mspire 0.5.0 → 0.6.1

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Files changed (107) hide show
  1. data/README.rdoc +24 -0
  2. data/Rakefile +51 -0
  3. data/VERSION +1 -0
  4. data/lib/cv/description.rb +18 -0
  5. data/lib/cv/param.rb +33 -0
  6. data/lib/cv.rb +3 -0
  7. data/lib/io/bookmark.rb +13 -0
  8. data/lib/merge.rb +7 -0
  9. data/lib/ms/cvlist.rb +76 -0
  10. data/lib/ms/digester.rb +245 -0
  11. data/lib/ms/fasta.rb +86 -0
  12. data/lib/ms/ident/peptide/db.rb +243 -0
  13. data/lib/ms/ident/peptide.rb +72 -0
  14. data/lib/ms/ident/peptide_hit/qvalue.rb +56 -0
  15. data/lib/ms/ident/peptide_hit.rb +26 -0
  16. data/lib/ms/ident/pepxml/modifications.rb +83 -0
  17. data/lib/ms/ident/pepxml/msms_pipeline_analysis.rb +70 -0
  18. data/lib/ms/ident/pepxml/msms_run_summary.rb +82 -0
  19. data/lib/ms/ident/pepxml/parameters.rb +14 -0
  20. data/lib/ms/ident/pepxml/sample_enzyme.rb +165 -0
  21. data/lib/ms/ident/pepxml/search_database.rb +49 -0
  22. data/lib/ms/ident/pepxml/search_hit/modification_info.rb +79 -0
  23. data/lib/ms/ident/pepxml/search_hit.rb +144 -0
  24. data/lib/ms/ident/pepxml/search_result.rb +35 -0
  25. data/lib/ms/ident/pepxml/search_summary.rb +92 -0
  26. data/lib/ms/ident/pepxml/spectrum_query.rb +85 -0
  27. data/lib/ms/ident/pepxml.rb +112 -0
  28. data/lib/ms/ident/protein.rb +33 -0
  29. data/lib/ms/ident/protein_group.rb +80 -0
  30. data/lib/ms/ident/search.rb +114 -0
  31. data/lib/ms/ident.rb +37 -0
  32. data/lib/ms/isotope/aa.rb +59 -0
  33. data/lib/ms/mascot.rb +6 -0
  34. data/lib/ms/mass/aa.rb +79 -0
  35. data/lib/ms/mass.rb +55 -0
  36. data/lib/ms/mzml/index_list.rb +98 -0
  37. data/lib/ms/mzml/plms1.rb +34 -0
  38. data/lib/ms/mzml.rb +197 -0
  39. data/lib/ms/obo.rb +38 -0
  40. data/lib/ms/plms1.rb +156 -0
  41. data/lib/ms/quant/qspec/protein_group_comparison.rb +22 -0
  42. data/lib/ms/quant/qspec.rb +112 -0
  43. data/lib/ms/spectrum.rb +154 -8
  44. data/lib/ms.rb +3 -10
  45. data/lib/msplat.rb +2 -0
  46. data/lib/obo/ims.rb +5 -0
  47. data/lib/obo/ms.rb +7 -0
  48. data/lib/obo/ontology.rb +41 -0
  49. data/lib/obo/unit.rb +5 -0
  50. data/lib/openany.rb +23 -0
  51. data/lib/write_file_or_string.rb +18 -0
  52. data/obo/ims.obo +562 -0
  53. data/obo/ms.obo +11677 -0
  54. data/obo/unit.obo +2563 -0
  55. data/spec/ms/cvlist_spec.rb +60 -0
  56. data/spec/ms/digester_spec.rb +351 -0
  57. data/spec/ms/fasta_spec.rb +100 -0
  58. data/spec/ms/ident/peptide/db_spec.rb +108 -0
  59. data/spec/ms/ident/pepxml/sample_enzyme_spec.rb +181 -0
  60. data/spec/ms/ident/pepxml/search_hit/modification_info_spec.rb +37 -0
  61. data/spec/ms/ident/pepxml_spec.rb +442 -0
  62. data/spec/ms/ident/protein_group_spec.rb +68 -0
  63. data/spec/ms/mass_spec.rb +8 -0
  64. data/spec/ms/mzml/index_list_spec.rb +122 -0
  65. data/spec/ms/mzml/plms1_spec.rb +62 -0
  66. data/spec/ms/mzml_spec.rb +50 -0
  67. data/spec/ms/plms1_spec.rb +38 -0
  68. data/spec/ms/quant/qspec_spec.rb +25 -0
  69. data/spec/msplat_spec.rb +24 -0
  70. data/spec/obo_spec.rb +25 -0
  71. data/spec/spec_helper.rb +25 -0
  72. data/spec/testfiles/ms/ident/peptide/db/uni_11_sp_tr.fasta +69 -0
  73. data/spec/testfiles/ms/ident/peptide/db/uni_11_sp_tr.msd_clvg2.min_aaseq4.yml +728 -0
  74. data/spec/testfiles/ms/mzml/j24z.idx_comp.3.mzML +271 -0
  75. data/spec/testfiles/ms/mzml/openms.noidx_nocomp.12.mzML +330 -0
  76. data/spec/testfiles/ms/quant/kill_extra_tabs.rb +13 -0
  77. data/spec/testfiles/ms/quant/max_quant_output.provenance.txt +15 -0
  78. data/spec/testfiles/ms/quant/max_quant_output.txt +199 -0
  79. data/spec/testfiles/ms/quant/pdcd5_final.killedextratabs.tsv +199 -0
  80. data/spec/testfiles/ms/quant/pdcd5_final.killedextratabs.tsv_qspecgp +199 -0
  81. data/spec/testfiles/ms/quant/pdcd5_final.killedextratabs.tsv_qspecgp.csv +199 -0
  82. data/spec/testfiles/ms/quant/pdcd5_final.txt +199 -0
  83. data/spec/testfiles/ms/quant/pdcd5_final.txt_qspecgp +0 -0
  84. data/spec/testfiles/ms/quant/pdcd5_lfq_qspec.CSV.csv +199 -0
  85. data/spec/testfiles/ms/quant/pdcd5_lfq_qspec.csv +199 -0
  86. data/spec/testfiles/ms/quant/pdcd5_lfq_qspec.oneprot.csv +199 -0
  87. data/spec/testfiles/ms/quant/pdcd5_lfq_qspec.oneprot.tsv +199 -0
  88. data/spec/testfiles/ms/quant/pdcd5_lfq_qspec.oneprot.tsv_qspecgp +199 -0
  89. data/spec/testfiles/ms/quant/pdcd5_lfq_qspec.oneprot.tsv_qspecgp.csv +199 -0
  90. data/spec/testfiles/ms/quant/pdcd5_lfq_qspec.txt +199 -0
  91. data/spec/testfiles/ms/quant/pdcd5_lfq_tabdel.txt +134 -0
  92. data/spec/testfiles/ms/quant/pdcd5_lfq_tabdel.txt_qspecgp +134 -0
  93. data/spec/testfiles/ms/quant/remove_rest_of_proteins.rb +13 -0
  94. data/spec/testfiles/ms/quant/unlog_transform.rb +13 -0
  95. data/spec/testfiles/plms1/output.key +0 -0
  96. metadata +157 -40
  97. data/README +0 -77
  98. data/changelog.txt +0 -196
  99. data/lib/ms/calc.rb +0 -32
  100. data/lib/ms/data/interleaved.rb +0 -60
  101. data/lib/ms/data/lazy_io.rb +0 -73
  102. data/lib/ms/data/lazy_string.rb +0 -15
  103. data/lib/ms/data/simple.rb +0 -59
  104. data/lib/ms/data/transposed.rb +0 -41
  105. data/lib/ms/data.rb +0 -57
  106. data/lib/ms/format/format_error.rb +0 -12
  107. data/lib/ms/support/binary_search.rb +0 -126
data/spec/testfiles/ms/mzml/openms.noidx_nocomp.12.mzML ADDED
@@ -0,0 +1,330 @@
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+ <?xml version="1.0" encoding="ISO-8859-1"?>
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+ <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">
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+ <cvList count="2">
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+ <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"/>
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+ <cv id="UO" fullName="Unit Ontology" URI="http://obo.cvs.sourceforge.net/obo/obo/ontology/phenotype/unit.obo"/>
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+ </cvList>
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+ <fileDescription>
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+ <fileContent>
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+ <cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum" />
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+ </fileContent>
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+ <sourceFileList count="1">
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+ <sourceFile id="sf_ru_0" name="file://CHEMBRI-EXTZA1B/t/Mouse_brain_Phosphoproteomics/may062011/11_110506125210.raw" location="">
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+ <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="826a6634f11d0bfd1948d06ecd033ce935175b0c" />
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+ <cvParam cvRef="MS" accession="MS:1000564" name="PSI mzData file" />
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+ <cvParam cvRef="MS" accession="MS:1000777" name="spectrum identifier nativeID format" />
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+ </sourceFile>
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+ </sourceFileList>
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+ </fileDescription>
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+ <sampleList count="1">
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+ <sample id="sa_0" name="">
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+ <cvParam cvRef="MS" accession="MS:1000004" name="sample mass" value="0" unitAccession="UO:0000021" unitName="gram" unitCvRef="UO" />
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+ <cvParam cvRef="MS" accession="MS:1000005" name="sample volume" value="0" unitAccession="UO:0000098" unitName="milliliter" unitCvRef="UO" />
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+ <cvParam cvRef="MS" accession="MS:1000006" name="sample concentration" value="0" unitAccession="UO:0000175" unitName="gram per liter" unitCvRef="UO" />
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+ </sample>
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+ </sampleList>
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+ <softwareList count="5">
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+ <software id="so_in_0" version="2.5.5" >
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+ <cvParam cvRef="MS" accession="MS:1000532" name="Xcalibur" />
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+ </software>
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+ <software id="so_default" version="" >
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+ <cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />
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+ </software>
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+ <software id="so_dp_sp_0_pm_0" version="4.3.1(build Sep 9 2009 12:30:29)" >
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+ <cvParam cvRef="MS" accession="MS:1000541" name="ReAdW" />
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+ </software>
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+ <software id="so_dp_sp_0_pm_1" version="1.7.0" >
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+ <cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="SpectrumCanvas" />
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+ </software>
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+ <software id="so_dp_sp_0_pm_2" version="1.7.0" >
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+ <cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="SpectrumCanvas" />
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+ </software>
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+ </softwareList>
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+ <instrumentConfigurationList count="1">
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+ <instrumentConfiguration id="ic_0">
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+ <cvParam cvRef="MS" accession="MS:1000031" name="instrument model" />
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+ <componentList count="3">
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+ <source order="0">
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+ <cvParam cvRef="MS" accession="MS:1000008" name="ionization type" />
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+ </source>
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+ <analyzer order="0">
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+ <cvParam cvRef="MS" accession="MS:1000014" name="accuracy" value="0" unitAccession="UO:0000169" unitName="parts per million" unitCvRef="UO" />
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+ <cvParam cvRef="MS" accession="MS:1000022" name="TOF Total Path Length" value="0" unitAccession="UO:0000008" unitName="meter" unitCvRef="UO" />
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+ <cvParam cvRef="MS" accession="MS:1000024" name="final MS exponent" value="0" />
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+ <cvParam cvRef="MS" accession="MS:1000025" name="magnetic field strength" value="0" unitAccession="UO:0000228" unitName="tesla" unitCvRef="UO" />
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+ <cvParam cvRef="MS" accession="MS:1000443" name="mass analyzer type" />
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+ </analyzer>
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+ <detector order="0">
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+ <cvParam cvRef="MS" accession="MS:1000028" name="detector resolution" value="0" />
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+ <cvParam cvRef="MS" accession="MS:1000029" name="sampling frequency" value="0" unitAccession="UO:0000106" unitName="hertz" unitCvRef="UO" />
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+ <cvParam cvRef="MS" accession="MS:1000026" name="detector type" />
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+ </detector>
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+ </componentList>
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+ <softwareRef ref="so_in_0" />
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+ </instrumentConfiguration>
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+ </instrumentConfigurationList>
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+ <dataProcessingList count="1">
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+ <dataProcessing id="dp_sp_0">
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+ <processingMethod order="0" softwareRef="so_dp_sp_0_pm_0">
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+ <cvParam cvRef="MS" accession="MS:1000035" name="peak picking" />
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+ <userParam name="#type" type="xsd:string" value="conversion"/>
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+ </processingMethod>
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+ <processingMethod order="0" softwareRef="so_dp_sp_0_pm_1">
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+ <cvParam cvRef="MS" accession="MS:1001486" name="data filtering" />
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+ <cvParam cvRef="MS" accession="MS:1000747" name="completion time" value="2011-05-19+20:22" />
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+ </processingMethod>
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+ <processingMethod order="0" softwareRef="so_dp_sp_0_pm_2">
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+ <cvParam cvRef="MS" accession="MS:1001486" name="data filtering" />
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+ <cvParam cvRef="MS" accession="MS:1000747" name="completion time" value="2011-06-10+09:32" />
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+ </processingMethod>
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+ </dataProcessing>
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+ </dataProcessingList>
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+ <run id="ru_0" defaultInstrumentConfigurationRef="ic_0" sampleRef="sa_0" defaultSourceFileRef="sf_ru_0">
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+ <spectrumList count="12" defaultDataProcessingRef="dp_sp_0">
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+ <spectrum id="scan=10929" index="0" defaultArrayLength="0" dataProcessingRef="dp_sp_0">
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+ <cvParam cvRef="MS" accession="MS:1000525" name="spectrum representation" />
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+ <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="1" />
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+ <cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum" />
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+ <cvParam cvRef="MS" accession="MS:1000130" name="positive scan" />
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+ <scanList count="1">
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+ <cvParam cvRef="MS" accession="MS:1000795" name="no combination" />
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+ <scan >
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+ </scan>
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+ </scanList>
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+ </spectrum>
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+ <spectrum id="scan=10930" index="1" defaultArrayLength="0">
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+ <cvParam cvRef="MS" accession="MS:1000525" name="spectrum representation" />
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+ <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="2" />
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+ <cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum" />
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+ <cvParam cvRef="MS" accession="MS:1000130" name="positive scan" />
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+ <scanList count="1">
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+ <cvParam cvRef="MS" accession="MS:1000795" name="no combination" />
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+ <scan >
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+ <cvParam cvRef="MS" accession="MS:1000016" name="scan start time" value="6605.5" unitAccession="UO:0000010" unitName="second" unitCvRef="UO" />
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+ </scan>
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+ </scanList>
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+ <precursorList count="1">
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+ <precursor>
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+ <isolationWindow>
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+ <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="696.86376953" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
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+ <cvParam cvRef="MS" accession="MS:1000828" name="isolation window lower offset" value="0" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
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+ </isolationWindow>
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+ <selectedIon>
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+ </selectedIonList>
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+ <activation>
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+ </precursor>
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+ <cvParam cvRef="MS" accession="MS:1000525" name="spectrum representation" />
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+ <cvParam cvRef="MS" accession="MS:1000130" name="positive scan" />
221
+ <scanList count="1">
222
+ <cvParam cvRef="MS" accession="MS:1000795" name="no combination" />
223
+ <scan >
224
+ <cvParam cvRef="MS" accession="MS:1000016" name="scan start time" value="6607.93" unitAccession="UO:0000010" unitName="second" unitCvRef="UO" />
225
+ </scan>
226
+ </scanList>
227
+ </spectrum>
228
+ <spectrum id="scan=10936" index="7" defaultArrayLength="0">
229
+ <cvParam cvRef="MS" accession="MS:1000525" name="spectrum representation" />
230
+ <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="2" />
231
+ <cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum" />
232
+ <cvParam cvRef="MS" accession="MS:1000130" name="positive scan" />
233
+ <scanList count="1">
234
+ <cvParam cvRef="MS" accession="MS:1000795" name="no combination" />
235
+ <scan >
236
+ <cvParam cvRef="MS" accession="MS:1000016" name="scan start time" value="6608.49" unitAccession="UO:0000010" unitName="second" unitCvRef="UO" />
237
+ </scan>
238
+ </scanList>
239
+ <precursorList count="1">
240
+ <precursor>
241
+ <isolationWindow>
242
+ <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="640.64752197" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
243
+ <cvParam cvRef="MS" accession="MS:1000828" name="isolation window lower offset" value="0" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
244
+ <cvParam cvRef="MS" accession="MS:1000829" name="isolation window upper offset" value="0" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
245
+ </isolationWindow>
246
+ <selectedIonList count="1">
247
+ <selectedIon>
248
+ <cvParam cvRef="MS" accession="MS:1000744" name="selected ion m/z" value="640.64752197" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
249
+ <cvParam cvRef="MS" accession="MS:1000041" name="charge state" value="3" />
250
+ <cvParam cvRef="MS" accession="MS:1000042" name="peak intensity" value="237991" unitAccession="MS:1000132" unitName="percent of base peak" unitCvRef="MS" />
251
+ </selectedIon>
252
+ </selectedIonList>
253
+ <activation>
254
+ <cvParam cvRef="MS" accession="MS:1000509" name="activation energy" value="0" unitAccession="UO:0000266" unitName="electronvolt" unitCvRef="UO" />
255
+ <cvParam cvRef="MS" accession="MS:1000044" name="dissociation method" />
256
+ </activation>
257
+ </precursor>
258
+ </precursorList>
259
+ </spectrum>
260
+ <spectrum id="scan=10937" index="8" defaultArrayLength="0">
261
+ <cvParam cvRef="MS" accession="MS:1000525" name="spectrum representation" />
262
+ <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="1" />
263
+ <cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum" />
264
+ <cvParam cvRef="MS" accession="MS:1000130" name="positive scan" />
265
+ <scanList count="1">
266
+ <cvParam cvRef="MS" accession="MS:1000795" name="no combination" />
267
+ <scan >
268
+ <cvParam cvRef="MS" accession="MS:1000016" name="scan start time" value="6608.92" unitAccession="UO:0000010" unitName="second" unitCvRef="UO" />
269
+ </scan>
270
+ </scanList>
271
+ </spectrum>
272
+ <spectrum id="scan=10938" index="9" defaultArrayLength="0">
273
+ <cvParam cvRef="MS" accession="MS:1000525" name="spectrum representation" />
274
+ <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="2" />
275
+ <cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum" />
276
+ <cvParam cvRef="MS" accession="MS:1000130" name="positive scan" />
277
+ <scanList count="1">
278
+ <cvParam cvRef="MS" accession="MS:1000795" name="no combination" />
279
+ <scan >
280
+ <cvParam cvRef="MS" accession="MS:1000016" name="scan start time" value="6609.49" unitAccession="UO:0000010" unitName="second" unitCvRef="UO" />
281
+ </scan>
282
+ </scanList>
283
+ <precursorList count="1">
284
+ <precursor>
285
+ <isolationWindow>
286
+ <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="460.55426025" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
287
+ <cvParam cvRef="MS" accession="MS:1000828" name="isolation window lower offset" value="0" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
288
+ <cvParam cvRef="MS" accession="MS:1000829" name="isolation window upper offset" value="0" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
289
+ </isolationWindow>
290
+ <selectedIonList count="1">
291
+ <selectedIon>
292
+ <cvParam cvRef="MS" accession="MS:1000744" name="selected ion m/z" value="460.55426025" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
293
+ <cvParam cvRef="MS" accession="MS:1000041" name="charge state" value="3" />
294
+ <cvParam cvRef="MS" accession="MS:1000042" name="peak intensity" value="182959" unitAccession="MS:1000132" unitName="percent of base peak" unitCvRef="MS" />
295
+ </selectedIon>
296
+ </selectedIonList>
297
+ <activation>
298
+ <cvParam cvRef="MS" accession="MS:1000509" name="activation energy" value="0" unitAccession="UO:0000266" unitName="electronvolt" unitCvRef="UO" />
299
+ <cvParam cvRef="MS" accession="MS:1000044" name="dissociation method" />
300
+ </activation>
301
+ </precursor>
302
+ </precursorList>
303
+ </spectrum>
304
+ <spectrum id="scan=10939" index="10" defaultArrayLength="0">
305
+ <cvParam cvRef="MS" accession="MS:1000525" name="spectrum representation" />
306
+ <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="1" />
307
+ <cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum" />
308
+ <cvParam cvRef="MS" accession="MS:1000130" name="positive scan" />
309
+ <scanList count="1">
310
+ <cvParam cvRef="MS" accession="MS:1000795" name="no combination" />
311
+ <scan >
312
+ <cvParam cvRef="MS" accession="MS:1000016" name="scan start time" value="6609.94" unitAccession="UO:0000010" unitName="second" unitCvRef="UO" />
313
+ </scan>
314
+ </scanList>
315
+ </spectrum>
316
+ <spectrum id="scan=10940" index="11" defaultArrayLength="0">
317
+ <cvParam cvRef="MS" accession="MS:1000525" name="spectrum representation" />
318
+ <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="1" />
319
+ <cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum" />
320
+ <cvParam cvRef="MS" accession="MS:1000130" name="positive scan" />
321
+ <scanList count="1">
322
+ <cvParam cvRef="MS" accession="MS:1000795" name="no combination" />
323
+ <scan >
324
+ <cvParam cvRef="MS" accession="MS:1000016" name="scan start time" value="6610.53" unitAccession="UO:0000010" unitName="second" unitCvRef="UO" />
325
+ </scan>
326
+ </scanList>
327
+ </spectrum>
328
+ </spectrumList>
329
+ </run>
330
+ </mzML>
data/spec/testfiles/ms/quant/kill_extra_tabs.rb ADDED
@@ -0,0 +1,13 @@
1
+ #!/usr/bin/env ruby
2
+
3
+ file = ARGV.shift
4
+
5
+ base = file.chomp(File.extname(file))
6
+
7
+ File.open(base + '.killedextratabs.tsv','w') do |out|
8
+ IO.foreach(file) do |line|
9
+ data = line.chomp.split("\t")
10
+ data = data[0,data.rindex {|v| !v.nil? }+1]
11
+ out.puts data.join("\t")
12
+ end
13
+ end
data/spec/testfiles/ms/quant/max_quant_output.provenance.txt ADDED
@@ -0,0 +1,15 @@
1
+ To get this file, used MaxQuant 1.2.2.5
2
+
3
+ Used Perseus 1.2.0.17 to transform the data:
4
+
5
+ First removed contaminants
6
+ Then removed those that showed up in reverse search
7
+ Ln of LFQ intensities
8
+ Imputation of LFQ int (normal distr) so that there are no zeros [ Width 0.3 and Downshift 1.8 ]
9
+
10
+ Columns selected (included):
11
+ LFQ Intensities
12
+ MS/MS
13
+ Protein ID's
14
+
15
+ note, the file is really tab delimited