File: FileMerger_6_output.mzML

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<?xml version="1.0" encoding="ISO-8859-1"?>
<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:1000579" name="MS1 spectrum" />
			<cvParam cvRef="MS" accession="MS:1000580" name="MSn spectrum" />
		</fileContent>
		<sourceFileList count="3">
			<sourceFile id="sf_ru_0" name="FileMerger_6_input2.mzML" location="<TEST_DATA_PATH>">
				<cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="6f3fd90af903c910d81d5d90088f805c33643ea5" />
				<cvParam cvRef="MS" accession="MS:1000584" name="mzML file" />
				<cvParam cvRef="MS" accession="MS:1000777" name="spectrum identifier nativeID format" />
			</sourceFile>
			<sourceFile id="sf_sp_0" name="FileMerger_6_input1.mzML" location="<TEST_DATA_PATH>">
				<cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="9caaed25a86b1e7306259612b4f74e461af7968e" />
				<cvParam cvRef="MS" accession="MS:1000584" name="mzML file" />
				<cvParam cvRef="MS" accession="MS:1000777" name="spectrum identifier nativeID format" />
			</sourceFile>
			<sourceFile id="sf_sp_2" name="tiny1.dta" location="file:///F:/data/Exp01">
				<cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="81be39fb2700ab2f3c8b2234b91274968b6899b1" />
				<cvParam cvRef="MS" accession="MS:1000613" name="DTA file" />
				<cvParam cvRef="MS" accession="MS:1000824" name="no nativeID format" />
			</sourceFile>
		</sourceFileList>
		<contact>
			<cvParam cvRef="MS" accession="MS:1000586" name="contact name" value="Pennington, William" />
			<cvParam cvRef="MS" accession="MS:1000590" name="contact organization" value="Higglesworth University" />
			<cvParam cvRef="MS" accession="MS:1000587" name="contact address" value="Higglesworth University, 12 Higglesworth Avenue, 12045, HI, USA" />
			<cvParam cvRef="MS" accession="MS:1000588" name="contact URL" value="http://www.higglesworth.edu/" />
			<cvParam cvRef="MS" accession="MS:1000589" name="contact email" value="wpennington@higglesworth.edu" />
			<userParam name="name" type="xsd:string" value="contact1"/>
		</contact>
	</fileDescription>
	<sampleList count="1">
		<sample id="sa_0" name="Sample1">
			<cvParam cvRef="MS" accession="MS:1000001" name="sample number" value="5" />
			<cvParam cvRef="MS" accession="MS:1000004" name="sample mass" value="11.7" unitAccession="UO:0000021" unitName="gram" unitCvRef="UO" />
			<cvParam cvRef="MS" accession="MS:1000005" name="sample volume" value="3.1" unitAccession="UO:0000098" unitName="milliliter" unitCvRef="UO" />
			<cvParam cvRef="MS" accession="MS:1000006" name="sample concentration" value="5.5" unitAccession="UO:0000175" unitName="gram per liter" unitCvRef="UO" />
			<userParam name="name" type="xsd:string" value="sample"/>
		</sample>
	</sampleList>
	<softwareList count="6">
		<software id="so_in_0" version="2.0.5" >
			<cvParam cvRef="MS" accession="MS:1000532" name="Xcalibur" />
		</software>
		<software id="so_default" version="" >
			<cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />
		</software>
		<software id="so_dp_sp_0_pm_0" version="2.0.5" >
			<cvParam cvRef="MS" accession="MS:1000532" name="Xcalibur" />
		</software>
		<software id="so_dp_sp_0_pm_1" version="version_string" >
			<cvParam cvRef="MS" accession="MS:1000758" name="FileMerger" />
		</software>
		<software id="so_dp_sp_1_pm_0" version="1.0" >
			<cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard" />
		</software>
		<software id="so_dp_sp_1_pm_1" version="version_string" >
			<cvParam cvRef="MS" accession="MS:1000758" name="FileMerger" />
		</software>
	</softwareList>
	<instrumentConfigurationList count="1">
		<instrumentConfiguration id="ic_0">
			<cvParam cvRef="MS" accession="MS:1000554" name="LCQ Deca" />
			<cvParam cvRef="MS" accession="MS:1000032" name="customization" value="Umbau" />
			<cvParam cvRef="MS" accession="MS:1000529" name="instrument serial number" value="23433"/>
			<userParam name="name" type="xsd:string" value="instrumentConfiguration"/>
			<componentList count="3">
				<source order="1">
					<cvParam cvRef="MS" accession="MS:1000056" name="direct inlet" />
					<cvParam cvRef="MS" accession="MS:1000073" name="electrospray ionization" />
					<userParam name="name" type="xsd:string" value="source"/>
				</source>
				<analyzer order="2">
					<cvParam cvRef="MS" accession="MS:1000014" name="accuracy" value="0" unitAccession="UO:0000169" unitName="parts per million" unitCvRef="UO" />
					<cvParam cvRef="MS" accession="MS:1000022" name="TOF Total Path Length" value="0" unitAccession="UO:0000008" unitName="meter" unitCvRef="UO" />
					<cvParam cvRef="MS" accession="MS:1000024" name="final MS exponent" value="0" />
					<cvParam cvRef="MS" accession="MS:1000025" name="magnetic field strength" value="14.56" unitAccession="UO:0000228" unitName="tesla" unitCvRef="UO" />
					<cvParam cvRef="MS" accession="MS:1000082" name="quadrupole ion trap" />
					<userParam name="name" type="xsd:string" value="analyzer1"/>
				</analyzer>
				<detector order="4">
					<cvParam cvRef="MS" accession="MS:1000028" name="detector resolution" value="5.1" />
					<cvParam cvRef="MS" accession="MS:1000029" name="sampling frequency" value="1.1" unitAccession="UO:0000106" unitName="hertz" unitCvRef="UO" />
					<cvParam cvRef="MS" accession="MS:1000119" name="time-digital converter" />
					<cvParam cvRef="MS" accession="MS:1000253" name="electron multiplier" />
					<userParam name="name" type="xsd:string" value="detector"/>
				</detector>
			</componentList>
			<softwareRef ref="so_in_0" />
		</instrumentConfiguration>
	</instrumentConfigurationList>
	<dataProcessingList count="2">
		<dataProcessing id="dp_sp_0">
			<processingMethod order="0" softwareRef="so_dp_sp_0_pm_0">
				<cvParam cvRef="MS" accession="MS:1000033" name="deisotoping" />
				<cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" />
				<userParam name="name" type="xsd:string" value="processingMethod"/>
				<userParam name="low_intensity_threshold" type="xsd:double" value="5.9"/>
			</processingMethod>
			<processingMethod order="0" softwareRef="so_dp_sp_0_pm_1">
				<cvParam cvRef="MS" accession="MS:1000530" name="file format conversion" />
				<cvParam cvRef="MS" accession="MS:1000747" name="completion time" value="1999-12-31+23:59" />
				<userParam name="parameter: mode" type="xsd:string" value="test_mode"/>
			</processingMethod>
		</dataProcessing>
		<dataProcessing id="dp_sp_1">
			<processingMethod order="0" softwareRef="so_dp_sp_1_pm_0">
				<cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" />
			</processingMethod>
			<processingMethod order="0" softwareRef="so_dp_sp_1_pm_1">
				<cvParam cvRef="MS" accession="MS:1000530" name="file format conversion" />
				<cvParam cvRef="MS" accession="MS:1000747" name="completion time" value="1999-12-31+23:59" />
				<userParam name="parameter: mode" type="xsd:string" value="test_mode"/>
			</processingMethod>
		</dataProcessing>
	</dataProcessingList>
	<run id="ru_0" defaultInstrumentConfigurationRef="ic_0" sampleRef="sa_0" startTimeStamp="2007-06-27T15:23:45" defaultSourceFileRef="sf_ru_0">
		<userParam name="int" type="xsd:integer" value="5"/>
		<userParam name="string" type="xsd:string" value="bla"/>
		<userParam name="flag" type="xsd:string" value=""/>
		<userParam name="float" type="xsd:double" value="5.11"/>
		<spectrumList count="3" defaultDataProcessingRef="dp_sp_0">
			<spectrum id="spectrum=0" index="0" defaultArrayLength="15" sourceFileRef="sf_sp_0" dataProcessingRef="dp_sp_0">
				<cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum" />
				<cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="1" />
				<cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" />
				<cvParam cvRef="MS" accession="MS:1000130" name="positive scan" />
				<cvParam cvRef="MS" accession="MS:1000528" name="lowest observed m/z" value="400.39" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS"/>
				<cvParam cvRef="MS" accession="MS:1000527" name="highest observed m/z" value="1795.56" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS"/>
				<cvParam cvRef="MS" accession="MS:1000504" name="base peak m/z" value="445.347" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS"/>
				<cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="16675500"/>
				<userParam name="name" type="xsd:string" value="scan1"/>
				<userParam name="filter string" type="xsd:string" value="+ c NSI Full ms [ 400.00-1800.00]"/>
				<userParam name="preset scan configuration" type="xsd:string" value="3"/>
				<scanList count="2">
					<cvParam cvRef="MS" accession="MS:1000795" name="no combination" />
					<scan externalSpectrumID="4711">
						<cvParam cvRef="MS" accession="MS:1000016" name="scan start time" value="5.89050006866455" unitAccession="UO:0000010" unitName="second" unitCvRef="UO" />
						<userParam name="name" type="xsd:string" value="acquisition1"/>
						<scanWindowList count="1">
							<scanWindow>
								<cvParam cvRef="MS" accession="MS:1000501" name="scan window lower limit" value="400" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
								<cvParam cvRef="MS" accession="MS:1000500" name="scan window upper limit" value="1800" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
							</scanWindow>
						</scanWindowList>
					</scan>
					<scan externalSpectrumID="4712">
						<userParam name="name" type="xsd:string" value="acquisition2"/>
					</scan>
				</scanList>
				<binaryDataArrayList count="2">
					<binaryDataArray encodedLength="160">
						<cvParam cvRef="MS" accession="MS:1000514" name="m/z array" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
						<cvParam cvRef="MS" accession="MS:1000523" name="64-bit float" />
						<cvParam cvRef="MS" accession="MS:1000576" name="no compression" />
						<binary>AAAAAAAAAAAAAAAAAADwPwAAAAAAAABAAAAAAAAACEAAAAAAAAAQQAAAAAAAABRAAAAAAAAAGEAAAAAAAAAcQAAAAAAAACBAAAAAAAAAIkAAAAAAAAAkQAAAAAAAACZAAAAAAAAAKEAAAAAAAAAqQAAAAAAAACxA</binary>
					</binaryDataArray>
					<binaryDataArray encodedLength="80">
						<cvParam cvRef="MS" accession="MS:1000515" name="intensity array" unitAccession="MS:1000131" unitName="number of counts" unitCvRef="MS"/>
						<cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" />
						<cvParam cvRef="MS" accession="MS:1000576" name="no compression" />
						<binary>AABwQQAAYEEAAFBBAABAQQAAMEEAACBBAAAQQQAAAEEAAOBAAADAQAAAoEAAAIBAAABAQAAAAEAAAIA/</binary>
					</binaryDataArray>
				</binaryDataArrayList>
			</spectrum>
			<spectrum id="spectrum=1" index="1" defaultArrayLength="10" dataProcessingRef="dp_sp_1">
				<cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum" />
				<cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="2" />
				<cvParam cvRef="MS" accession="MS:1000580" name="MSn spectrum" />
				<cvParam cvRef="MS" accession="MS:1000130" name="positive scan" />
				<cvParam cvRef="MS" accession="MS:1000528" name="lowest observed m/z" value="320.39" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS"/>
				<cvParam cvRef="MS" accession="MS:1000527" name="highest observed m/z" value="1003.56" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS"/>
				<cvParam cvRef="MS" accession="MS:1000504" name="base peak m/z" value="456.347" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS"/>
				<cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="16675500"/>
				<userParam name="name" type="xsd:string" value="scan2"/>
				<userParam name="filter string" type="xsd:string" value="+ c d Full ms2  445.35@cid35.00 [ 110.00-905.00]"/>
				<userParam name="preset scan configuration" type="xsd:string" value="4"/>
				<scanList count="1">
					<cvParam cvRef="MS" accession="MS:1000795" name="no combination" />
					<scan externalSpectrumID="0">
						<cvParam cvRef="MS" accession="MS:1000016" name="scan start time" value="5.99049997329712" unitAccession="UO:0000010" unitName="second" unitCvRef="UO" />
						<scanWindowList count="1">
							<scanWindow>
								<cvParam cvRef="MS" accession="MS:1000501" name="scan window lower limit" value="110" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
								<cvParam cvRef="MS" accession="MS:1000500" name="scan window upper limit" value="905" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
							</scanWindow>
						</scanWindowList>
					</scan>
				</scanList>
			<precursorList count="1">
					<precursor>
						<isolationWindow>
							<cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="445.34" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
							<cvParam cvRef="MS" accession="MS:1000828" name="isolation window lower offset" value="0" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
							<cvParam cvRef="MS" accession="MS:1000829" name="isolation window upper offset" value="0" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
						</isolationWindow>
						<selectedIonList count="1">
							<selectedIon>
								<cvParam cvRef="MS" accession="MS:1000744" name="selected ion m/z" value="445.34" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
								<cvParam cvRef="MS" accession="MS:1000041" name="charge state" value="2" />
								<cvParam cvRef="MS" accession="MS:1000042" name="peak intensity" value="120053" unitAccession="MS:1000132" unitName="percent of base peak" unitCvRef="MS" />
							</selectedIon>
						</selectedIonList>
						<activation>
							<cvParam cvRef="MS" accession="MS:1000509" name="activation energy" value="35" unitAccession="UO:0000266" unitName="electronvolt" unitCvRef="UO" />
							<cvParam cvRef="MS" accession="MS:1000133" name="collision-induced dissociation" />
						</activation>
					</precursor>
			</precursorList>
				<binaryDataArrayList count="2">
					<binaryDataArray encodedLength="108">
						<cvParam cvRef="MS" accession="MS:1000514" name="m/z array" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
						<cvParam cvRef="MS" accession="MS:1000523" name="64-bit float" />
						<cvParam cvRef="MS" accession="MS:1000576" name="no compression" />
						<binary>AAAAAAAAAAAAAAAAAAAAQAAAAAAAABBAAAAAAAAAGEAAAAAAAAAgQAAAAAAAACRAAAAAAAAAKEAAAAAAAAAsQAAAAAAAADBAAAAAAAAAMkA=</binary>
					</binaryDataArray>
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						<cvParam cvRef="MS" accession="MS:1000515" name="intensity array" unitAccession="MS:1000131" unitName="number of counts" unitCvRef="MS"/>
						<cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" />
						<cvParam cvRef="MS" accession="MS:1000576" name="no compression" />
						<binary>AACgQQAAkEEAAIBBAABgQQAAQEEAACBBAAAAQQAAwEAAAIBAAAAAQA==</binary>
					</binaryDataArray>
				</binaryDataArrayList>
			</spectrum>
			<spectrum id="spectrum=2" index="2" defaultArrayLength="0" sourceFileRef="sf_sp_2" dataProcessingRef="dp_sp_1">
				<cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum" />
				<cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="1" />
				<cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" />
				<cvParam cvRef="MS" accession="MS:1000130" name="positive scan" />
				<userParam name="name" type="xsd:string" value="spectrum3"/>
				<scanList count="1">
					<cvParam cvRef="MS" accession="MS:1000795" name="no combination" />
					<scan externalSpectrumID="0">
						<cvParam cvRef="MS" accession="MS:1000016" name="scan start time" value="6.09049987792969" unitAccession="UO:0000010" unitName="second" unitCvRef="UO" />
					</scan>
				</scanList>
			</spectrum>
		</spectrumList>
	</run>
</mzML>