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<div class="title">XTandemAdapter </div> </div>
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<div class="textblock"><p>Identifies peptides in MS/MS spectra via XTandem.</p>
<center> <table class="doxtable">
<tr>
<td align="center" bgcolor="#EBEBEB">pot. predecessor tools </td><td valign="middle" rowspan="2"><img class="formulaInl" alt="$ \longrightarrow $" src="form_91.png"/> XTandemAdapter <img class="formulaInl" alt="$ \longrightarrow $" src="form_91.png"/> </td><td align="center" bgcolor="#EBEBEB">pot. successor tools </td></tr>
<tr>
<td valign="middle" align="center" rowspan="1">any signal-/preprocessing tool <br/>
(in mzML format) </td><td valign="middle" align="center" rowspan="1"><a class="el" href="TOPP_IDFilter.html">IDFilter</a> or <br/>
any protein/peptide processing tool </td></tr>
</table>
</center><p><em>X!Tandem</em> must be installed before this wrapper can be used. This wrapper has been successfully tested with several versions of X!Tandem. The last known version to work is 2009-04-01. We encountered problems with later versions (namely 2010-01-01).</p>
<p>To speed up computations, FASTA databases can be compressed using the fasta_pro.exe tool of <em>X!Tandem</em>. It is contained in the "bin" folder of the <em>X!Tandem</em> installation. Refer to the docu of <em>X!Tandem</em> for further information about settings.</p>
<p>This adapter supports relative database filenames, which (when not found in the current working directory) is looked up in the directories specified by 'OpenMS.ini:id_db_dir' (see <a class="el" href="TOPP_advanced.html">TOPP for Advanced Users</a>).</p>
<p>The major part of the setting can be directly adjusted using the "default_input.xml" of <em>X!Tandem</em>. Parameters set by this wrapper overwrite the default settings given in the "default_input.xml", even those parameters not set explicitly, but defaulting to a value. An example of such a "default_input.xml" is contained in the "bin" folder of the <em>X!Tandem</em> installation. The parameter "default_input_file" must point to a valid file. "Masterfiles" for "default_input.xml" parameter importing other xml input files are not recommended, use at own risk.</p>
<p><b>The command line parameters of this tool are:</b> </p>
<pre class="fragment">
XTandemAdapter -- Annotates MS/MS spectra using XTandem.
Version: 1.11.1 Nov 14 2013, 11:18:15, Revision: 11976
Usage:
XTandemAdapter <options>
Options (mandatory options marked with '*'):
-in <file>* Input file (valid formats: 'mzML')
-out <file>* Output file (valid formats: 'idXML')
-precursor_mass_tolerance <tolerance> Precursor mass tolerance (default: '1.5')
-fragment_mass_tolerance <tolerance> Fragment mass error (default: '0.3')
-precursor_error_units <unit> Parent monoisotopic mass error units (default: 'ppm' valid: 'ppm',
'Da')
-fragment_error_units <unit> Fragment monoisotopic mass error units (default: 'Da' valid: 'ppm',
'Da')
-database <file>* FASTA file or pro file. Non-existing relative file-names are looked
up via'OpenMS.ini:id_db_dir' (valid formats: 'FASTA')
-min_precursor_charge <charge> Minimum precursor charge (default: '1')
-max_precursor_charge <charge> Maximum precursor charge (default: '4')
-fixed_modifications <mods> Fixed modifications, specified using UniMod (www.unimod.org) terms,
e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)' (valid: '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)', 'AEB
S (K)', 'AEBS (S)', 'AEBS (Y)', 'AEC-MAEC (S)', 'AEC-MAEC (T)', 'AEC
...
mino (Y)', 'thioacylPA (K)', 'trifluoro (L)')
-variable_modifications <mods> Variable modifications, specified using UniMod (www.unimod.org) term
s, e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)' (valid: '15dB-bioti
n (C)', '2-succinyl (C)', '2HPG (R)', '3-deoxyglucosone (R)', '3sulf
o (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)', 'AEB
S (K)', 'AEBS (S)', 'AEBS (Y)', 'AEC-MAEC (S)', 'AEC-MAEC (T)', 'AEC
...
mino (Y)', 'thioacylPA (K)', 'trifluoro (L)')
-missed_cleavages <num> Number of possible cleavage sites missed by the enzyme (default:
'1')
-xtandem_executable <executable>* X!Tandem executable of the installation e.g. 'tandem.exe'
-default_input_file <file> Default parameters input file, if not given default parameters are
used
-minimum_fragment_mz <num> Minimum fragment mz (default: '150')
-cleavage_site <cleavage site> Cleavage site of the used enzyme as regular expression ([RK]|{P}
(i.e. tryptic clevage) is default, [X]|[X] (i.e. every site) would
be best for peptide input or unspecific digestion). (default: '[RK]|
{P}')
-max_valid_expect <E-Value> Maximal E-Value of a hit to be reported (default: '0.1')
-refinement Enable the refinement. For most applications (especially when using
FDR, PEP approaches) it is NOT recommended to set this flag.
-semi_cleavage If set, both termini must NOT follow the cutting rule. For most appl
ications it is NOT recommended to set this flag.
Common TOPP options:
-ini <file> Use the given TOPP INI file
-threads <n> Sets the number of threads allowed to be used by the TOPP tool (defa
ult: '1')
-write_ini <file> Writes the default configuration file
--help Shows options
--helphelp Shows all options (including advanced)
</pre><p> <b>INI file documentation of this tool:</b> <div class="ini_global">
<div class="legend">
<b>Legend:</b><br>
<div class="item item_required">required parameter</div>
<div class="item item_advanced">advanced parameter</div>
</div>
<div class="node"><span class="node_name">+XTandemAdapter</span><span class="node_description">Annotates MS/MS spectra using XTandem.</span></div>
<div class="item item_advanced"><span class="item_name" style="padding-left:16px;">version</span><span class="item_value">1.11.1</span>
<span class="item_description">Version of the tool that generated this parameters file.</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="node"><span class="node_name">++1</span><span class="node_description">Instance '1' section for 'XTandemAdapter'</span></div>
<div class="item"><span class="item_name item_required" style="padding-left:24px;">in</span><span class="item_value"></span>
<span class="item_description">Input file</span><span class="item_tags">input file</span><span class="item_restrictions">*.mzML</span></div> <div class="item"><span class="item_name item_required" style="padding-left:24px;">out</span><span class="item_value"></span>
<span class="item_description">Output file</span><span class="item_tags">output file</span><span class="item_restrictions">*.idXML</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">precursor_mass_tolerance</span><span class="item_value">1.5</span>
<span class="item_description">Precursor mass tolerance</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:24px;">fragment_mass_tolerance</span><span class="item_value">0.3</span>
<span class="item_description">Fragment mass error</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:24px;">precursor_error_units</span><span class="item_value">ppm</span>
<span class="item_description">Parent monoisotopic mass error units</span><span class="item_tags"></span><span class="item_restrictions">ppm,Da</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">fragment_error_units</span><span class="item_value">Da</span>
<span class="item_description">Fragment monoisotopic mass error units</span><span class="item_tags"></span><span class="item_restrictions">ppm,Da</span></div> <div class="item"><span class="item_name item_required" style="padding-left:24px;">database</span><span class="item_value"></span>
<span class="item_description">FASTA file or pro file. Non-existing relative file-names are looked up via'OpenMS.ini:id_db_dir'</span><span class="item_tags">input file</span><span class="item_restrictions">*.FASTA</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">min_precursor_charge</span><span class="item_value">1</span>
<span class="item_description">Minimum precursor charge</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:24px;">max_precursor_charge</span><span class="item_value">4</span>
<span class="item_description">Maximum precursor charge</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:24px;">fixed_modifications</span><span class="item_value">[]</span>
<span class="item_description">Fixed modifications, specified using UniMod (www.unimod.org) terms, e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'</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:24px;">variable_modifications</span><span class="item_value">[]</span>
<span class="item_description">Variable modifications, specified using UniMod (www.unimod.org) terms, e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'</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:24px;">missed_cleavages</span><span class="item_value">1</span>
<span class="item_description">Number of possible cleavage sites missed by the enzyme</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name item_required" style="padding-left:24px;">xtandem_executable</span><span class="item_value">tandem</span>
<span class="item_description">X!Tandem executable of the installation e.g. 'tandem.exe'</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;">default_input_file</span><span class="item_value"></span>
<span class="item_description">Default parameters input file, if not given default parameters are used</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;">minimum_fragment_mz</span><span class="item_value">150</span>
<span class="item_description">Minimum fragment mz</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:24px;">cleavage_site</span><span class="item_value">[RK]|{P}</span>
<span class="item_description">Cleavage site of the used enzyme as regular expression ([RK]|{P} (i.e. tryptic clevage) is default, [X]|[X] (i.e. every site) would be best for peptide input or unspecific digestion).</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:24px;">max_valid_expect</span><span class="item_value">0.1</span>
<span class="item_description">Maximal E-Value of a hit to be reported</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:24px;">refinement</span><span class="item_value">false</span>
<span class="item_description">Enable the refinement. For most applications (especially when using FDR, PEP approaches) it is NOT recommended to set this flag.</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;">semi_cleavage</span><span class="item_value">false</span>
<span class="item_description">If set, both termini must NOT follow the cutting rule. For most applications it is NOT recommended to set this flag.</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:24px;">log</span><span class="item_value"></span>
<span class="item_description">Name of log file (created only when specified)</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:24px;">debug</span><span class="item_value">0</span>
<span class="item_description">Sets the debug level</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:24px;">threads</span><span class="item_value">1</span>
<span class="item_description">Sets the number of threads allowed to be used by the TOPP tool</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:24px;">no_progress</span><span class="item_value">false</span>
<span class="item_description">Disables progress logging to command line</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:24px;">test</span><span class="item_value">false</span>
<span class="item_description">Enables the test mode (needed for internal use only)</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div></div>
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<TD><font color="#c0c0c0">OpenMS / TOPP release 1.11.1</font></TD>
<TD align="right"><font color="#c0c0c0">Documentation generated on Thu Nov 14 2013 11:19:24 using doxygen 1.8.5</font></TD>
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