Lars Nilse lars20070
lars20070
/ LabelFree_Mascot_QExactive_20170723.toppas
Created
July 23, 2017 10:30
OpenMS workflow, label free quantification, Mascot, Thermo Q Exactive, 23/07/2017
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| <?xml version="1.0" encoding="ISO-8859-1"?> | |
| <PARAMETERS version="1.6.2" xsi:noNamespaceSchemaLocation="http://open-ms.sourceforge.net/schemas/Param_1_6_2.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"> | |
| <NODE name="info" description=""> | |
| <ITEM name="version" value="2.2.0" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="num_vertices" value="25" type="int" description="" required="false" advanced="false" /> | |
| <ITEM name="num_edges" value="27" type="int" description="" required="false" advanced="false" /> | |
| <ITEM name="description" value="<![CDATA[<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd"> | |
| <html><head><meta name="qrichtext" content="1" /><style type="text/css"> | |
| p, li { white-space: pre-wrap; } | |
| </style></head><body style=" font-family:'Arial'; font-size:12pt; font-weight:400; font-style:normal;&quo |
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| <?xml version="1.0" encoding="ISO-8859-1"?> | |
| <featureMap version="1.9" id="fm_2471938744762100408" xsi:noNamespaceSchemaLocation="http://open-ms.sourceforge.net/schemas/FeatureXML_1_9.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"> | |
| <UserParam type="stringList" name="spectra_data" value="[file:///CC271_20170216.raw]"/> | |
| <dataProcessing completion_time="2017-02-16T16:09:33"> | |
| <software name="IDMapper" version="2.1.0" /> | |
| <processingAction name="Identification mapping" /> | |
| <UserParam type="string" name="parameter: id" value="C:/Users/lars/AppData/Local/Temp/2/2017-02-16_142625_ukmz1005immz_416_1/TOPPAS_tmp/QuantAndID_Trypsin_QExactive_20170118/012_IDFilter/out/CC271_20170216.idXML"/> | |
| <UserParam type="string" name="parameter: in" value="C:/Users/lars/AppData/Local/Temp/2/2017-02-16_142625_ukmz1005immz_416_1/TOPPAS_tmp/QuantAndID_Trypsin_QExactive_20170118/004_FeatureFinderMultiplex/out_features/CC271_20170216.featureXML"/> | |
| <UserParam type="string" name="parameter: out" value="C:\Users\lars\AppD |
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| <?xml version="1.0" encoding="UTF-8"?> | |
| <?xml-stylesheet type="text/xsl" href="http://open-ms.sourceforge.net/XSL/IdXML.xsl" ?> | |
| <IdXML version="1.4" xsi:noNamespaceSchemaLocation="http://open-ms.sourceforge.net/SCHEMAS/IdXML_1_4.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"> | |
| <SearchParameters id="SP_0" db="D:\data\proteome-databases-OpenMS\uniprot-human-Nov26-2013-reference-reviewed-canonical-without-isoforms-plus-shuffled.fasta" db_version="" taxonomy="" mass_type="monoisotopic" charges="" enzyme="trypsin" missed_cleavages="1000" precursor_peak_tolerance="20" precursor_peak_tolerance_ppm="false" peak_mass_tolerance="0" peak_mass_tolerance_ppm="false" > | |
| <FixedModification name="Carbamidomethyl (C)" /> | |
| <VariableModification name="Methyl (K)" /> | |
| <UserParam type="string" name="MS:1001211" value=""/> | |
| <UserParam type="string" name="MS:1001256" value=""/> | |
| <UserParam type="string" name="ChargeCarrierMass" value="1.00727649"/> | |
| <UserParam type="string" name="FragmentMethod" value="As w |
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| <?xml version="1.0" encoding="ISO-8859-1"?> | |
| <featureMap version="1.9" id="fm_18258434481825381329" xsi:noNamespaceSchemaLocation="http://open-ms.sourceforge.net/schemas/FeatureXML_1_9.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"> | |
| <UserParam type="stringList" name="spectra_data" value="[file:///BM3415.raw]"/> | |
| <dataProcessing completion_time="2017-05-09T15:54:51"> | |
| <software name="IDMapper" version="2.1.0" /> | |
| <processingAction name="Identification mapping" /> | |
| <UserParam type="string" name="parameter: id" value="C:/Users/lars/AppData/Local/Temp/14/2017-05-09_154011_ukmz1005immz_9124_1/TOPPAS_tmp/PeptideQuant_ThermoQExactive_Dimethyl_20170124/016_IDFilter/out/BM3415.idXML"/> | |
| <UserParam type="string" name="parameter: in" value="C:/Users/lars/AppData/Local/Temp/14/2017-05-09_154011_ukmz1005immz_9124_1/TOPPAS_tmp/PeptideQuant_ThermoQExactive_Dimethyl_20170124/006_FeatureFinderMultiplex/out_features/BM3415.featureXML"/> | |
| <UserParam type="string" name="parameter: out" value="C:\Users\lars\AppDa |
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| <?xml version="1.0" encoding="UTF-8"?> | |
| <?xml-stylesheet type="text/xsl" href="http://open-ms.sourceforge.net/XSL/IdXML.xsl" ?> | |
| <IdXML version="1.4" xsi:noNamespaceSchemaLocation="http://open-ms.sourceforge.net/SCHEMAS/IdXML_1_4.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"> | |
| <SearchParameters id="SP_0" db="" db_version="" taxonomy="" mass_type="monoisotopic" charges="" enzyme="unknown_enzyme" missed_cleavages="0" precursor_peak_tolerance="0" precursor_peak_tolerance_ppm="false" peak_mass_tolerance="0" peak_mass_tolerance_ppm="false" > | |
| <FixedModification name="Carbamidomethyl (C)" /> | |
| <FixedModification name="Dimethyl" /> | |
| <FixedModification name="Dimethyl (K)" /> | |
| <FixedModification name="Dimethyl:2H(4)13C(2)" /> | |
| <FixedModification name="Dimethyl:2H(4)13C(2) (K)" /> | |
| </SearchParameters> |
lars20070
/ PeptideQuant_ThermoQExactive_Dimethyl_20170124.toppas
Created
May 9, 2017 13:48
PeptideQuant_ThermoQExactive_Dimethyl_20170124.toppas
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| <?xml version="1.0" encoding="ISO-8859-1"?> | |
| <PARAMETERS version="1.6.2" xsi:noNamespaceSchemaLocation="http://open-ms.sourceforge.net/schemas/Param_1_6_2.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"> | |
| <NODE name="info" description=""> | |
| <ITEM name="version" value="2.1.0" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="num_vertices" value="24" type="int" description="" required="false" advanced="false" /> | |
| <ITEM name="num_edges" value="27" type="int" description="" required="false" advanced="false" /> | |
| <ITEM name="description" value="<![CDATA[<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd"> <html><head><meta name="qrichtext" content="1" /><style type="text/css"> p, li { white-space: pre-wrap; } </style></head><body style=" font-family:'Arial'; font-size:12pt; font-weight:400; font-style:normal;&quo |
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| <?xml version="1.0" encoding="UTF-8"?> | |
| <?xml-stylesheet type="text/xsl" href="http://open-ms.sourceforge.net/XSL/IdXML.xsl" ?> | |
| <IdXML version="1.4" xsi:noNamespaceSchemaLocation="http://open-ms.sourceforge.net/SCHEMAS/IdXML_1_4.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"> | |
| <SearchParameters id="SP_0" db="" db_version="" taxonomy="" mass_type="monoisotopic" charges="" enzyme="unknown_enzyme" missed_cleavages="0" precursor_peak_tolerance="0" precursor_peak_tolerance_ppm="false" peak_mass_tolerance="0" peak_mass_tolerance_ppm="false" > | |
| <FixedModification name="Carbamidomethyl (C)" /> | |
| <FixedModification name="Dimethyl" /> | |
| <FixedModification name="Dimethyl (K)" /> | |
| <FixedModification name="Dimethyl:2H(4)13C(2)" /> | |
| <FixedModification name="Dimethyl:2H(4)13C(2) (K)" /> | |
| </SearchParameters> |
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| <?xml version="1.0" encoding="ISO-8859-1"?> | |
| <PARAMETERS version="1.6.2" xsi:noNamespaceSchemaLocation="http://open-ms.sourceforge.net/schemas/Param_1_6_2.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"> | |
| <NODE name="info" description=""> | |
| <ITEM name="version" value="2.1.0" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="num_vertices" value="10" type="int" description="" required="false" advanced="false" /> | |
| <ITEM name="num_edges" value="13" type="int" description="" required="false" advanced="false" /> | |
| <ITEM name="description" value="<![CDATA[]]>" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="vertices" description=""> | |
| <NODE name="0" description=""> |
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| <?xml version="1.0" encoding="ISO-8859-1"?> | |
| <PARAMETERS version="1.6.2" xsi:noNamespaceSchemaLocation="http://open-ms.sourceforge.net/schemas/Param_1_6_2.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"> | |
| <NODE name="info" description=""> | |
| <ITEM name="version" value="2.1.0" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="num_vertices" value="9" type="int" description="" required="false" advanced="false" /> | |
| <ITEM name="num_edges" value="12" type="int" description="" required="false" advanced="false" /> | |
| <ITEM name="description" value="<![CDATA[]]>" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="vertices" description=""> | |
| <NODE name="0" description=""> |
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| During the workflow conversion from TOPPAS to Knime we encountered a number of questions/problems. | |
| Some reflect our incomplete knowledge of Knime, others might lead hopefully to future Knime improvements. | |
| (1) unimod database | |
| The unimod.xml can easily be changed in /OpenMS/share/OpenMS/CHEMISTRY/unimod.xml when using TOPPAS. | |
| In Knime a re-installation of the OpenMS module is necessary, which cannot easily be done by the users. | |
| (2) Some tools such as ProteinQuantifier give different results in TOPPAS and Knime. | |
| (3) third party software |