mzml 0.3.1 → 0.3.2

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Files changed (11) hide show
  1. data/lib/mzml/spectrum.rb +3 -2
  2. data/lib/mzml/version.rb +1 -1
  3. data/test/test_mzml.rb +2 -0
  4. metadata +10 -24
  5. data/spec/mzml_spec.rb +0 -114
  6. data/spec/sample.compressed.mzML +0 -3108
  7. data/spec/sample.mgf +0 -10705
  8. data/spec/sample.mzML +0 -3108
  9. data/spec/sample.unindexed.mzML +0 -221
  10. data/spec/spec.opts +0 -1
  11. data/spec/spec_helper.rb +0 -29
data/spec/sample.unindexed.mzML DELETED
@@ -1,221 +0,0 @@
1
- <?xml version="1.0" encoding="ISO-8859-1"?>
2
- <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" accession="" version="1.1.0">
3
- <cvList count="2">
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- <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/>
5
- <cv id="UO" fullName="Unit Ontology" URI="http://obo.cvs.sourceforge.net/obo/obo/ontology/phenotype/unit.obo"/>
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- </cvList>
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- <fileDescription>
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- <fileContent>
9
- <cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum" />
10
- </fileContent>
11
- <sourceFileList count="1">
12
- <sourceFile id="sf_ru_0" name="file://MSALLY2/S/RAW/HEK_cells/Hek_cells_100904050914.RAW" location="">
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- <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="2b6ebe1d5f900a445f82adb40b24cd77ed476ecb" />
14
- <cvParam cvRef="MS" accession="MS:1000564" name="PSI mzData file" />
15
- <cvParam cvRef="MS" accession="MS:1000777" name="spectrum identifier nativeID format" />
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- </sourceFile>
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- </sourceFileList>
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- </fileDescription>
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- <sampleList count="1">
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- <sample id="sa_0" name="">
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- <cvParam cvRef="MS" accession="MS:1000004" name="sample mass" value="0" unitAccession="UO:0000021" unitName="gram" unitCvRef="UO" />
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- <cvParam cvRef="MS" accession="MS:1000005" name="sample volume" value="0" unitAccession="UO:0000098" unitName="milliliter" unitCvRef="UO" />
23
- <cvParam cvRef="MS" accession="MS:1000006" name="sample concentration" value="0" unitAccession="UO:0000175" unitName="gram per liter" unitCvRef="UO" />
24
- </sample>
25
- </sampleList>
26
- <softwareList count="4">
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- <software id="so_in_0" version="2.5.5" >
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- <cvParam cvRef="MS" accession="MS:1000532" name="Xcalibur" />
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- </software>
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- <software id="so_default" version="" >
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- <cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />
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- </software>
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- <software id="so_dp_sp_0_pm_0" version="4.3.1(build Sep 9 2009 12:30:29)" >
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- <cvParam cvRef="MS" accession="MS:1000541" name="ReAdW" />
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- </software>
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- <software id="so_dp_sp_0_pm_1" version="1.7.0" >
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- <cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="SpectrumCanvas" />
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- </software>
39
- </softwareList>
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- <instrumentConfigurationList count="1">
41
- <instrumentConfiguration id="ic_0">
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- <cvParam cvRef="MS" accession="MS:1000031" name="instrument model" />
43
- <componentList count="3">
44
- <source order="0">
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- <cvParam cvRef="MS" accession="MS:1000008" name="ionization type" />
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- </source>
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- <analyzer order="0">
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- <cvParam cvRef="MS" accession="MS:1000014" name="accuracy" value="0" unitAccession="UO:0000169" unitName="parts per million" unitCvRef="UO" />
49
- <cvParam cvRef="MS" accession="MS:1000022" name="TOF Total Path Length" value="0" unitAccession="UO:0000008" unitName="meter" unitCvRef="UO" />
50
- <cvParam cvRef="MS" accession="MS:1000024" name="final MS exponent" value="0" />
51
- <cvParam cvRef="MS" accession="MS:1000025" name="magnetic field strength" value="0" unitAccession="UO:0000228" unitName="tesla" unitCvRef="UO" />
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- <cvParam cvRef="MS" accession="MS:1000443" name="mass analyzer type" />
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- </analyzer>
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- <detector order="0">
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- <cvParam cvRef="MS" accession="MS:1000028" name="detector resolution" value="0" />
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- <cvParam cvRef="MS" accession="MS:1000029" name="sampling frequency" value="0" unitAccession="UO:0000106" unitName="hertz" unitCvRef="UO" />
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- <cvParam cvRef="MS" accession="MS:1000026" name="detector type" />
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- </detector>
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- </componentList>
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- <softwareRef ref="so_in_0" />
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- </instrumentConfiguration>
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- </instrumentConfigurationList>
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- <dataProcessingList count="1">
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- <dataProcessing id="dp_sp_0">
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- <processingMethod order="0" softwareRef="so_dp_sp_0_pm_0">
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- <cvParam cvRef="MS" accession="MS:1000035" name="peak picking" />
67
- <userParam name="#type" type="xsd:string" value="conversion"/>
68
- </processingMethod>
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- <processingMethod order="0" softwareRef="so_dp_sp_0_pm_1">
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- <cvParam cvRef="MS" accession="MS:1001486" name="data filtering" />
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- <cvParam cvRef="MS" accession="MS:1000747" name="completion time" value="2011-02-07+21:50" />
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- </processingMethod>
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- </dataProcessing>
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- </dataProcessingList>
75
- <run id="ru_0" defaultInstrumentConfigurationRef="ic_0" sampleRef="sa_0" defaultSourceFileRef="sf_ru_0">
76
- <spectrumList count="5" defaultDataProcessingRef="dp_sp_0">
77
- <spectrum id="scan=9033" index="562" defaultArrayLength="75">
78
- <cvParam cvRef="MS" accession="MS:1000525" name="spectrum representation" />
79
- <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="1" />
80
- <cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum" />
81
- <cvParam cvRef="MS" accession="MS:1000130" name="positive scan" />
82
- <scanList count="1">
83
- <cvParam cvRef="MS" accession="MS:1000795" name="no combination" />
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- <scan>
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- <cvParam cvRef="MS" accession="MS:1000016" name="scan start time" value="5207.31" unitAccession="UO:0000010" unitName="second" unitCvRef="UO" />
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- </scan>
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- </scanList>
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- <binaryDataArrayList count="2">
89
- <binaryDataArray encodedLength="800">
90
- <cvParam cvRef="MS" accession="MS:1000514" name="m/z array" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
91
- <cvParam cvRef="MS" accession="MS:1000523" name="64-bit float" />
92
- <cvParam cvRef="MS" accession="MS:1000576" name="no compression" />
93
- <binary>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</binary>
94
- </binaryDataArray>
95
- <binaryDataArray encodedLength="400">
96
- <cvParam cvRef="MS" accession="MS:1000515" name="intensity array" unitAccession="MS:1000131" unitName="number of counts" unitCvRef="MS"/>
97
- <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" />
98
- <cvParam cvRef="MS" accession="MS:1000576" name="no compression" />
99
- <binary>CZMLRfdvCEWM1ydFdZ/pRDWvDUapXF5FlQ4eRRgd20W1P3BFe9EqRecTCEWk6gdF1TyQRf3eDEblhfxEGkkWRua92UXCoaVFknjfRD2F80RS3hxFwbDrRHJiRkUUbSBFv2McRTEaQ0VvUwlFi68fRUv5hkVEwIZFBrRRRdTF6UVEzxJF+UYTRd/nH0Ui83tFox8MRUrwG0X3gWpFmtUURQjH20UWMTRFwc8pRTNRCEWsaQlFcrUXRSkJwUWZkBxGrgIxRuMio0WU/etEmWwtReGvbEUa4JZFyoffRPtHlEUI/lBFsW2ARV4xUEWtvS5FBi06RdwJEkWojBJGPIxHRvKcE0UAqGNGzdmkRQ+aFkXsqlpFvtcwRRLkYUV/WFRFSJQLRQy4BkV29CNF</binary>
100
- </binaryDataArray>
101
- </binaryDataArrayList>
102
- </spectrum>
103
- <spectrum id="scan=9034" index="563" defaultArrayLength="79">
104
- <cvParam cvRef="MS" accession="MS:1000525" name="spectrum representation" />
105
- <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="1" />
106
- <cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum" />
107
- <cvParam cvRef="MS" accession="MS:1000130" name="positive scan" />
108
- <scanList count="1">
109
- <cvParam cvRef="MS" accession="MS:1000795" name="no combination" />
110
- <scan>
111
- <cvParam cvRef="MS" accession="MS:1000016" name="scan start time" value="5208.68" unitAccession="UO:0000010" unitName="second" unitCvRef="UO" />
112
- </scan>
113
- </scanList>
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- <binaryDataArrayList count="2">
115
- <binaryDataArray encodedLength="844">
116
- <cvParam cvRef="MS" accession="MS:1000514" name="m/z array" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
117
- <cvParam cvRef="MS" accession="MS:1000523" name="64-bit float" />
118
- <cvParam cvRef="MS" accession="MS:1000576" name="no compression" />
119
- <binary>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</binary>
120
- </binaryDataArray>
121
- <binaryDataArray encodedLength="424">
122
- <cvParam cvRef="MS" accession="MS:1000515" name="intensity array" unitAccession="MS:1000131" unitName="number of counts" unitCvRef="MS"/>
123
- <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" />
124
- <cvParam cvRef="MS" accession="MS:1000576" name="no compression" />
125
- <binary>pb8PRZMGWEVVn1lFubaqRfkR9kQDlm9FT/ACRWNkKEWd/O9Ep2c3RawNg0XKUEtFGxvcRdjRFUZWyWdFw0hhRVb/BkUlNVtFoqkRRZLe+USzSApFXQv6RLsYMkWBsjFFk6OBRXLSNUVydedEVt7jRE/ECkUVMA5FHQ4YRbGREUWA9fZE+j5lRY5hx0UBRAxFY6cBRc2+OkU4JBBFsFsiRcmD+0Q9B4dF327GRZ1oDkVZ1w5FF5sLRfppFEW51lJFmBM4RXZCpEUdjvREDS6TRftxVUY/pL1FGRb1RCPjUEU0HGVFckCBRfDWH0V+wx9FkXcrRlr3bEVTNjdFvosIRVkXc0U5klxGCiYnRt0xHEa/RsVF1IQNRUNWNEXMaftEvNkPRRWB+ETuG19FMOLURL+sQUUdew5FuDkARQ==</binary>
126
- </binaryDataArray>
127
- </binaryDataArrayList>
128
- </spectrum>
129
- <spectrum id="scan=9035" index="564" defaultArrayLength="0">
130
- <cvParam cvRef="MS" accession="MS:1000525" name="spectrum representation" />
131
- <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="2" />
132
- <cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum" />
133
- <cvParam cvRef="MS" accession="MS:1000130" name="positive scan" />
134
- <scanList count="1">
135
- <cvParam cvRef="MS" accession="MS:1000795" name="no combination" />
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- <scan>
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- <cvParam cvRef="MS" accession="MS:1000016" name="scan start time" value="5209.18" unitAccession="UO:0000010" unitName="second" unitCvRef="UO" />
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- </scan>
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- </scanList>
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- <precursorList count="1">
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- <precursor>
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- <isolationWindow>
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- <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="868.46765137" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
144
- <cvParam cvRef="MS" accession="MS:1000828" name="isolation window lower offset" value="0" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
145
- <cvParam cvRef="MS" accession="MS:1000829" name="isolation window upper offset" value="0" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
146
- </isolationWindow>
147
- <selectedIonList count="1">
148
- <selectedIon>
149
- <cvParam cvRef="MS" accession="MS:1000744" name="selected ion m/z" value="868.46765137" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
150
- <cvParam cvRef="MS" accession="MS:1000041" name="charge state" value="3" />
151
- <cvParam cvRef="MS" accession="MS:1000042" name="peak intensity" value="12840.7001953125" unitAccession="MS:1000132" unitName="percent of base peak" unitCvRef="MS" />
152
- </selectedIon>
153
- </selectedIonList>
154
- <activation>
155
- <cvParam cvRef="MS" accession="MS:1000509" name="activation energy" value="0" unitAccession="UO:0000266" unitName="electronvolt" unitCvRef="UO" />
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- <cvParam cvRef="MS" accession="MS:1000044" name="dissociation method" />
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- </activation>
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- </precursor>
159
- </precursorList>
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- </spectrum>
161
- <spectrum id="scan=9036" index="565" defaultArrayLength="83">
162
- <cvParam cvRef="MS" accession="MS:1000525" name="spectrum representation" />
163
- <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="1" />
164
- <cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum" />
165
- <cvParam cvRef="MS" accession="MS:1000130" name="positive scan" />
166
- <scanList count="1">
167
- <cvParam cvRef="MS" accession="MS:1000795" name="no combination" />
168
- <scan>
169
- <cvParam cvRef="MS" accession="MS:1000016" name="scan start time" value="5209.63" unitAccession="UO:0000010" unitName="second" unitCvRef="UO" />
170
- </scan>
171
- </scanList>
172
- <binaryDataArrayList count="2">
173
- <binaryDataArray encodedLength="888">
174
- <cvParam cvRef="MS" accession="MS:1000514" name="m/z array" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
175
- <cvParam cvRef="MS" accession="MS:1000523" name="64-bit float" />
176
- <cvParam cvRef="MS" accession="MS:1000576" name="no compression" />
177
- <binary>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</binary>
178
- </binaryDataArray>
179
- <binaryDataArray encodedLength="444">
180
- <cvParam cvRef="MS" accession="MS:1000515" name="intensity array" unitAccession="MS:1000131" unitName="number of counts" unitCvRef="MS"/>
181
- <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" />
182
- <cvParam cvRef="MS" accession="MS:1000576" name="no compression" />
183
- <binary>Q4ImReexMkXWN0VF1fbbRA9nB0Xe/Q1Fa/urRX8rTEWmbiRFiZoORfixFUUuPEZFPmYCRftqzURuxC9FfZg1RbgrYEYmLB5FsK+FRoIRlEUDV4NF+TAaRecZNUW5phhFoIsjRa5JBUU+ezVFC3PqRNAl80TsNepE+vMgRfW5hEVv6VxFHYMFRV2NEUXvJCpFvHYNRQXMUUVMBFBFvGrvRLUEBEXs2OpEd8n6RBYJJkWzmyhFEaklRXVEp0UrKVtGKosjRUYeJEUJ8FVGN5knRjHQ7kX6AUNFxeEpRdmiD0V8QjpFpaUaRSSwn0UBmPZFtF8TRYJfB0VugzZF+AwJRf/G8EWjC4hGhv0sRYyvq0XuxoxFuKYdRaJqBEWvwCFFaZYgRdncL0W/dR1FrHL4REkECkUJ8lJFRDYXRatv+0Tha01Fr8E2RWCNDkU=</binary>
184
- </binaryDataArray>
185
- </binaryDataArrayList>
186
- </spectrum>
187
- <spectrum id="scan=9037" index="566" defaultArrayLength="0">
188
- <cvParam cvRef="MS" accession="MS:1000525" name="spectrum representation" />
189
- <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="2" />
190
- <cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum" />
191
- <cvParam cvRef="MS" accession="MS:1000130" name="positive scan" />
192
- <scanList count="1">
193
- <cvParam cvRef="MS" accession="MS:1000795" name="no combination" />
194
- <scan>
195
- <cvParam cvRef="MS" accession="MS:1000016" name="scan start time" value="5210.17" unitAccession="UO:0000010" unitName="second" unitCvRef="UO" />
196
- </scan>
197
- </scanList>
198
- <precursorList count="1">
199
- <precursor>
200
- <isolationWindow>
201
- <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="1045.84021" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
202
- <cvParam cvRef="MS" accession="MS:1000828" name="isolation window lower offset" value="0" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
203
- <cvParam cvRef="MS" accession="MS:1000829" name="isolation window upper offset" value="0" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
204
- </isolationWindow>
205
- <selectedIonList count="1">
206
- <selectedIon>
207
- <cvParam cvRef="MS" accession="MS:1000744" name="selected ion m/z" value="1045.84021" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
208
- <cvParam cvRef="MS" accession="MS:1000041" name="charge state" value="3" />
209
- <cvParam cvRef="MS" accession="MS:1000042" name="peak intensity" value="17405.5" unitAccession="MS:1000132" unitName="percent of base peak" unitCvRef="MS" />
210
- </selectedIon>
211
- </selectedIonList>
212
- <activation>
213
- <cvParam cvRef="MS" accession="MS:1000509" name="activation energy" value="0" unitAccession="UO:0000266" unitName="electronvolt" unitCvRef="UO" />
214
- <cvParam cvRef="MS" accession="MS:1000044" name="dissociation method" />
215
- </activation>
216
- </precursor>
217
- </precursorList>
218
- </spectrum>
219
- </spectrumList>
220
- </run>
221
- </mzML>
data/spec/spec.opts DELETED
@@ -1 +0,0 @@
1
- --color
data/spec/spec_helper.rb DELETED
@@ -1,29 +0,0 @@
1
- $LOAD_PATH.unshift(File.dirname(__FILE__))
2
- $LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
3
- require 'rubygems'
4
- require 'mzml'
5
- require 'spec'
6
- require 'spec/autorun'
7
-
8
- class Mgf < Struct.new(:title, :mz, :intensity); end
9
-
10
- def parse_mgf(fname)
11
- mgf = Mgf.new(nil,[],[])
12
- File.open(fname).each do |l|
13
- l.chomp!
14
- case l
15
- when /^TITLE=(.+)/
16
- mgf.title = $1
17
- when /^\d/
18
- m,i = l.split(' ').map{|e| (e.to_f * 1000).to_i() / 1000.0 }
19
- mgf.mz << m
20
- mgf.intensity << i
21
- when /^END IONS/
22
- break
23
- end
24
- end
25
- return mgf
26
- end
27
-
28
- Spec::Runner.configure do |config|
29
- end