client/servlet/conf/omssa_default_etd.xml

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2915 27 Oct 08 olle 1 <?xml version="1.0"?>
2915 27 Oct 08 olle 2 <MSSearchSettings
2915 27 Oct 08 olle 3   xmlns="http://www.ncbi.nlm.nih.gov"
2915 27 Oct 08 olle 4   xmlns:xs="http://www.w3.org/2001/XMLSchema-instance"
2915 27 Oct 08 olle 5   xs:schemaLocation="http://www.ncbi.nlm.nih.gov OMSSA.xsd"
2915 27 Oct 08 olle 6 >
2915 27 Oct 08 olle 7   <MSSearchSettings_precursorsearchtype>
2915 27 Oct 08 olle 8     <MSSearchType value="average">1</MSSearchType>
2915 27 Oct 08 olle 9   </MSSearchSettings_precursorsearchtype>
2915 27 Oct 08 olle 10   <MSSearchSettings_productsearchtype>
2915 27 Oct 08 olle 11     <MSSearchType value="monoisotopic">0</MSSearchType>
2915 27 Oct 08 olle 12   </MSSearchSettings_productsearchtype>
2915 27 Oct 08 olle 13   <MSSearchSettings_ionstosearch>
2915 27 Oct 08 olle 14     <MSIonType value="c">2</MSIonType>
2915 27 Oct 08 olle 15     <MSIonType value="z">5</MSIonType>
2915 27 Oct 08 olle 16   </MSSearchSettings_ionstosearch>
2915 27 Oct 08 olle 17   <MSSearchSettings_peptol>2</MSSearchSettings_peptol>
2915 27 Oct 08 olle 18   <MSSearchSettings_msmstol>0.8</MSSearchSettings_msmstol>
2915 27 Oct 08 olle 19   <MSSearchSettings_zdep>
2915 27 Oct 08 olle 20     <MSZdependence value="linearwithz">1</MSZdependence>
2915 27 Oct 08 olle 21   </MSSearchSettings_zdep>
2915 27 Oct 08 olle 22   <MSSearchSettings_cutoff>1</MSSearchSettings_cutoff>
2915 27 Oct 08 olle 23   <MSSearchSettings_cutlo>0</MSSearchSettings_cutlo>
2915 27 Oct 08 olle 24   <MSSearchSettings_cuthi>0.2</MSSearchSettings_cuthi>
2915 27 Oct 08 olle 25   <MSSearchSettings_cutinc>0.0005</MSSearchSettings_cutinc>
2915 27 Oct 08 olle 26   <MSSearchSettings_singlewin>20</MSSearchSettings_singlewin>
2915 27 Oct 08 olle 27   <MSSearchSettings_doublewin>14</MSSearchSettings_doublewin>
2915 27 Oct 08 olle 28   <MSSearchSettings_singlenum>2</MSSearchSettings_singlenum>
2915 27 Oct 08 olle 29   <MSSearchSettings_doublenum>2</MSSearchSettings_doublenum>
2915 27 Oct 08 olle 30   <MSSearchSettings_fixed></MSSearchSettings_fixed>
2915 27 Oct 08 olle 31   <MSSearchSettings_variable></MSSearchSettings_variable>
2915 27 Oct 08 olle 32   <MSSearchSettings_enzyme>
2915 27 Oct 08 olle 33     <MSEnzymes value="trypsin">0</MSEnzymes>
2915 27 Oct 08 olle 34   </MSSearchSettings_enzyme>
2915 27 Oct 08 olle 35   <MSSearchSettings_missedcleave>1</MSSearchSettings_missedcleave>
2915 27 Oct 08 olle 36   <MSSearchSettings_hitlistlen>10</MSSearchSettings_hitlistlen>
2915 27 Oct 08 olle 37   <MSSearchSettings_db>nr</MSSearchSettings_db>
2915 27 Oct 08 olle 38   <MSSearchSettings_tophitnum>20</MSSearchSettings_tophitnum>
2915 27 Oct 08 olle 39   <MSSearchSettings_minhit>2</MSSearchSettings_minhit>
2915 27 Oct 08 olle 40   <MSSearchSettings_minspectra>4</MSSearchSettings_minspectra>
2915 27 Oct 08 olle 41   <MSSearchSettings_scale>1000</MSSearchSettings_scale>
2915 27 Oct 08 olle 42   <MSSearchSettings_maxmods>64</MSSearchSettings_maxmods>
2915 27 Oct 08 olle 43   <MSSearchSettings_chargehandling>
2915 27 Oct 08 olle 44     <MSChargeHandle>
2915 27 Oct 08 olle 45       <MSChargeHandle_calcplusone>
2915 27 Oct 08 olle 46         <MSCalcPlusOne>1</MSCalcPlusOne>
2915 27 Oct 08 olle 47       </MSChargeHandle_calcplusone>
2915 27 Oct 08 olle 48       <MSChargeHandle_calccharge>
2915 27 Oct 08 olle 49         <MSCalcCharge>2</MSCalcCharge>
2915 27 Oct 08 olle 50       </MSChargeHandle_calccharge>
2915 27 Oct 08 olle 51       <MSChargeHandle_mincharge>1</MSChargeHandle_mincharge>
2915 27 Oct 08 olle 52       <MSChargeHandle_maxcharge>6</MSChargeHandle_maxcharge>
2915 27 Oct 08 olle 53       <MSChargeHandle_considermult>7</MSChargeHandle_considermult>
2915 27 Oct 08 olle 54       <MSChargeHandle_plusone>0.95</MSChargeHandle_plusone>
2915 27 Oct 08 olle 55       <MSChargeHandle_maxproductcharge>2</MSChargeHandle_maxproductcharge>
2915 27 Oct 08 olle 56     </MSChargeHandle>
2915 27 Oct 08 olle 57   </MSSearchSettings_chargehandling>
2915 27 Oct 08 olle 58   <MSSearchSettings_pseudocount>1</MSSearchSettings_pseudocount>
2915 27 Oct 08 olle 59   <MSSearchSettings_searchb1>1</MSSearchSettings_searchb1>
2915 27 Oct 08 olle 60   <MSSearchSettings_searchctermproduct>0</MSSearchSettings_searchctermproduct>
2915 27 Oct 08 olle 61   <MSSearchSettings_maxproductions>100</MSSearchSettings_maxproductions>
2915 27 Oct 08 olle 62   <MSSearchSettings_minnoenzyme>4</MSSearchSettings_minnoenzyme>
2915 27 Oct 08 olle 63   <MSSearchSettings_maxnoenzyme>40</MSSearchSettings_maxnoenzyme>
2915 27 Oct 08 olle 64   <MSSearchSettings_exactmass>1446.94</MSSearchSettings_exactmass>
2915 27 Oct 08 olle 65   <MSSearchSettings_settingid>0</MSSearchSettings_settingid>
2915 27 Oct 08 olle 66   <MSSearchSettings_iterativesettings>
2915 27 Oct 08 olle 67     <MSIterativeSettings>
2915 27 Oct 08 olle 68       <MSIterativeSettings_researchthresh>0.01</MSIterativeSettings_researchthresh>
2915 27 Oct 08 olle 69       <MSIterativeSettings_subsetthresh>0</MSIterativeSettings_subsetthresh>
2915 27 Oct 08 olle 70       <MSIterativeSettings_replacethresh>0</MSIterativeSettings_replacethresh>
2915 27 Oct 08 olle 71     </MSIterativeSettings>
2915 27 Oct 08 olle 72   </MSSearchSettings_iterativesettings>
2915 27 Oct 08 olle 73   <MSSearchSettings_precursorcull>1</MSSearchSettings_precursorcull>
2915 27 Oct 08 olle 74   <MSSearchSettings_nocorrelationscore>1</MSSearchSettings_nocorrelationscore>
2915 27 Oct 08 olle 75   <MSSearchSettings_probfollowingion>0.5</MSSearchSettings_probfollowingion>
2915 27 Oct 08 olle 76   <MSSearchSettings_nmethionine value="true"/>
2915 27 Oct 08 olle 77   <MSSearchSettings_automassadjust>1.0</MSSearchSettings_automassadjust>
2915 27 Oct 08 olle 78   <MSSearchSettings_species>9606</MSSearchSettings_species>
2915 27 Oct 08 olle 79 </MSSearchSettings>

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