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annotate test-data/tiny.mzML @ 14:9d6e0ad4d600 draft

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Docker support and update for protk 1.4
author iracooke
date Thu, 26 Mar 2015 19:53:53 -0400
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14
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1 <?xml version="1.0" encoding="ISO-8859-1"?>
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2 <indexedmzML xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.1_idx.xsd">
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3 <mzML xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0.xsd" id="tiny" version="1.1.0">
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4 <cvList count="2">
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5 <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="3.7.3" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/>
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6 <cv id="UO" fullName="Unit Ontology" version="18:03:2011" URI="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo"/>
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7 </cvList>
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8 <fileDescription>
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9 <fileContent>
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10 <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value=""/>
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11 <cvParam cvRef="MS" accession="MS:1000580" name="MSn spectrum" value=""/>
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12 <cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum" value=""/>
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13 </fileContent>
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14 <sourceFileList count="2">
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15 <sourceFile id="sourceFile" name="ANALYSIS.BAF" location="Q:/Data/MALDI/1110/MT573/Tilo%20Knobs%20S2_BAF.d">
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16 <cvParam cvRef="MS" accession="MS:1000772" name="Bruker BAF nativeID format" value=""/>
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17 <cvParam cvRef="MS" accession="MS:1000815" name="Bruker BAF file" value=""/>
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18 <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="2107bc8ebc6160293e3c95b1848d4afa96435c39"/>
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19 </sourceFile>
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20 <sourceFile id="tiny.mzML" name="tiny.mzML" location="file://.">
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21 <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="c52beeb6ca5b6865b55e67b919317a96a064854b"/>
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22 </sourceFile>
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23 </sourceFileList>
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24 <contact>
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25 <cvParam cvRef="MS" accession="MS:1000586" name="contact name" value=" pfaou"/>
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26 <cvParam cvRef="MS" accession="MS:1000590" name="contact organization" value=""/>
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27 </contact>
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28 </fileDescription>
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29 <sampleList count="1">
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30 <sample id="sample" name="">
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31 </sample>
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32 </sampleList>
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33 <softwareList count="3">
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34 <software id="exportSoftware" version="3.0.1">
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35 <cvParam cvRef="MS" accession="MS:1000717" name="CompassXport" value=""/>
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36 </software>
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37 <software id="instrumentSoftware" version="3.3.85.0">
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38 <cvParam cvRef="MS" accession="MS:1000692" name="Bruker software" value=""/>
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39 <userParam name="AcquisitionProgram" value="flexControl"/>
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40 </software>
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41 <software id="pwiz_2.2.0_x0020__x0028_TPP_x0020_v4.6_x0020_OCCUPY_x0020_rev_x0020_1_x002c__x0020_Build_x0020_201210300824_x0020__x0028_linux_x0029__x0029_" version="2.2.0 (TPP v4.6 OCCUPY rev 1, Build 201210300824 (linux))">
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42 <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard" value=""/>
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43 </software>
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44 </softwareList>
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45 <instrumentConfigurationList count="1">
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46 <instrumentConfiguration id="instrument">
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47 <cvParam cvRef="MS" accession="MS:1000705" name="ultraflex III TOF/TOF" value=""/>
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48 <componentList count="3">
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49 <source order="1">
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50 <cvParam cvRef="MS" accession="MS:1000075" name="matrix-assisted laser desorption ionization" value=""/>
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51 </source>
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52 <analyzer order="2">
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53 <cvParam cvRef="MS" accession="MS:1000084" name="time-of-flight" value=""/>
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54 </analyzer>
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55 <detector order="3">
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56 <cvParam cvRef="MS" accession="MS:1000026" name="detector type" value=""/>
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57 </detector>
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58 </componentList>
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59 <softwareRef ref="instrumentSoftware"/>
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60 </instrumentConfiguration>
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61 </instrumentConfigurationList>
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62 <dataProcessingList count="2">
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63 <dataProcessing id="exportation">
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64 <processingMethod order="1" softwareRef="instrumentSoftware">
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65 <cvParam cvRef="MS" accession="MS:1000035" name="peak picking" value=""/>
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66 </processingMethod>
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67 <processingMethod order="2" softwareRef="exportSoftware">
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68 <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value=""/>
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69 <cvParam cvRef="MS" accession="MS:1000747" name="completion time" value="2011-10-11T01:50:11"/>
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70 </processingMethod>
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71 </dataProcessing>
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72 <dataProcessing id="pwiz_Reader_conversion">
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73 <processingMethod order="0" softwareRef="pwiz_2.2.0_x0020__x0028_TPP_x0020_v4.6_x0020_OCCUPY_x0020_rev_x0020_1_x002c__x0020_Build_x0020_201210300824_x0020__x0028_linux_x0029__x0029_">
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74 <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value=""/>
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75 </processingMethod>
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76 </dataProcessing>
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77 </dataProcessingList>
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78 <run id="tiny" defaultInstrumentConfigurationRef="instrument" startTimeStamp="2011-10-01T12:55:24.000+00:00">
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79 <spectrumList count="6" defaultDataProcessingRef="pwiz_Reader_conversion">
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80 <spectrum index="0" id="scan=1" defaultArrayLength="1">
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81 <cvParam cvRef="MS" accession="MS:1000130" name="positive scan" value=""/>
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82 <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value=""/>
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83 <cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum" value=""/>
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84 <cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="292.75354107"/>
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85 <cvParam cvRef="MS" accession="MS:1000504" name="base peak m/z" value="1251.52908446" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
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86 <cvParam cvRef="MS" accession="MS:1000505" name="base peak intensity" value="292.75354107" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of counts"/>
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87 <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="1"/>
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88 <cvParam cvRef="MS" accession="MS:1000527" name="highest observed m/z" value="1251.52908446" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
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89 <cvParam cvRef="MS" accession="MS:1000528" name="lowest observed m/z" value="1251.52908446" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
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90 <scanList count="1">
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91 <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value=""/>
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92 <scan>
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93 <cvParam cvRef="MS" accession="MS:1000016" name="scan start time" value="24" unitCvRef="UO" unitAccession="UO:0000031" unitName="minute"/>
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94 </scan>
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95 </scanList>
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96 <binaryDataArrayList count="2">
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97 <binaryDataArray encodedLength="12">
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98 <cvParam cvRef="MS" accession="MS:1000523" name="64-bit float" value=""/>
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99 <cvParam cvRef="MS" accession="MS:1000576" name="no compression" value=""/>
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100 <cvParam cvRef="MS" accession="MS:1000514" name="m/z array" value="" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
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101 <binary>AAAAwB2Ok0A=</binary>
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102 </binaryDataArray>
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103 <binaryDataArray encodedLength="8">
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104 <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value=""/>
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105 <cvParam cvRef="MS" accession="MS:1000576" name="no compression" value=""/>
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106 <cvParam cvRef="MS" accession="MS:1000515" name="intensity array" value="" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of counts"/>
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107 <binary>dGCSQw==</binary>
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108 </binaryDataArray>
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109 </binaryDataArrayList>
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110 </spectrum>
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111 <spectrum index="1" id="scan=2" defaultArrayLength="3">
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112 <cvParam cvRef="MS" accession="MS:1000130" name="positive scan" value=""/>
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114 <cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum" value=""/>
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115 <cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="635.53870230"/>
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116 <cvParam cvRef="MS" accession="MS:1000504" name="base peak m/z" value="977.60470404" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
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117 <cvParam cvRef="MS" accession="MS:1000505" name="base peak intensity" value="355.11991292" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of counts"/>
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118 <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="1"/>
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120 <cvParam cvRef="MS" accession="MS:1000528" name="lowest observed m/z" value="977.60470404" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
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121 <scanList count="1">
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122 <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value=""/>
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123 <scan>
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124 <cvParam cvRef="MS" accession="MS:1000016" name="scan start time" value="24.1667" unitCvRef="UO" unitAccession="UO:0000031" unitName="minute"/>
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125 </scan>
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126 </scanList>
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127 <binaryDataArrayList count="2">
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128 <binaryDataArray encodedLength="32">
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