily/openms/wily

« back to all changes in this revision

Viewing changes to doc/html/TOPP_PILISModelCV.html

  • Committer: Package Import Robot
  • Author(s): Filippo Rusconi
  • Date: 2013-12-20 11:30:16 UTC
  • mfrom: (5.1.2 sid)
  • Revision ID: package-import@ubuntu.com-20131220113016-wre5g9bteeheq6he
Tags: 1.11.1-3
* remove version number from libbost development package names;
* ensure that AUTHORS is correctly shipped in all packages.

Show diffs side-by-side

added added

removed removed

Lines of Context:
doc/html/TOPP_PILISModelCV.html
 
1
<HTML>
 
2
<HEAD>
 
3
<TITLE>PILISModelCV</TITLE>
 
4
<LINK HREF="doxygen.css" REL="stylesheet" TYPE="text/css">
 
5
<LINK HREF="style_ini.css" REL="stylesheet" TYPE="text/css">
 
6
</HEAD>
 
7
<BODY BGCOLOR="#FFFFFF">
 
8
<A href="index.html">Home</A> &nbsp;&middot;
 
9
<A href="classes.html">Classes</A> &nbsp;&middot;
 
10
<A href="annotated.html">Annotated Classes</A> &nbsp;&middot;
 
11
<A href="modules.html">Modules</A> &nbsp;&middot;
 
12
<A href="functions_func.html">Members</A> &nbsp;&middot;
 
13
<A href="namespaces.html">Namespaces</A> &nbsp;&middot;
 
14
<A href="pages.html">Related Pages</A>
 
15
<HR style="height:1px; border:none; border-top:1px solid #c0c0c0;">
 
16
<!-- Generated by Doxygen 1.8.5 -->
 
17
</div><!-- top -->
 
18
<div class="header">
 
19
  <div class="headertitle">
 
20
<div class="title">PILISModelCV </div>  </div>
 
21
</div><!--header-->
 
22
<div class="contents">
 
23
<div class="textblock"><p>Perform a cross validation of the PILIS model parameters</p>
 
24
<dl class="experimental"><dt><b><a class="el" href="experimental.html#_experimental000016">Experimental classes:</a></b></dt><dd>This TOPP-tool is not well tested and not all features might be properly implemented and tested!</dd></dl>
 
25
<center> <table class="doxtable">
 
26
<tr>
 
27
<td align="center" bgcolor="#EBEBEB">pot. predecessor tools  </td><td valign="middle" rowspan="3"><img class="formulaInl" alt="$ \longrightarrow $" src="form_91.png"/> PILISModelCV <img class="formulaInl" alt="$ \longrightarrow $" src="form_91.png"/> </td><td align="center" bgcolor="#EBEBEB">pot. successor tools   </td></tr>
 
28
<tr>
 
29
<td valign="middle" align="center" rowspan="1"><a class="el" href="TOPP_MascotAdapter.html">MascotAdapter</a> (or other ID engines)  </td><td valign="middle" align="center" rowspan="1"><a class="el" href="TOPP_PILISIdentification.html">PILISIdentification</a>   </td></tr>
 
30
<tr>
 
31
<td rowspan="1"></td><td valign="middle" align="center" rowspan="1"><a class="el" href="TOPP_PILISModelTrainer.html">PILISModelTrainer</a>   </td></tr>
 
32
</table>
 
33
</center><p>A cross validation is performed to find the best parameters. The ini file contains for each parameter that can be optimized a flag, whether it should be used, a min value, a max value and a step size. These parameters are used to perform a grid search on the parameter. The result is a model with best performing parameter set. More on the cross validation can be found at the docu of the PILISCrossValidation class.</p>
 
34
<p><b>The command line parameters of this tool are:</b> </p>
 
35
<pre class="fragment">
 
36
PILISModelCV -- Perform a cross validation of the PILIS model parameters
 
37
Version: 1.11.1 Nov 14 2013, 11:18:15, Revision: 11976
 
38
 
 
39
Usage:
 
40
  PILISModelCV &lt;options&gt;
 
41
 
 
42
This tool has algoritm parameters that are not shown here! Please check the ini file for a detailed descripti
 
43
on or use the --helphelp option.
 
44
 
 
45
Options (mandatory options marked with '*'):
 
46
  -in &lt;file&gt;                  Input files for the spectra in mzML or MSP format. (valid formats: 'mzML', 'msp
 
47
                              ')
 
48
  -id_in &lt;file&gt;               Input files for the annotations in idXML format (if not given in MSP format). 
 
49
                              (valid formats: 'idXML')
 
50
  -model_file &lt;file&gt;          Input model file, used for generation mode or as basis for training. If not 
 
51
                              given, a default parameters are used for training.
 
52
  -trained_model_file &lt;file&gt;  The output file of the trained model, used in training mode.
 
53
  -min_charge &lt;charge&gt;        The minimal charge state used for training (other peptides are ignored) and 
 
54
                              for 'generation' mode if peptides have charge 0. (default: '1' min: '1')
 
55
  -max_charge &lt;charge&gt;        The maximal charge state used for training (other peptides are ignored) and 
 
56
                              for 'generation' mode if peptides have charge 0. (default: '3' min: '1')
 
57
  -score_filtering            If this flag is enabled the used spectra for training or cross validation are 
 
58
                              filtered using the 'score_treshold' parameter.
 
59
  -score_threshold &lt;score&gt;    The score threshold that must be passed in order to be used for training if 
 
60
                              'score_filtering' is enabled. (default: '0')
 
61
                              
 
62
                              
 
63
Common TOPP options:
 
64
  -ini &lt;file&gt;                 Use the given TOPP INI file
 
65
  -threads &lt;n&gt;                Sets the number of threads allowed to be used by the TOPP tool (default: '1')
 
66
  -write_ini &lt;file&gt;           Writes the default configuration file
 
67
  --help                      Shows options
 
68
  --helphelp                  Shows all options (including advanced)
 
69
 
 
70
The following configuration subsections are valid:
 
71
 - PILIS_parameters              PILIS model parameters
 
72
 - cross_validation_parameters   Parameters for the PILIS cross validation.
 
73
 - grid_search_parameters        Parameters for the PILIS grid search.
 
74
 
 
75
You can write an example INI file using the '-write_ini' option.
 
76
Documentation of subsection parameters can be found in the doxygen documentation or the INIFileEditor.
 
77
Have a look at the OpenMS documentation for more information.
 
78
 
 
79
</pre><p> <b>INI file documentation of this tool:</b> <div class="ini_global">
 
80
<div class="legend">
 
81
<b>Legend:</b><br>
 
82
 <div class="item item_required">required parameter</div>
 
83
 <div class="item item_advanced">advanced parameter</div>
 
84
</div>
 
85
  <div class="node"><span class="node_name">+PILISModelCV</span><span class="node_description">Perform a cross validation of the PILIS model parameters</span></div>
 
86
    <div class="item item_advanced"><span class="item_name" style="padding-left:16px;">version</span><span class="item_value">1.11.1</span>
 
87
<span class="item_description">Version of the tool that generated this parameters file.</span><span class="item_tags"></span><span class="item_restrictions"> </span></div>    <div class="node"><span class="node_name">++1</span><span class="node_description">Instance '1' section for 'PILISModelCV'</span></div>
 
88
      <div class="item"><span class="item_name" style="padding-left:24px;">in</span><span class="item_value">[]</span>
 
89
<span class="item_description">Input files for the spectra in mzML or MSP format.</span><span class="item_tags">input file</span><span class="item_restrictions">*.mzML,*.msp</span></div>      <div class="item"><span class="item_name" style="padding-left:24px;">id_in</span><span class="item_value">[]</span>
 
90
<span class="item_description">Input files for the annotations in idXML format (if not given in MSP format).</span><span class="item_tags">input file</span><span class="item_restrictions">*.idXML</span></div>      <div class="item"><span class="item_name" style="padding-left:24px;">model_file</span><span class="item_value"></span>
 
91
<span class="item_description">Input model file, used for generation mode or as basis for training. If not given, a default parameters are used for training.</span><span class="item_tags">input file</span><span class="item_restrictions"> </span></div>      <div class="item"><span class="item_name" style="padding-left:24px;">trained_model_file</span><span class="item_value"></span>
 
92
<span class="item_description">The output file of the trained model, used in training mode.</span><span class="item_tags">output file</span><span class="item_restrictions"> </span></div>      <div class="item"><span class="item_name" style="padding-left:24px;">min_charge</span><span class="item_value">1</span>
 
93
<span class="item_description">The minimal charge state used for training (other peptides are ignored) and for 'generation' mode if peptides have charge 0.</span><span class="item_tags"></span><span class="item_restrictions">1:&#8734;</span></div>      <div class="item"><span class="item_name" style="padding-left:24px;">max_charge</span><span class="item_value">3</span>
 
94
<span class="item_description">The maximal charge state used for training (other peptides are ignored) and for 'generation' mode if peptides have charge 0.</span><span class="item_tags"></span><span class="item_restrictions">1:&#8734;</span></div>      <div class="item"><span class="item_name" style="padding-left:24px;">score_filtering</span><span class="item_value">false</span>
 
95
<span class="item_description">If this flag is enabled the used spectra for training or cross validation are filtered using the 'score_treshold' parameter.</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div>      <div class="item"><span class="item_name" style="padding-left:24px;">score_threshold</span><span class="item_value">0</span>
 
96
<span class="item_description">The score threshold that must be passed in order to be used for training if 'score_filtering' is enabled.</span><span class="item_tags"></span><span class="item_restrictions"> </span></div>      <div class="item item_advanced"><span class="item_name" style="padding-left:24px;">log</span><span class="item_value"></span>
 
97
<span class="item_description">Name of log file (created only when specified)</span><span class="item_tags"></span><span class="item_restrictions"> </span></div>      <div class="item item_advanced"><span class="item_name" style="padding-left:24px;">debug</span><span class="item_value">0</span>
 
98
<span class="item_description">Sets the debug level</span><span class="item_tags"></span><span class="item_restrictions"> </span></div>      <div class="item"><span class="item_name" style="padding-left:24px;">threads</span><span class="item_value">1</span>
 
99
<span class="item_description">Sets the number of threads allowed to be used by the TOPP tool</span><span class="item_tags"></span><span class="item_restrictions"> </span></div>      <div class="item item_advanced"><span class="item_name" style="padding-left:24px;">no_progress</span><span class="item_value">false</span>
 
100
<span class="item_description">Disables progress logging to command line</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div>      <div class="item item_advanced"><span class="item_name" style="padding-left:24px;">test</span><span class="item_value">false</span>
 
101
<span class="item_description">Enables the test mode (needed for internal use only)</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div>      <div class="node"><span class="node_name">+++PILIS_parameters</span><span class="node_description">PILIS model parameters</span></div>
 
102
        <div class="item"><span class="item_name" style="padding-left:32px;">upper_mz</span><span class="item_value">2000</span>
 
103
<span class="item_description">Max m/z value of product ions in the simulated spectrum</span><span class="item_tags"></span><span class="item_restrictions"> </span></div>        <div class="item"><span class="item_name" style="padding-left:32px;">lower_mz</span><span class="item_value">200</span>
 
104
<span class="item_description">Lowest m/z value of product ions in the simulated spectrum</span><span class="item_tags"></span><span class="item_restrictions"> </span></div>        <div class="item"><span class="item_name" style="padding-left:32px;">charge_remote_threshold</span><span class="item_value">0.3</span>
 
105
<span class="item_description">If the probability for the proton at the N-terminus is lower than this value, enable charge-remote pathways</span><span class="item_tags"></span><span class="item_restrictions"> </span></div>        <div class="item"><span class="item_name" style="padding-left:32px;">charge_directed_threshold</span><span class="item_value">0.3</span>
 
106
<span class="item_description">Limit the proton availability at the N-terminus to at least this value for charge-directed pathways</span><span class="item_tags"></span><span class="item_restrictions"> </span></div>        <div class="item item_advanced"><span class="item_name" style="padding-left:32px;">model_depth</span><span class="item_value">10</span>
 
107
<span class="item_description">The number of explicitly modeled backbone cleavages from N-terminus and C-terminus, would be 9 for the default value</span><span class="item_tags"></span><span class="item_restrictions"> </span></div>        <div class="item item_advanced"><span class="item_name" style="padding-left:32px;">visible_model_depth</span><span class="item_value">50</span>
 
108
<span class="item_description">The maximal possible size of a peptide to be modeled</span><span class="item_tags"></span><span class="item_restrictions"> </span></div>        <div class="item"><span class="item_name" style="padding-left:32px;">precursor_mass_tolerance</span><span class="item_value">3</span>
 
109
<span class="item_description">Mass tolerance of the precursor peak, used to identify the precursor peak and its loss peaks for training</span><span class="item_tags"></span><span class="item_restrictions"> </span></div>        <div class="item"><span class="item_name" style="padding-left:32px;">fragment_mass_tolerance</span><span class="item_value">0.3</span>
 
110
<span class="item_description">Peak mass tolerance of the product ions, used to identify the ions for training</span><span class="item_tags"></span><span class="item_restrictions"> </span></div>        <div class="item"><span class="item_name" style="padding-left:32px;">variable_modifications</span><span class="item_value">[Oxidation (M), Carbamyl (K)]</span>
 
111
<span class="item_description">Modifications which should be included in the model, represented by PSI-MOD accessions.</span><span class="item_tags"></span><span class="item_restrictions">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)</span></div>        <div class="item"><span class="item_name" style="padding-left:32px;">fixed_modifications</span><span class="item_value">[]</span>
 
112
<span class="item_description">Modifications which should replace the unmodified amino acid, represented by PSI-MOD accessions.</span><span class="item_tags"></span><span class="item_restrictions">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)</span></div>        <div class="item item_advanced"><span class="item_name" style="padding-left:32px;">min_enhancement_factor</span><span class="item_value">2</span>
 
113
<span class="item_description">Minimal factor for bxyz backbone cleavages.</span><span class="item_tags"></span><span class="item_restrictions"> </span></div>        <div class="item item_advanced"><span class="item_name" style="padding-left:32px;">min_y_ion_intensity</span><span class="item_value">0</span>
 
114
<span class="item_description">Minimal intensity for y ions.</span><span class="item_tags"></span><span class="item_restrictions"> </span></div>        <div class="item item_advanced"><span class="item_name" style="padding-left:32px;">min_b_ion_intensity</span><span class="item_value">0</span>
 
115
<span class="item_description">Minimal intensity for b ions.</span><span class="item_tags"></span><span class="item_restrictions"> </span></div>        <div class="item item_advanced"><span class="item_name" style="padding-left:32px;">min_a_ion_intensity</span><span class="item_value">0</span>
 
116
<span class="item_description">Minimal intensity for a ions.</span><span class="item_tags"></span><span class="item_restrictions"> </span></div>        <div class="item item_advanced"><span class="item_name" style="padding-left:32px;">min_y_loss_intensity</span><span class="item_value">0</span>
 
117
<span class="item_description">Minimal intensity for y ions with neutral loss.</span><span class="item_tags"></span><span class="item_restrictions"> </span></div>        <div class="item item_advanced"><span class="item_name" style="padding-left:32px;">min_b_loss_intensity</span><span class="item_value">0</span>
 
118
<span class="item_description">Minimal intensity for b ions with neutral loss.</span><span class="item_tags"></span><span class="item_restrictions"> </span></div>        <div class="item"><span class="item_name" style="padding-left:32px;">side_chain_activation</span><span class="item_value">0.2</span>
 
119
<span class="item_description">Additional activation of proton sitting at side chain, especially important at lysine and histidine residues</span><span class="item_tags"></span><span class="item_restrictions"> </span></div>        <div class="item item_advanced"><span class="item_name" style="padding-left:32px;">pseudo_counts</span><span class="item_value">1e-15</span>
 
120
<span class="item_description">Value which is added for every transition trained of the underlying hidden Markov model</span><span class="item_tags"></span><span class="item_restrictions"> </span></div>        <div class="item"><span class="item_name" style="padding-left:32px;">max_isotope</span><span class="item_value">2</span>
 
121
<span class="item_description">Maximal isotope peak which is reported by the model, 0 means all isotope peaks are reported</span><span class="item_tags"></span><span class="item_restrictions"> </span></div>        <div class="item"><span class="item_name" style="padding-left:32px;">max_fragment_charge_training</span><span class="item_value">2</span>
 
122
<span class="item_description">Maximal allowed charge states for ions to be considered for training</span><span class="item_tags"></span><span class="item_restrictions"> </span></div>        <div class="item"><span class="item_name" style="padding-left:32px;">max_fragment_charge</span><span class="item_value">4</span>
 
123
<span class="item_description">Maximal charge state allowed for fragment ions</span><span class="item_tags"></span><span class="item_restrictions"> </span></div>      <div class="node"><span class="node_name">+++cross_validation_parameters</span><span class="node_description">Parameters for the PILIS cross validation.</span></div>
 
124
        <div class="item"><span class="item_name" style="padding-left:32px;">nfold</span><span class="item_value">10</span>
 
125
<span class="item_description">Number of partitions to use for cross validation</span><span class="item_tags"></span><span class="item_restrictions"> </span></div>        <div class="item"><span class="item_name" style="padding-left:32px;">optimization_method</span><span class="item_value">tophit_against_all_others</span>
 
126
<span class="item_description">Scoring method used for optimization</span><span class="item_tags"></span><span class="item_restrictions">tophit_against_all_others,only_top_hit,top_n_ions,top_n_ions_by</span></div>        <div class="item"><span class="item_name" style="padding-left:32px;">compare_function</span><span class="item_value">SpectrumAlignmentScore</span>
 
127
<span class="item_description">Spectra scoring function to use</span><span class="item_tags"></span><span class="item_restrictions">SpectrumAlignmentScore,ZhangSimilarityScore</span></div>        <div class="item"><span class="item_name" style="padding-left:32px;">num_top_peaks</span><span class="item_value">2</span>
 
128
<span class="item_description">Number of highest abundant peaks to consider with top_n_ion and top_n_ions_by optimization_methods</span><span class="item_tags"></span><span class="item_restrictions"> </span></div>        <div class="item"><span class="item_name" style="padding-left:32px;">min_intensity</span><span class="item_value">0.3</span>
 
129
<span class="item_description">Min relative intensity of highest abundant peaks to consider in top_n_ions_by</span><span class="item_tags"></span><span class="item_restrictions"> </span></div>        <div class="item"><span class="item_name" style="padding-left:32px;">fragment_mass_tolerance</span><span class="item_value">0.5</span>
 
130
<span class="item_description">Fragment mass tolerance, mainly used in compare function.</span><span class="item_tags"></span><span class="item_restrictions"> </span></div>        <div class="item"><span class="item_name" style="padding-left:32px;">normalize_to_TIC</span><span class="item_value">true</span>
 
131
<span class="item_description">Whether the spectra should be normalized to TIC before training, to max of one otherwise.</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div>      <div class="node"><span class="node_name">+++grid_search_parameters</span><span class="node_description">Parameters for the PILIS grid search.</span></div>
 
132
        <div class="item"><span class="item_name" style="padding-left:32px;">number_of_repeats</span><span class="item_value">2</span>
 
133
<span class="item_description">The grid search is performed 'number_of_repeats' times, to optimize the values.</span><span class="item_tags"></span><span class="item_restrictions">1:&#8734;</span></div>        <div class="item item_advanced"><span class="item_name" style="padding-left:32px;">grid_search_lower_mz</span><span class="item_value">true</span>
 
134
<span class="item_description">Enables the grid search for the 'lower_mz' parameter</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div>        <div class="item item_advanced"><span class="item_name" style="padding-left:32px;">lower_mz_min</span><span class="item_value">0</span>
 
135
<span class="item_description">Minimal value of the 'lower_mz' parameter.</span><span class="item_tags"></span><span class="item_restrictions"> </span></div>        <div class="item item_advanced"><span class="item_name" style="padding-left:32px;">lower_mz_max</span><span class="item_value">500</span>
 
136
<span class="item_description">Maximal value of the 'lower_mz' parameter.</span><span class="item_tags"></span><span class="item_restrictions"> </span></div>        <div class="item item_advanced"><span class="item_name" style="padding-left:32px;">lower_mz_step_size</span><span class="item_value">20</span>
 
137
<span class="item_description">Step size for increasing the parameter 'lower_mz' during grid search</span><span class="item_tags"></span><span class="item_restrictions"> </span></div>        <div class="item item_advanced"><span class="item_name" style="padding-left:32px;">grid_search_charge_remote_threshold</span><span class="item_value">true</span>
 
138
<span class="item_description">Enables the grid search for the parameter 'charge_remote_threshold'.</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div>        <div class="item item_advanced"><span class="item_name" style="padding-left:32px;">charge_remote_threshold_min</span><span class="item_value">0.01</span>
 
139
<span class="item_description">Minimal value of the 'charge_remote_threshold' parameter.</span><span class="item_tags"></span><span class="item_restrictions"> </span></div>        <div class="item item_advanced"><span class="item_name" style="padding-left:32px;">charge_remote_threshold_max</span><span class="item_value">0.8</span>
 
140
<span class="item_description">Maximal value of the 'charge_remote_threshold' parameter.</span><span class="item_tags"></span><span class="item_restrictions"> </span></div>        <div class="item item_advanced"><span class="item_name" style="padding-left:32px;">charge_remote_threshold_step_size</span><span class="item_value">0.1</span>
 
141
<span class="item_description">Step size for increasing the parameter 'charge_remote_threshold' during the grid search.</span><span class="item_tags"></span><span class="item_restrictions"> </span></div>        <div class="item item_advanced"><span class="item_name" style="padding-left:32px;">grid_search_charge_directed_threshold</span><span class="item_value">true</span>
 
142
<span class="item_description">Enables the grid search for the parameter 'charge_directed_threshold'.</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div>        <div class="item item_advanced"><span class="item_name" style="padding-left:32px;">charge_directed_threshold_min</span><span class="item_value">0</span>
 
143
<span class="item_description">Minimal value of the 'charge_directed_threshold' parameter.</span><span class="item_tags"></span><span class="item_restrictions"> </span></div>        <div class="item item_advanced"><span class="item_name" style="padding-left:32px;">charge_directed_threshold_max</span><span class="item_value">0.8</span>
 
144
<span class="item_description">Maximal value of the 'charge_directed_threshold' parameter.</span><span class="item_tags"></span><span class="item_restrictions"> </span></div>        <div class="item item_advanced"><span class="item_name" style="padding-left:32px;">charge_directed_threshold_step_size</span><span class="item_value">0.1</span>
 
145
<span class="item_description">Step size for increasing the parameter 'charge_directed_threshold' during the grid search.</span><span class="item_tags"></span><span class="item_restrictions"> </span></div>        <div class="item item_advanced"><span class="item_name" style="padding-left:32px;">grid_search_min_enhancement_factor</span><span class="item_value">true</span>
 
146
<span class="item_description">Enables the grid search for the parameter 'min_enhancement_factor'.</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div>        <div class="item item_advanced"><span class="item_name" style="padding-left:32px;">min_enhancement_factor_min</span><span class="item_value">0.1</span>
 
147
<span class="item_description">Minimal value of the 'min_enhancement_factor' parameter.</span><span class="item_tags"></span><span class="item_restrictions"> </span></div>        <div class="item item_advanced"><span class="item_name" style="padding-left:32px;">min_enhancement_factor_max</span><span class="item_value">2</span>
 
148
<span class="item_description">Maximal value of the 'min_enhancement_factor' parameter.</span><span class="item_tags"></span><span class="item_restrictions"> </span></div>        <div class="item item_advanced"><span class="item_name" style="padding-left:32px;">min_enhancement_factor_step_size</span><span class="item_value">0.3</span>
 
149
<span class="item_description">Step size for increasing the parameter 'min_enhancement_factor' during the grid search.</span><span class="item_tags"></span><span class="item_restrictions"> </span></div>        <div class="item item_advanced"><span class="item_name" style="padding-left:32px;">grid_search_side_chain_activation</span><span class="item_value">true</span>
 
150
<span class="item_description">Enables the grid search for the parameter 'side_chain_activation'.</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div>        <div class="item item_advanced"><span class="item_name" style="padding-left:32px;">side_chain_activation_min</span><span class="item_value">0</span>
 
151
<span class="item_description">Minimal value of the 'side_chain_activation' parameter.</span><span class="item_tags"></span><span class="item_restrictions"> </span></div>        <div class="item item_advanced"><span class="item_name" style="padding-left:32px;">side_chain_activation_max</span><span class="item_value">0.8</span>
 
152
<span class="item_description">Maximal value of the 'side_chain_activation' parameter.</span><span class="item_tags"></span><span class="item_restrictions"> </span></div>        <div class="item item_advanced"><span class="item_name" style="padding-left:32px;">side_chain_activation_step_size</span><span class="item_value">0.05</span>
 
153
<span class="item_description">Step size for increasing the parameter 'side_chain_activation' during the grid search.</span><span class="item_tags"></span><span class="item_restrictions"> </span></div>        <div class="item item_advanced"><span class="item_name" style="padding-left:32px;">grid_search_model_depth</span><span class="item_value">true</span>
 
154
<span class="item_description">Enables the grid search for the parameter 'model_depth'.</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div>        <div class="item item_advanced"><span class="item_name" style="padding-left:32px;">model_depth_min</span><span class="item_value">4</span>
 
155
<span class="item_description">Minimal value of the 'model_depth' parameter.</span><span class="item_tags"></span><span class="item_restrictions"> </span></div>        <div class="item item_advanced"><span class="item_name" style="padding-left:32px;">model_depth_max</span><span class="item_value">10</span>
 
156
<span class="item_description">Maximal value of the 'model_depth' parameter.</span><span class="item_tags"></span><span class="item_restrictions"> </span></div>        <div class="item item_advanced"><span class="item_name" style="padding-left:32px;">model_depth_step_size</span><span class="item_value">1</span>
 
157
<span class="item_description">Step size for increasing the parameter 'model_depth' during the grid search.</span><span class="item_tags"></span><span class="item_restrictions"> </span></div>        <div class="item item_advanced"><span class="item_name" style="padding-left:32px;">grid_search_min_a_ion_intensity</span><span class="item_value">true</span>
 
158
<span class="item_description">Enables the grid search for the parameter 'min_a_ion_intensity'.</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div>        <div class="item item_advanced"><span class="item_name" style="padding-left:32px;">min_a_ion_intensity_min</span><span class="item_value">0</span>
 
159
<span class="item_description">Minimal value of the 'min_a_ion_intensity' parameter.</span><span class="item_tags"></span><span class="item_restrictions"> </span></div>        <div class="item item_advanced"><span class="item_name" style="padding-left:32px;">min_a_ion_intensity_max</span><span class="item_value">0.5</span>
 
160
<span class="item_description">Maximal value of the 'min_a_ion_intensity' parameter.</span><span class="item_tags"></span><span class="item_restrictions"> </span></div>        <div class="item item_advanced"><span class="item_name" style="padding-left:32px;">min_a_ion_intensity_step_size</span><span class="item_value">0.05</span>
 
161
<span class="item_description">Step size for increasing the parameter 'min_a_ion_intensity' during the grid search.</span><span class="item_tags"></span><span class="item_restrictions"> </span></div>        <div class="item item_advanced"><span class="item_name" style="padding-left:32px;">grid_search_min_b_ion_intensity</span><span class="item_value">true</span>
 
162
<span class="item_description">Enables the grid search for the parameter 'min_b_ion_intensity'.</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div>        <div class="item item_advanced"><span class="item_name" style="padding-left:32px;">min_b_ion_intensity_min</span><span class="item_value">0</span>
 
163
<span class="item_description">Minimal value of the 'min_b_ion_intensity' parameter.</span><span class="item_tags"></span><span class="item_restrictions"> </span></div>        <div class="item item_advanced"><span class="item_name" style="padding-left:32px;">min_b_ion_intensity_max</span><span class="item_value">0.8</span>
 
164
<span class="item_description">Maximal value of the 'min_b_ion_intensity' parameter.</span><span class="item_tags"></span><span class="item_restrictions"> </span></div>        <div class="item item_advanced"><span class="item_name" style="padding-left:32px;">min_b_ion_intensity_step_size</span><span class="item_value">0.05</span>
 
165
<span class="item_description">Step size for increasing the parameter 'min_b_ion_intensity' during the grid search.</span><span class="item_tags"></span><span class="item_restrictions"> </span></div>        <div class="item item_advanced"><span class="item_name" style="padding-left:32px;">grid_search_min_y_ion_intensity</span><span class="item_value">true</span>
 
166
<span class="item_description">Enables the grid search for the parameter 'min_y_ion_intensity'.</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div>        <div class="item item_advanced"><span class="item_name" style="padding-left:32px;">min_y_ion_intensity_min</span><span class="item_value">0</span>
 
167
<span class="item_description">Minimal value of the 'min_y_ion_intensity' parameter.</span><span class="item_tags"></span><span class="item_restrictions"> </span></div>        <div class="item item_advanced"><span class="item_name" style="padding-left:32px;">min_y_ion_intensity_max</span><span class="item_value">0.8</span>
 
168
<span class="item_description">Maximal value of the 'min_y_ion_intensity' parameter.</span><span class="item_tags"></span><span class="item_restrictions"> </span></div>        <div class="item item_advanced"><span class="item_name" style="padding-left:32px;">min_y_ion_intensity_step_size</span><span class="item_value">0.05</span>
 
169
<span class="item_description">Step size for increasing the parameter 'min_y_ion_intensity' during the grid search.</span><span class="item_tags"></span><span class="item_restrictions"> </span></div>        <div class="item item_advanced"><span class="item_name" style="padding-left:32px;">grid_search_min_b_loss_intensity</span><span class="item_value">true</span>
 
170
<span class="item_description">Enables the grid search for the parameter 'min_b_loss_intensity'.</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div>        <div class="item item_advanced"><span class="item_name" style="padding-left:32px;">min_b_loss_intensity_min</span><span class="item_value">0</span>
 
171
<span class="item_description">Minimal value of the 'min_b_loss_intensity' parameter.</span><span class="item_tags"></span><span class="item_restrictions"> </span></div>        <div class="item item_advanced"><span class="item_name" style="padding-left:32px;">min_b_loss_intensity_max</span><span class="item_value">0.5</span>
 
172
<span class="item_description">Maximal value of the 'min_b_loss_intensity' parameter.</span><span class="item_tags"></span><span class="item_restrictions"> </span></div>        <div class="item item_advanced"><span class="item_name" style="padding-left:32px;">min_b_loss_intensity_step_size</span><span class="item_value">0.05</span>
 
173
<span class="item_description">Step size for increasing the parameter 'min_b_loss_intensity' during the grid search.</span><span class="item_tags"></span><span class="item_restrictions"> </span></div>        <div class="item item_advanced"><span class="item_name" style="padding-left:32px;">grid_search_min_y_loss_intensity</span><span class="item_value">true</span>
 
174
<span class="item_description">Enables the grid search for the parameter 'min_y_loss_intensity'.</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div>        <div class="item item_advanced"><span class="item_name" style="padding-left:32px;">min_y_loss_intensity_min</span><span class="item_value">0</span>
 
175
<span class="item_description">Minimal value of the 'min_y_loss_intensity' parameter.</span><span class="item_tags"></span><span class="item_restrictions"> </span></div>        <div class="item item_advanced"><span class="item_name" style="padding-left:32px;">min_y_loss_intensity_max</span><span class="item_value">0.5</span>
 
176
<span class="item_description">Maximal value of the 'min_y_loss_intensity' parameter.</span><span class="item_tags"></span><span class="item_restrictions"> </span></div>        <div class="item item_advanced"><span class="item_name" style="padding-left:32px;">min_y_loss_intensity_step_size</span><span class="item_value">0.05</span>
 
177
<span class="item_description">Step size for increasing the parameter 'min_y_loss_intensity' during the grid search.</span><span class="item_tags"></span><span class="item_restrictions"> </span></div>        <div class="item item_advanced"><span class="item_name" style="padding-left:32px;">grid_search_max_fragment_charge</span><span class="item_value">true</span>
 
178
<span class="item_description">Enables the grid search for the parameter 'max_fragment_charge'.</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div>        <div class="item item_advanced"><span class="item_name" style="padding-left:32px;">max_fragment_charge_min</span><span class="item_value">1</span>
 
179
<span class="item_description">Minimal value of the 'max_fragment_charge' parameter.</span><span class="item_tags"></span><span class="item_restrictions"> </span></div>        <div class="item item_advanced"><span class="item_name" style="padding-left:32px;">max_fragment_charge_max</span><span class="item_value">3</span>
 
180
<span class="item_description">Maximal value of the 'max_fragment_charge' parameter.</span><span class="item_tags"></span><span class="item_restrictions"> </span></div>        <div class="item item_advanced"><span class="item_name" style="padding-left:32px;">max_fragment_charge_step_size</span><span class="item_value">1</span>
 
181
<span class="item_description">Step size for increasing the parameter 'max_fragment_charge' during the grid search.</span><span class="item_tags"></span><span class="item_restrictions"> </span></div>        <div class="item item_advanced"><span class="item_name" style="padding-left:32px;">grid_search_max_isotope</span><span class="item_value">true</span>
 
182
<span class="item_description">Enables the grid search for the parameter 'max_isotope'.</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div>        <div class="item item_advanced"><span class="item_name" style="padding-left:32px;">max_isotope_min</span><span class="item_value">1</span>
 
183
<span class="item_description">Minimal value of the 'max_isotope' parameter.</span><span class="item_tags"></span><span class="item_restrictions"> </span></div>        <div class="item item_advanced"><span class="item_name" style="padding-left:32px;">max_isotope_max</span><span class="item_value">4</span>
 
184
<span class="item_description">Maximal value of the 'max_isotope' parameter.</span><span class="item_tags"></span><span class="item_restrictions"> </span></div>        <div class="item item_advanced"><span class="item_name" style="padding-left:32px;">max_isotope_step_size</span><span class="item_value">1</span>
 
185
<span class="item_description">Step size for increasing the parameter 'max_isotope' during the grid search.</span><span class="item_tags"></span><span class="item_restrictions"> </span></div>        <div class="item item_advanced"><span class="item_name" style="padding-left:32px;">grid_search_max_fragment_charge_training</span><span class="item_value">true</span>
 
186
<span class="item_description">Enables the grid search for the parameter 'max_fragment_charge_training'.</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div>        <div class="item item_advanced"><span class="item_name" style="padding-left:32px;">max_fragment_charge_training_min</span><span class="item_value">1</span>
 
187
<span class="item_description">Minimal value of the 'max_fragment_charge_training' parameter.</span><span class="item_tags"></span><span class="item_restrictions"> </span></div>        <div class="item item_advanced"><span class="item_name" style="padding-left:32px;">max_fragment_charge_training_max</span><span class="item_value">3</span>
 
188
<span class="item_description">Maximal value of the 'max_fragment_charge_training' parameter.</span><span class="item_tags"></span><span class="item_restrictions"> </span></div>        <div class="item item_advanced"><span class="item_name" style="padding-left:32px;">max_fragment_charge_training_step_size</span><span class="item_value">1</span>
 
189
<span class="item_description">Step size for increasing the parameter 'max_fragment_charge_training' during the grid search.</span><span class="item_tags"></span><span class="item_restrictions"> </span></div></div>
 
190
 </div></div><!-- contents -->
 
191
<HR style="height:1px; border:none; border-top:1px solid #c0c0c0;">
 
192
<TABLE width="100%" border="0">
 
193
<TR>
 
194
<TD><font color="#c0c0c0">OpenMS / TOPP release 1.11.1</font></TD>
 
195
<TD align="right"><font color="#c0c0c0">Documentation generated on Thu Nov 14 2013 11:19:24 using doxygen 1.8.5</font></TD>
 
196
</TR>
 
197
</TABLE>
 
198
</BODY>
 
199
</HTML>