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<?xml version="1.0" encoding="ISO-8859-1"?>
<PARAMETERS version="1.1" xsi:noNamespaceSchemaLocation="http://open-ms.sourceforge.net/schemas/Param_1_1.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
<NODE name="SequestAdapter" description="">
<NODE name="1" description="">
<ITEM name="charges" value="1,3" type="string" description="" />
<ITEM name="cleavage" value="Trypsin" type="string" description="" />
<ITEM name="contact_info" value="unknown" type="string" description="" />
<ITEM name="contact_institution" value="unknown" type="string" description="" />
<ITEM name="contact_name" value="unknown" type="string" description="" />
<ITEM name="db" value="" type="string" description="" />
<ITEM name="db_directory_network" value="Sequest_FASTAFile_test.fasta" type="string" description="" />
<ITEM name="debug" value="0" type="int" description="" />
<ITEM name="enzyme_info" value="TEST_enzyme,1,K,-" type="string" description="" />
<ITEM name="header_filter" value="human,!mouse" type="string" description="" />
<ITEM name="ion_cutoff" value="0.3" type="float" description="" />
<ITEM name="ion_series_weights" value="0,1.0,0,0,0,0,0,1.0,0" type="string" description="" />
<ITEM name="keep_dta_files" value="false" type="string" description="" />
<ITEM name="keep_out_files" value="false" type="string" description="" />
<ITEM name="log" value="TOPP.log" type="string" description="" />
<ITEM name="mass_type_peak" value="false" type="string" description="" />
<ITEM name="mass_type_precursor" value="false" type="string" description="" />
<ITEM name="match_peak_allowed_error" value="4" type="int" description="" />
<ITEM name="match_peak_count" value="2" type="int" description="" />
<ITEM name="match_peak_tol" value="0.3" type="float" description="" />
<ITEM name="max_num_dif_AA_per_mod" value="2" type="int" description="" />
<ITEM name="max_num_dif_mods_per_peptide" value="4" type="int" description="" />
<ITEM name="max_num_int_cleav_sites" value="3" type="int" description="" />
<ITEM name="max_prot_mass_or_tol" value="0.5" type="float" description="" />
<ITEM name="modifications" value="10.3+,KRLNH,stat:Phosphorylation:16,C:HCNO,*,nterminal,Carbamylation:H2C,CHKNQRILDEST,dyn,Methylation:16-,cterminal:16-,nterminal_dyn:16-,cterminal_dyn:16-,nterminal_prot:16-,cterminal_prot" type="string" description="" />
<ITEM name="modifications_xml_file" value="" type="string" description="" />
<ITEM name="mz_files" value="" type="string" description="" />
<ITEM name="neutral_loss_ABY" value="011" type="string" description="" />
<ITEM name="normalize_xcorr" value="false" type="string" description="" />
<ITEM name="nuc_reading_frame" value="0" type="int" description="" />
<ITEM name="num_results" value="2" type="int" description="" />
<ITEM name="p_value" value="1" type="float" description="" />
<ITEM name="partial_sequence" value="ABC" type="string" description="" />
<ITEM name="password" value="" type="string" description="" />
<ITEM name="peak_mass_tolerance" value="0.5" type="float" description="" />
<ITEM name="pep_mass_unit" value="0" type="int" description="" />
<ITEM name="precursor_mass_tolerance" value="1" type="float" description="" />
<ITEM name="prot_mass" value="0" type="float" description="" />
<ITEM name="remove_precursor_peak" value="false" type="string" description="" />
<ITEM name="residues_in_lower_case" value="false" type="string" description="" />
<ITEM name="sequest_computer" value="buche" type="string" description="" />
<ITEM name="sequest_directory_win" value="C:\Inetpub\etc\XCalibur" type="string" description="" />
<ITEM name="sequest_in" value="false" type="string" description="" />
<ITEM name="sequest_input" value="" type="string" description="" />
<ITEM name="sequest_input_directory_network" value="\\TEST\SequestAdapter_1_output.sequest_in" type="string" description="" />
<ITEM name="sequest_out" value="false" type="string" description="" />
<ITEM name="show_enzymes" value="false" type="string" description="" />
<ITEM name="show_fragment_ions" value="true" type="string" description="" />
<ITEM name="temp_data_directory" value="./tmp/" type="string" description="" />
<ITEM name="temp_data_directory_network" value="\\TEST" type="string" description="" />
<ITEM name="temp_data_directory_win" value="X:" type="string" description="" />
<ITEM name="use_monoisotopic_mod_mass" value="false" type="string" description="" />
<ITEM name="user" value="" type="string" description="" />
</NODE>
</NODE>
</PARAMETERS>
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