Mercurial > repos > lecorguille > xcms_xcmsset

diff test-data/xcms_plot_raw_testdata.mzML @ 34:6550698fe60f draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
author workflow4metabolomics
date Mon, 15 Jul 2024 16:02:04 +0000
parents
children
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/xcms_plot_raw_testdata.mzML	Mon Jul 15 16:02:04 2024 +0000
@@ -0,0 +1,212 @@
+<?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:1000294" name="mass spectrum" />
+		</fileContent>
+		<sourceFileList count="1">
+			<sourceFile id="sf_ru_0" name="RCX_06_shortened.mzML" location="file:///C:/Users/473355/Downloads">
+				<cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="6c9fc5a54e7e588b4940994f66c953de66f8e8c5" />
+				<cvParam cvRef="MS" accession="MS:1000584" name="mzML format" />
+				<cvParam cvRef="MS" accession="MS:1000777" name="spectrum identifier nativeID format" />
+			</sourceFile>
+		</sourceFileList>
+	</fileDescription>
+	<sampleList count="1">
+		<sample id="sa_0" name="">
+			<cvParam cvRef="MS" accession="MS:1000004" name="sample mass" value="0" unitAccession="UO:0000021" unitName="gram" unitCvRef="UO" />
+			<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" />
+		</sample>
+	</sampleList>
+	<softwareList count="2">
+		<software id="so_in_0" version="" >
+			<cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />
+		</software>
+		<software id="so_default" version="" >
+			<cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />
+		</software>
+	</softwareList>
+	<instrumentConfigurationList count="1">
+		<instrumentConfiguration id="ic_0">
+			<cvParam cvRef="MS" accession="MS:1000031" name="instrument model" />
+			<softwareRef ref="so_in_0" />
+		</instrumentConfiguration>
+	</instrumentConfigurationList>
+	<dataProcessingList count="1">
+		<dataProcessing id="dp_sp_0">
+			<processingMethod order="0" softwareRef="so_default">
+				<cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" />
+				<userParam name="warning" type="xsd:string" value="fictional processing method used to fulfill format requirements" />
+			</processingMethod>
+		</dataProcessing>
+	</dataProcessingList>
+	<run id="ru_0" defaultInstrumentConfigurationRef="ic_0" sampleRef="sa_0" defaultSourceFileRef="sf_ru_0">
+		<userParam name="mzml_id" type="xsd:string" value="MZmine mzML export"/>
+		<spectrumList count="4" defaultDataProcessingRef="dp_sp_0">
+			<spectrum id="scan=126" index="0" defaultArrayLength="31" dataProcessingRef="dp_sp_0">
+				<cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" />
+				<cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="1" />
+				<cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum" />
+				<cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="6.0450043e09"/>
+				<cvParam cvRef="MS" accession="MS:1000528" name="lowest observed m/z" value="108.907723264639685" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS"/>
+				<cvParam cvRef="MS" accession="MS:1000527" name="highest observed m/z" value="1111.100247713231283" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS"/>
+				<userParam name="filter string" type="xsd:string" value="FTMS + p ESI Full ms [110.0000-1100.0000]"/>
+				<scanList count="1">
+					<cvParam cvRef="MS" accession="MS:1000795" name="no combination" />
+					<scan >
+						<cvParam cvRef="MS" accession="MS:1000016" name="scan start time" value="171.55917" unitAccession="UO:0000010" unitName="second" unitCvRef="UO" />
+						<userParam name="MS:1000130" type="xsd:string" value=""/>
+						<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="1100" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
+							</scanWindow>
+						</scanWindowList>
+					</scan>
+				</scanList>
+				<binaryDataArrayList count="2">
+					<binaryDataArray encodedLength="332">
+						<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>r5exsg4iY0CIh5zHECJjQFnOh9wSImNAI2xz8RQiY0DoYF8GFyJjQKWsSxsZImNAXU84MBsiY0ANSSVFHSJjQLiZElofImNAXUEAbyEiY0D8P+6DIyJjQJOV3JglImNAJkLLrSciY0DAvI+5WyJjQNE+h85dImNA4Bd/418iY0DqR3f4YSJjQO/Obw1kImNA8qxoImYiY0DPgTgP4yJjQHoaRiTlImNAJgpUOeciY0DTUGJO6SJjQIDucGPrImNAL+N/eO0iY0AdcL2ZPCNjQC+m2a4+I2NARjP2w0AjY0BhFxPZQiNjQIBSMO5EI2NAo+RNA0cjY0A=</binary>
+					</binaryDataArray>
+					<binaryDataArray encodedLength="168">
+						<cvParam cvRef="MS" accession="MS:1000515" name="intensity array" unitAccession="MS:1000131" unitName="number of detector counts" unitCvRef="MS"/>
+						<cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" />
+						<cvParam cvRef="MS" accession="MS:1000576" name="no compression" />
+						<binary>n7xcRxLCpkdqnyZJdS8vSqhE/UqdaFZLB+CHS17TUEvmdfVKVOwpSrriTEnEfoNIuSX9R9s+AkfErrtHYdANSIrABki7tKBH5HDURtM8ekc5hvNHwH4WSPywAkjmQaxHN1ktR2ZZFEeHy8hHHs8kSFVNMEgs2v1HAyl6Rw==</binary>
+					</binaryDataArray>
+				</binaryDataArrayList>
+			</spectrum>
+			<spectrum id="scan=127" index="1" defaultArrayLength="25">
+				<cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" />
+				<cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="1" />
+				<cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum" />
+				<cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="7.4992742e09"/>
+				<cvParam cvRef="MS" accession="MS:1000528" name="lowest observed m/z" value="108.907733023156396" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS"/>
+				<cvParam cvRef="MS" accession="MS:1000527" name="highest observed m/z" value="1111.100738826513407" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS"/>
+				<userParam name="filter string" type="xsd:string" value="FTMS + p ESI Full ms [110.0000-1100.0000]"/>
+				<scanList count="1">
+					<cvParam cvRef="MS" accession="MS:1000795" name="no combination" />
+					<scan >
+						<cvParam cvRef="MS" accession="MS:1000016" name="scan start time" value="171.92241" unitAccession="UO:0000010" unitName="second" unitCvRef="UO" />
+						<userParam name="MS:1000130" type="xsd:string" value=""/>
+						<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="1100" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
+							</scanWindow>
+						</scanWindowList>
+					</scan>
+				</scanList>
+				<binaryDataArrayList count="2">
+					<binaryDataArray encodedLength="268">
+						<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>dPjCarchY0C7p59/uSFjQPetfJS7IWNAKgtaqb0hY0BUvze+vyFjQHPKFdPBIWNAiiz058MhY0Bu8yXYDiJjQFnnEO0QImNAPTL8ARMiY0Ab1OcWFSJjQPPM0ysXImNAwxzAQBkiY0COw6xVGyJjQFPBmWodImNAEBaHfx8iY0DIwXSUISJjQHrEYqkjImNAJR5RviUiY0AdSg3KWSJjQEd5BN9bImNAa//7810iY0CN3PMIYCJjQKsQ7B1iImNAxJvkMmQiY0A=</binary>
+					</binaryDataArray>
+					<binaryDataArray encodedLength="136">
+						<cvParam cvRef="MS" accession="MS:1000515" name="intensity array" unitAccession="MS:1000131" unitName="number of detector counts" unitCvRef="MS"/>
+						<cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" />
+						<cvParam cvRef="MS" accession="MS:1000576" name="no compression" />
+						<binary>weaTRwOtJUhmbmtIh5J4SCCxVEjhYRNIjwmRR+TAMEdkshZIpwk/SSEqK0oxl+hKWLdCS2T2dEsDhjxLo73dSiRWF0r3fBRJ/KUYRzb5mkf1fQ5IkJ9ASD4EO0hfe+dHrvn+Rg==</binary>
+					</binaryDataArray>
+				</binaryDataArrayList>
+			</spectrum>
+			<spectrum id="scan=128" index="2" defaultArrayLength="18">
+				<cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" />
+				<cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="1" />
+				<cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum" />
+				<cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="6.3630976e09"/>
+				<cvParam cvRef="MS" accession="MS:1000528" name="lowest observed m/z" value="108.907709764292704" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS"/>
+				<cvParam cvRef="MS" accession="MS:1000527" name="highest observed m/z" value="1111.100125670347097" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS"/>
+				<userParam name="filter string" type="xsd:string" value="FTMS + p ESI Full ms [110.0000-1100.0000]"/>
+				<scanList count="1">
+					<cvParam cvRef="MS" accession="MS:1000795" name="no combination" />
+					<scan >
+						<cvParam cvRef="MS" accession="MS:1000016" name="scan start time" value="172.28342" unitAccession="UO:0000010" unitName="second" unitCvRef="UO" />
+						<userParam name="MS:1000130" type="xsd:string" value=""/>
+						<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="1100" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
+							</scanWindow>
+						</scanWindowList>
+					</scan>
+				</scanList>
+				<binaryDataArrayList count="2">
+					<binaryDataArray encodedLength="192">
+						<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>ccJIT7shY0AdGCZkvSFjQL/EA3m/IWNAV8jhjcEhY0DlIsCiwyFjQGvUnrfFIWNAt3Dwkg4iY0AbXdunECJjQHigxrwSImNAzjqy0RQiY0AeLJ7mFiJjQGd0ivsYImNAqhN3EBsiY0DmCWQlHSJjQBxXUTofImNATPs+TyEiY0B39ixkIyJjQJpIG3klImNA</binary>
+					</binaryDataArray>
+					<binaryDataArray encodedLength="96">
+						<cvParam cvRef="MS" accession="MS:1000515" name="intensity array" unitAccession="MS:1000131" unitName="number of detector counts" unitCvRef="MS"/>
+						<cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" />
+						<cvParam cvRef="MS" accession="MS:1000576" name="no compression" />
+						<binary>MpSAR7CKlkfSH7ZH8ADIR47vl0elaPRGkTmOR/0nH0gVxxNJXw/6SSlRrkpz4hJLaZY8S4KkE0vEPa5KZiHvSTSj30hQKRBH</binary>
+					</binaryDataArray>
+				</binaryDataArrayList>
+			</spectrum>
+			<spectrum id="scan=129" index="3" defaultArrayLength="31">
+				<cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" />
+				<cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="1" />
+				<cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum" />
+				<cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="5.5177718e09"/>
+				<cvParam cvRef="MS" accession="MS:1000528" name="lowest observed m/z" value="108.907641099520376" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS"/>
+				<cvParam cvRef="MS" accession="MS:1000527" name="highest observed m/z" value="1111.099388375058879" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS"/>
+				<userParam name="filter string" type="xsd:string" value="FTMS + p ESI Full ms [110.0000-1100.0000]"/>
+				<scanList count="1">
+					<cvParam cvRef="MS" accession="MS:1000795" name="no combination" />
+					<scan >
+						<cvParam cvRef="MS" accession="MS:1000016" name="scan start time" value="172.64467" unitAccession="UO:0000010" unitName="second" unitCvRef="UO" />
+						<userParam name="MS:1000130" type="xsd:string" value=""/>
+						<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="1100" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
+							</scanWindow>
+						</scanWindowList>
+					</scan>
+				</scanList>
+				<binaryDataArrayList count="2">
+					<binaryDataArray encodedLength="332">
+						<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>v/C4pr4hY0B13Za7wCFjQCMhddDCIWNAx7tT5cQhY0BirTL6xiFjQPT1EQ/JIWNAwtKM1Q8iY0A9/3fqESJjQLGCY/8TImNAH11PFBYiY0CGjjspGCJjQOgWKD4aImNAQvYUUxwiY0CWLAJoHiJjQOW573wgImNALZ7dkSIiY0Bu2cumJCJjQKprursmImNA4VSp0CgiY0CGbJeIVCJjQE3PjZ1WImNAEImEslgiY0DPmXvHWiJjQIkBc9xcImNAQcBq8V4iY0D01WIGYSJjQKGC19E/I2NAY0z05kEjY0ApbRH8QyNjQPTkLhFGI2NAwrNMJkgjY0A=</binary>
+					</binaryDataArray>
+					<binaryDataArray encodedLength="168">
+						<cvParam cvRef="MS" accession="MS:1000515" name="intensity array" unitAccession="MS:1000131" unitName="number of detector counts" unitCvRef="MS"/>
+						<cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" />
+						<cvParam cvRef="MS" accession="MS:1000576" name="no compression" />
+						<binary>fv0oRj9abEfoz8tHM/PIR0Q2f0eGNfFGwRgcSAr2V0icrD9JxtcqSvxEwErt4BlLlFcpSyPp6UqapnlK1o6YSfuKpEjqzglIZ2WBR8B3u0bDlYJHQfIASNx2I0hHr5NH7dsiRw69pUYm4wdHO6CKR0+FkEcPBkJHQvz1Rg==</binary>
+					</binaryDataArray>
+				</binaryDataArrayList>
+			</spectrum>
+		</spectrumList>
+	</run>
+</mzML>
+<indexList count="1">
+	<index name="spectrum">
+		<offset idRef="scan=126">3577</offset>
+		<offset idRef="scan=127">6508</offset>
+		<offset idRef="scan=128">9315</offset>
+		<offset idRef="scan=129">12005</offset>
+	</index>
+</indexList>
+<indexListOffset>14938</indexListOffset>
+<fileChecksum>0</fileChecksum>
+</indexedmzML>
\ No newline at end of file