Lars Nilse lars20070
lars20070
/ interact.pep.csv
Created
March 5, 2015 08:10
plain text versions of interact.pep.xml, TPP analysis of HEK Q Exactive dataset LN1
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| probability,spectrum,start_scan,expect,ions2,peptide,protein,calc_neutral_pep_mass,xpress,light_area,heavy_area,retention_time_sec,RT,RT_score | |
| 0.7911,H_LN1.01671.01671.2,1671,0.033,Jul-30,R.n[35.07]TGSESSQTGTSTTSSRc[17.00].N,sp|P23588|IF4B_HUMAN,1606.7499,4.11,1.10E+07,2.68E+06,383.877,72.48,1.36 | |
| 0.9133,H_LN1.01790.01790.3,1790,0.17,Jun-44,K.n[35.07]YHTVNGHNC[160.03]EVRc[17.00].K,sp|P09651|ROA1_HUMAN,1518.7214,3.19,2.10E+07,6.59E+06,398.955,70.44,1.38 | |
| 1,H_LN1.01829.01829.3,1829,0.00082,Jun-44,K.n[35.07]LAEAHQQEC[160.03]C[160.03]QK[162.16]c[17.00].F,sp|Q9Y5X3|SNX5_HUMAN,1568.7716,3.5,1.79E+07,5.12E+06,403.923,569.9,0.3 | |
| 1,H_LN1.01843.01843.3,1843,0.0015,Aug-40,R.n[35.07]TSVPENHAQSRc[17.00].L,sp|Q9UQ35|SRRM2_HUMAN,1258.6482,4.21,1.23E+07,2.93E+06,405.58,207.99,1.09 | |
| 1,H_LN1.02003.02003.3,2003,2.20E-08,Dec-48,R.n[35.07]EESGK[162.16]PGAHVTVK[162.16]c[17.00].K,sp|P22626|ROA2_HUMAN,1439.8837,3.68,2.76E+08,7.51E+07,426.112,605.54,0.26 | |
| 1,H_LN1.02042.02042.3,2042,0.0002,Oct-48,K.n[35.07]HGDPGDAAQQEAK[162.16]c[17.00].H,s |
lars20070
/ interact.prot.csv
Created
March 5, 2015 08:14
plain text versions of interact.prot.xml, TPP analysis of HEK Q Exactive dataset LN1
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| entry no.,group probability,protein,protein link,protein probability,percent coverage,xpress ratio mean,xpress stdev,xpress num peptides,xpress link,num unique peps,tot indep spectra,percent share of spectrum ids,description | |
| 1,1,"sp|B5ME19|EIFCL_HUMAN,sp|Q99613|EIF3C_HUMAN","http://localhost/tpp-bin/comet-fastadb.cgi?Ref=sp|B5ME19|EIFCL_HUMAN&Db=c:/Inetpub/wwwroot/ISB/data/user-data/proteome-databases/uniprot-human-Nov26-2013-reference-reviewed-canonical-without-isoforms_plus-shuffled.fasta&Pep=DFESHITSYK+GTEITHAVVIK+LGSLVENNER+MDEEFTK+QLTPPEGSSK+TCHSFIINEK,http://localhost/tpp-bin/comet-fastadb.cgi?Ref=sp|Q99613|EIF3C_HUMAN&Db=c:/Inetpub/wwwroot/ISB/data/user-data/proteome-databases/uniprot-human-Nov26-2013-reference-reviewed-canonical-without-isoforms_plus-shuffled.fasta&Pep=DFESHITSYK+GTEITHAVVIK+LGSLVENNER+MDEEFTK+QLTPPEGSSK+TCHSFIINEK",1,6.4,7.18,3.22,7,http://localhost/tpp-bin/XPressCGIProteinDisplayParser.cgi?cgihome=/tpp-bin/&protein=sp|B5ME19|EIFCL_HUMAN&peptide_string=LGSLVENNER+QLTPPEGSSK+GTEITHAVV |
lars20070
/ Proteins_MSGFplusFido_DoubleDimethyl.toppas
Created
April 30, 2015 09:16
MSGF+ Fido protein identification
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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="2.0.0" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="num_vertices" value="22" type="int" description="" required="false" advanced="false" /> | |
| <ITEM name="num_edges" value="24" 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"?> | |
| <?xml-stylesheet type="text/xsl" href="file:////Users/lars/Code/git/OpenMs/share/OpenMS/XSL/ConsensusXML.xsl"?> | |
| <consensusXML version="1.5" experiment_type="labeled_MS1" xsi:noNamespaceSchemaLocation="http://open-ms.sourceforge.net/schemas/ConsensusXML_1_4.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"> | |
| <dataProcessing completion_time="2015-05-29T15:42:15"> | |
| <software name="IDMapper" version="2.0.0" /> | |
| <processingAction name="Identification mapping" /> | |
| <userParam type="string" name="parameter: id" value="D:/data/Lars/temp/2015-05-29_102730_ukmz1005immz_12048_1/TOPPAS_tmp/peptide_identification_and_mapping/017_IDFilter/out/WL383.idXML"/> | |
| <userParam type="string" name="parameter: in" value="D:\data\Weng\20150309_FFPE_TAILS\WL383_388\OpenMS\dimethylation\results_peptide_quant\WL383.consensusXML"/> | |
| <userParam type="string" name="parameter: out" value="D:\data\Lars\temp\2015-05-29_102730_ukmz1005immz_12048_1\TOPPAS_tmp\peptide_identification_and_map |
lars20070
/ peptide_identification_and_mapping.toppas
Created
June 7, 2015 08:17
peptide identification and mapping
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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="2.0.0" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="num_vertices" value="31" type="int" description="" required="false" advanced="false" /> | |
| <ITEM name="num_edges" value="35" 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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| MTD mzTab-version 1.0.0 | |
| MTD mzTab-mode Summary | |
| MTD mzTab-type Identification | |
| MTD description Export from idXML | |
| MTD protein_search_engine_score[1] [, , custom score, ] | |
| MTD psm_search_engine_score[1] null | |
| MTD ms_run[1]-location D:/data/Lars/temp/2015-06-15_134751_ukmz1005immz_9764_1/TOPPAS_tmp/protein_inference2/002_IDFilter/out/AGA116.idXML | |
| PRH accession description taxid species database database_version search_engine best_search_engine_score[1] ambiguity_members modifications protein_coverage opt_global_protein_group_type | |
| PRT sp|A2A8L5|PTPRF_MOUSE Receptor-type tyrosine-protein phosphatase F OS=Mus musculus GN=Ptprf PE=1 SV=1 null null null null null 0 null null null null |
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| protein group accessions description taxid species database database_version search_engine best_search_engine_score[1] ambiguity_members modifications protein_coverage opt_global_protein_group_type gene | |
| 1 A2A4P0 ATP-dependent RNA helicase DHX8 OS=Mus musculus GN=Dhx8 PE=2 SV=1 null null null null null 0.933762490749359 null null null null DHX8_MOUSE | |
| 1 A2A8L5 Receptor-type tyrosine-protein phosphatase F OS=Mus musculus GN=Ptprf PE=1 SV=1 null null null null null 0 null null null null PTPRF_MOUSE | |
| 1 A2AJI0 MAP7 domain-containing protein 1 OS=Mus musculus GN=Map7d1 PE=1 SV=1 null null null null null 0.933762490749359 null null null null MA7D1_MOUSE | |
| 1 A2AQP0 Myosin-7B OS=Mus musculus GN=Myh7b PE=3 SV=1 null null null null null 0.933762490749359 null null null null MYH7B_MOUSE | |
| 1 A2ASS6 Titin OS=Mus musculus GN=Ttn PE=1 SV=1 null null null null null 0.933937430381775 null null null null TITIN_MOUSE | |
| 1 A3KFM7 Chromodomain-helicase-DNA-binding protein 6 OS=Mus musculus GN=Chd6 PE=1 SV=1 null null null null null 0.93376 |
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| MTD mzTab-version 1.0.0 | |
| MTD mzTab-mode Summary | |
| MTD mzTab-type Quantification | |
| MTD description Export from consensusXML | |
| MTD peptide_search_engine_score[1] null | |
| MTD psm_search_engine_score[1] null | |
| MTD ms_run[1]-location /Users/lars/Desktop/GW/WL383.consensusXML | |
| PEH sequence accession unique database database_version search_engine best_search_engine_score[1] search_engine_score[1]_ms_run[1] modifications retention_time retention_time_window charge mass_to_charge spectra_ref peptide_abundance_study_variable[1] peptide_abundance_stdev_study_variable[1] peptide_abundance_std_error_study_variable[1] peptide_abundance_study_variable[2] peptide_abundance_stdev_study_variable[2] peptide_abundance_std_error_study_variable[2] opt_global_modified_sequence opt_psm_SpecEValue_score opt_psm_consensus_support opt_psm_protein_references opt_psm_target_decoy | |
| PEP TATPQQAQEVH sp|P17751|TPIS_MOUSE 1 null null null 0 null null 493.487117891973 null 2 619.312272206878 null 287630016 null null 244726000 null null (Dimethyl:2H(4)13C(2 |
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| sequence accession unique database database_version search_engine best_search_engine_score[1] search_engine_score[1]_ms_run[1] modifications retention_time retention_time_window charge mass_to_charge spectra_ref peptide_abundance_study_variable[1] peptide_abundance_stdev_study_variable[1] peptide_abundance_std_error_study_variable[1] peptide_abundance_study_variable[2] peptide_abundance_stdev_study_variable[2] peptide_abundance_std_error_study_variable[2] peptide_abundance_study_variable[3] peptide_abundance_stdev_study_variable[3] peptide_abundance_std_error_study_variable[3] opt_global_modified_sequence opt_psm_Posterior Error Probability_score opt_psm_consensus_support opt_psm_protein_references opt_psm_target_decoy gene | |
| TATPQQAQEVH P17751 1 null null null 0 null null 493.487117891973 null 2 619.312272206878 null 287630016 null null 244726000 null null null null null (Dimethyl:2H(4)13C(2))TATPQQAQEVH 0.0012867650458559 0 unique target TPIS_MOUSE | |
| NHIADPDIDKK Q922Q2 1 null null null 0.0454022988505747 null 1 |
lars20070
/ peptide_pair_detection.toppas
Last active
August 29, 2015 14:23
peptide pair detection for Q Exactive data (using FeatureFinderMultiplex)
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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="2.0.0" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="num_vertices" value="4" type="int" description="" required="false" advanced="false" /> | |
| <ITEM name="num_edges" value="3" 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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