File: FileFilter_28_output.mzML

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<?xml version="1.0" encoding="ISO-8859-1"?>
<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/mzML1.1.0_idx.xsd">
<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">
	<cvList count="5">
		<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"/>
		<cv id="UO" fullName="Unit Ontology" URI="http://obo.cvs.sourceforge.net/obo/obo/ontology/phenotype/unit.obo"/>
		<cv id="BTO" fullName="BrendaTissue545" version="unknown" URI="http://www.brenda-enzymes.info/ontology/tissue/tree/update/update_files/BrendaTissueOBO"/>
		<cv id="GO" fullName="Gene Ontology - Slim Versions" version="unknown" URI="http://www.geneontology.org/GO_slims/goslim_goa.obo"/>
		<cv id="PATO" fullName="Quality ontology" version="unknown" URI="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/quality.obo"/>
	</cvList>
	<fileDescription>
		<fileContent>
			<cvParam cvRef="MS" accession="MS:1000580" name="MSn spectrum" />
		</fileContent>
		<sourceFileList count="1">
			<sourceFile id="sf_ru_0" name="Toni_20121101_GM_70_Cel_pSILAC_16h_02.raw" location="file://">
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				<cvParam cvRef="MS" accession="MS:1000563" name="Thermo RAW format" />
				<cvParam cvRef="MS" accession="MS:1000768" name="Thermo nativeID format" />
			</sourceFile>
		</sourceFileList>
	</fileDescription>
	<sampleList count="1">
		<sample id="sa_0" name="">
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			<cvParam cvRef="MS" accession="MS:1000005" name="sample volume" value="0" unitAccession="UO:0000098" unitName="milliliter" unitCvRef="UO" />
			<cvParam cvRef="MS" accession="MS:1000006" name="sample concentration" value="0" unitAccession="UO:0000175" unitName="gram per liter" unitCvRef="UO" />
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	</sampleList>
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		</software>
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			<componentList count="3">
				<source order="1">
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				</source>
				<analyzer order="2">
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			</componentList>
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	</instrumentConfigurationList>
	<dataProcessingList count="2">
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			<processingMethod order="0" softwareRef="so_dp_sp_0_pm_0">
				<cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" />
			</processingMethod>
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				<cvParam cvRef="MS" accession="MS:1000747" name="completion time" value="2013-01-25+13:32" />
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				<userParam name="parameter: out_type" type="xsd:string" value=""/>
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				<userParam name="parameter: rm_pc_charge" type="xsd:string" value="[]"/>
				<userParam name="parameter: level" type="xsd:string" value="[1, 2, 3]"/>
				<userParam name="parameter: sort_peaks" type="xsd:string" value="false"/>
				<userParam name="parameter: no_chromatograms" type="xsd:string" value="false"/>
				<userParam name="parameter: remove_chromatograms" type="xsd:string" value="false"/>
				<userParam name="parameter: mz_precision" type="xsd:string" value="64"/>
				<userParam name="parameter: int_precision" type="xsd:string" value="32"/>
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				<userParam name="parameter: remove_mode" type="xsd:string" value=""/>
				<userParam name="parameter: remove_activation" type="xsd:string" value=""/>
				<userParam name="parameter: select_zoom" type="xsd:string" value="false"/>
				<userParam name="parameter: select_mode" type="xsd:string" value=""/>
				<userParam name="parameter: select_activation" type="xsd:string" value=""/>
				<userParam name="parameter: charge" type="xsd:string" value=":"/>
				<userParam name="parameter: size" type="xsd:string" value=":"/>
				<userParam name="parameter: remove_meta" type="xsd:string" value="[]"/>
				<userParam name="parameter: q" type="xsd:string" value=":"/>
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				<userParam name="parameter: map_and" type="xsd:string" value="false"/>
				<userParam name="parameter: log" type="xsd:string" value=""/>
				<userParam name="parameter: debug" type="xsd:integer" value="0"/>
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				<userParam name="parameter: no_progress" type="xsd:string" value="false"/>
				<userParam name="parameter: test" type="xsd:string" value="false"/>
				<userParam name="parameter: id:remove_clashes" type="xsd:string" value="false"/>
				<userParam name="parameter: id:keep_best_score_id" type="xsd:string" value="false"/>
				<userParam name="parameter: id:sequences_whitelist" type="xsd:string" value="[]"/>
				<userParam name="parameter: id:accessions_whitelist" type="xsd:string" value="[]"/>
				<userParam name="parameter: id:remove_annotated_features" type="xsd:string" value="false"/>
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				<userParam name="parameter: id:remove_unassigned_ids" type="xsd:string" value="false"/>
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				<userParam name="parameter: id:mz" type="xsd:double" value="0.001"/>
				<userParam name="parameter: id:blacklist_imperfect" type="xsd:string" value="false"/>
				<userParam name="parameter: algorithm:SignalToNoise:max_intensity" type="xsd:integer" value="-1"/>
				<userParam name="parameter: algorithm:SignalToNoise:auto_max_stdev_factor" type="xsd:double" value="3"/>
				<userParam name="parameter: algorithm:SignalToNoise:auto_max_percentile" type="xsd:integer" value="95"/>
				<userParam name="parameter: algorithm:SignalToNoise:auto_mode" type="xsd:integer" value="0"/>
				<userParam name="parameter: algorithm:SignalToNoise:win_len" type="xsd:double" value="200"/>
				<userParam name="parameter: algorithm:SignalToNoise:bin_count" type="xsd:integer" value="30"/>
				<userParam name="parameter: algorithm:SignalToNoise:min_required_elements" type="xsd:integer" value="10"/>
				<userParam name="parameter: algorithm:SignalToNoise:noise_for_empty_window" type="xsd:double" value="1e+20"/>
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				<userParam name="parameter: out" type="xsd:string" value="in.mzML"/>
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				<userParam name="parameter: algorithm:SignalToNoise:min_required_elements" type="xsd:integer" value="10"/>
				<userParam name="parameter: algorithm:SignalToNoise:noise_for_empty_window" type="xsd:double" value="1e+20"/>
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