OSCR

Brain defence by the extracellular matrix protein Cochlin.

Code ↔ Paper

9 matches between paragraphs of the paper and lines of its authors' code, computed by the harvester (lexical-v1). Click a colored paragraph or line to see its counterpart.

The 9 matches · 1 of them tie a paragraph to a whole file, not to given lines: a weak match, whose lines are not tinted
  1. [1] § Methods › Gene ontology annotation and filtering ↔ subCellularLocationMap.r, lines 284–364 · score 0.73 · biological process, gene annotations, gene ID, bitr, enrichment, GO
  2. [2] § Methods › Extraction and proteomics of adult zebrafish cerebrospinal fluid ↔ fragger.sh, lines 231–312 · score 0.71 · allowed miss cleavage, variable modifications, MBR, ppm, DIA, mass
  3. [3] § Methods › Gene ontology annotation and filtering ↔ get-syn-salmIg.pl, the whole file · a weak match · score 0.69 · drerio_gene_ensembl, BioMart, Ensembl gene ID, attributes, filtered
  4. [4] § Methods › Extraction and proteomics of adult zebrafish cerebrospinal fluid ↔ dePepComet.py, lines 118–159 · score 0.63 · allowed miss cleavage, variable modifications, spectrum, mass, MS, peptide
  5. [5] § Methods › Extraction and proteomics of adult zebrafish cerebrospinal fluid ↔ fragger.sh, lines 166–229 · score 0.61 · timsTOF, dry, PASEF, spectrometry, DIA, mass
  6. [6] § Methods › Analysis of pineal gland single-cell RNA sequencing data ↔ scratch.nb, lines 61–137 · score 0.59 · FindClusters, nearest neighbor, dimensions, graph, log2, Clustering
  7. [7] § Methods › Analysis of single-cell RNA sequencing data for the rat pineal gland ↔ scratch.nb, lines 61–137 · score 0.58 · FindClusters, nearest neighbor, Dimension, graph, Clustering
  8. [8] § Methods › Analysis of single-cell RNA sequencing data for the rat pineal gland ↔ predPHOsite.rmd, lines 77–130 · score 0.56 · nearest neighbor, Dimension reduction, PCA
  9. [9] § Methods › Analysis of pineal gland single-cell RNA sequencing data ↔ predPHOsite.rmd, lines 77–130 · score 0.55 · nearest neighbor, Dimension reduction, PCA

Paper

Loaded from Europe PMC by your browser, not stored by OSCR: doi.org · Europe PMC

The paper is loaded when this pane is shown.

The authors' code

Shell · 398 lines · 35 KB · GPL-2.0 · 2 matches

  1. C:\Users\animeshs\GD\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck
  2. java -jar -Dfile.encoding=UTF-8 -Xmx57G C:\Users\animeshs\GD\fragpipe\tools\MSFragger-3.1\MSFragger-3.1.jar F:\SINTEF\fragger.params F:\SINTEF\200925_SINTEF_sample-T2-M3_positionA8.raw F:\SINTEF\200925_SINTEF_sample-T2-M4_positionB5.raw F:\SINTEF\200925_SINTEF_sample-T2-M5_positionA6.raw F:\SINTEF\200925_SINTEF_sample-T2-M6_positionB6.raw F:\SINTEF\200925_SINTEF_sample-T2-M7_positionB3.raw F:\SINTEF\200925_SINTEF_sample-T2-M8_positionB8.raw F:\SINTEF\200925_SINTEF_sample-T5-M3_positionB1.raw F:\SINTEF\200925_SINTEF_sample-T5-M4_positionC1.raw F:\SINTEF\200925_SINTEF_sample-T5-M5_positionA3.raw F:\SINTEF\200925_SINTEF_sample-T5-M6_positionA2.raw F:\SINTEF\200925_SINTEF_sample-T5-M7_positionA4.raw F:\SINTEF\200925_SINTEF_sample-T5-M8_positionB7.raw F:\SINTEF\200925_SINTEF_sample-T6-M7_positionB2.raw F:\SINTEF\200925_SINTEF_sample-T6-M8_positionA5.raw F:\SINTEF\200925_SINTEF_sample-T7-M3_positionA1.raw F:\SINTEF\200925_SINTEF_sample-T7-M4_positionC2.raw F:\SINTEF\200925_SINTEF_sample-T7-M5_positionB4.raw F:\SINTEF\200925_SINTEF_sample-T7-M6_positionA7.raw
  3. java -cp C:\Users\animeshs\GD\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove F:\SINTEF\200925_SINTEF_sample-T2-M3_positionA8.pepXML
  4. java -cp C:\Users\animeshs\GD\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove --no-err F:\SINTEF\200925_SINTEF_sample-T2-M3_positionA8.tsv F:\SINTEF\200925_SINTEF_sample-T2-M3_positionA8\200925_SINTEF_sample-T2-M3_positionA8.tsv
  5. java -Dbatmass.io.libs.thermo.dir="C:\Users\animeshs\GD\fragpipe\tools\MSFragger-3.1\ext\thermo" -Xmx57G -cp "C:\Users\animeshs\GD\fragpipe\tools\original-crystalc-1.3.2.jar;C:\Users\animeshs\GD\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\animeshs\GD\fragpipe\tools\grppr-0.3.23.jar" crystalc.Run F:\SINTEF\200925_SINTEF_sample-T2-M3_positionA8\crystalc-1-200925_SINTEF_sample-T2-M3_positionA8.pepXML.params F:\SINTEF\200925_SINTEF_sample-T2-M3_positionA8\200925_SINTEF_sample-T2-M3_positionA8.pepXML
  6. C:\Users\animeshs\GD\fragpipe\tools\philosopher\philosopher.exe peptideprophet --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --decoy rev_ --database F:\SINTEF\2020-10-28-decoys-contam-AP-004_translations.fa.fas --combine 200925_SINTEF_sample-T2-M3_positionA8_c.pepXML
  7. java -cp C:\Users\animeshs\GD\fragpipe\lib/* com.dmtavt.fragpipe.util.RewritePepxml F:\SINTEF\200925_SINTEF_sample-T5-M3_positionB1\interact.pep.xml F:\SINTEF\200925_SINTEF_sample-T5-M3_positionB1.raw
  8. java -cp C:\Users\animeshs\GD\fragpipe\lib/* com.dmtavt.fragpipe.util.RewritePepxml F:\SINTEF\200925_SINTEF_sample-T2-M3_positionA8\interact.pep.xml F:\SINTEF\200925_SINTEF_sample-T2-M3_positionA8.raw
  9. C:\Users\animeshs\GD\fragpipe\tools\philosopher\philosopher.exe proteinprophet --maxppmdiff 2000000 --output combined F:\SINTEF\200925_SINTEF_sample-T5-M5_positionA3\interact.pep.xml F:\SINTEF\200925_SINTEF_sample-T7-M3_positionA1\interact.pep.xml F:\SINTEF\200925_SINTEF_sample-T6-M8_positionA5\interact.pep.xml F:\SINTEF\200925_SINTEF_sample-T2-M3_positionA8\interact.pep.xml F:\SINTEF\200925_SINTEF_sample-T2-M4_positionB5\interact.pep.xml F:\SINTEF\200925_SINTEF_sample-T7-M4_positionC2\interact.pep.xml F:\SINTEF\200925_SINTEF_sample-T7-M5_positionB4\interact.pep.xml F:\SINTEF\200925_SINTEF_sample-T7-M6_positionA7\interact.pep.xml F:\SINTEF\200925_SINTEF_sample-T5-M8_positionB7\interact.pep.xml F:\SINTEF\200925_SINTEF_sample-T5-M7_positionA4\interact.pep.xml F:\SINTEF\200925_SINTEF_sample-T5-M6_positionA2\interact.pep.xml F:\SINTEF\200925_SINTEF_sample-T5-M4_positionC1\interact.pep.xml F:\SINTEF\200925_SINTEF_sample-T2-M5_positionA6\interact.pep.xml F:\SINTEF\200925_SINTEF_sample-T6-M7_positionB2\interact.pep.xml F:\SINTEF\200925_SINTEF_sample-T5-M3_positionB1\interact.pep.xml F:\SINTEF\200925_SINTEF_sample-T2-M7_positionB3\interact.pep.xml F:\SINTEF\200925_SINTEF_sample-T2-M8_positionB8\interact.pep.xml F:\SINTEF\200925_SINTEF_sample-T2-M6_positionB6\interact.pep.xml
  10. PhilosopherDbAnnotate [Work dir: F:\SINTEF\200925_SINTEF_sample-T7-M5_positionB4]
  11. C:\Users\animeshs\GD\fragpipe\tools\philosopher\philosopher.exe database --annotate F:\SINTEF\2020-10-28-decoys-contam-AP-004_translations.fa.fas --prefix rev_
  12. PhilosopherDbAnnotate [Work dir: F:\SINTEF\200925_SINTEF_sample-T5-M8_positionB7]
  13. C:\Users\animeshs\GD\fragpipe\tools\philosopher\philosopher.exe database --annotate F:\SINTEF\2020-10-28-decoys-contam-AP-004_translations.fa.fas --prefix rev_
  14. PhilosopherDbAnnotate [Work dir: F:\SINTEF\200925_SINTEF_sample-T5-M6_positionA2]
  15. C:\Users\animeshs\GD\fragpipe\tools\philosopher\philosopher.exe database --annotate F:\SINTEF\2020-10-28-decoys-contam-AP-004_translations.fa.fas --prefix rev_
  16. PhilosopherDbAnnotate [Work dir: F:\SINTEF\200925_SINTEF_sample-T7-M3_positionA1]
  17. C:\Users\animeshs\GD\fragpipe\tools\philosopher\philosopher.exe database --annotate F:\SINTEF\2020-10-28-decoys-contam-AP-004_translations.fa.fas --prefix rev_
  18. PhilosopherDbAnnotate [Work dir: F:\SINTEF\200925_SINTEF_sample-T6-M8_positionA5]
  19. C:\Users\animeshs\GD\fragpipe\tools\philosopher\philosopher.exe database --annotate F:\SINTEF\2020-10-28-decoys-contam-AP-004_translations.fa.fas --prefix rev_
  20. PhilosopherDbAnnotate [Work dir: F:\SINTEF]
  21. C:\Users\animeshs\GD\fragpipe\tools\philosopher\philosopher.exe database --annotate F:\SINTEF\2020-10-28-decoys-contam-AP-004_translations.fa.fas --prefix rev_
  22. PhilosopherDbAnnotate [Work dir: F:\SINTEF\200925_SINTEF_sample-T2-M4_positionB5]
  23. C:\Users\animeshs\GD\fragpipe\tools\philosopher\philosopher.exe database --annotate F:\SINTEF\2020-10-28-decoys-contam-AP-004_translations.fa.fas --prefix rev_
  24. PhilosopherDbAnnotate [Work dir: F:\SINTEF\200925_SINTEF_sample-T5-M3_positionB1]
  25. C:\Users\animeshs\GD\fragpipe\tools\philosopher\philosopher.exe database --annotate F:\SINTEF\2020-10-28-decoys-contam-AP-004_translations.fa.fas --prefix rev_
  26. PhilosopherDbAnnotate [Work dir: F:\SINTEF\200925_SINTEF_sample-T6-M7_positionB2]
  27. C:\Users\animeshs\GD\fragpipe\tools\philosopher\philosopher.exe database --annotate F:\SINTEF\2020-10-28-decoys-contam-AP-004_translations.fa.fas --prefix rev_
  28. PhilosopherDbAnnotate [Work dir: F:\SINTEF\200925_SINTEF_sample-T7-M4_positionC2]
  29. C:\Users\animeshs\GD\fragpipe\tools\philosopher\philosopher.exe database --annotate F:\SINTEF\2020-10-28-decoys-contam-AP-004_translations.fa.fas --prefix rev_
  30. PhilosopherDbAnnotate [Work dir: F:\SINTEF\200925_SINTEF_sample-T2-M8_positionB8]
  31. C:\Users\animeshs\GD\fragpipe\tools\philosopher\philosopher.exe database --annotate F:\SINTEF\2020-10-28-decoys-contam-AP-004_translations.fa.fas --prefix rev_
  32. PhilosopherDbAnnotate [Work dir: F:\SINTEF\200925_SINTEF_sample-T2-M3_positionA8]
  33. C:\Users\animeshs\GD\fragpipe\tools\philosopher\philosopher.exe database --annotate F:\SINTEF\2020-10-28-decoys-contam-AP-004_translations.fa.fas --prefix rev_
  34. PhilosopherDbAnnotate [Work dir: F:\SINTEF\200925_SINTEF_sample-T7-M6_positionA7]
  35. C:\Users\animeshs\GD\fragpipe\tools\philosopher\philosopher.exe database --annotate F:\SINTEF\2020-10-28-decoys-contam-AP-004_translations.fa.fas --prefix rev_
  36. PhilosopherDbAnnotate [Work dir: F:\SINTEF\200925_SINTEF_sample-T2-M6_positionB6]
  37. C:\Users\animeshs\GD\fragpipe\tools\philosopher\philosopher.exe database --annotate F:\SINTEF\2020-10-28-decoys-contam-AP-004_translations.fa.fas --prefix rev_
  38. PhilosopherDbAnnotate [Work dir: F:\SINTEF\200925_SINTEF_sample-T5-M5_positionA3]
  39. C:\Users\animeshs\GD\fragpipe\tools\philosopher\philosopher.exe database --annotate F:\SINTEF\2020-10-28-decoys-contam-AP-004_translations.fa.fas --prefix rev_
  40. PhilosopherDbAnnotate [Work dir: F:\SINTEF\200925_SINTEF_sample-T5-M7_positionA4]
  41. C:\Users\animeshs\GD\fragpipe\tools\philosopher\philosopher.exe database --annotate F:\SINTEF\2020-10-28-decoys-contam-AP-004_translations.fa.fas --prefix rev_
  42. PhilosopherDbAnnotate [Work dir: F:\SINTEF\200925_SINTEF_sample-T2-M5_positionA6]
  43. C:\Users\animeshs\GD\fragpipe\tools\philosopher\philosopher.exe database --annotate F:\SINTEF\2020-10-28-decoys-contam-AP-004_translations.fa.fas --prefix rev_
  44. PhilosopherDbAnnotate [Work dir: F:\SINTEF\200925_SINTEF_sample-T5-M4_positionC1]
  45. C:\Users\animeshs\GD\fragpipe\tools\philosopher\philosopher.exe database --annotate F:\SINTEF\2020-10-28-decoys-contam-AP-004_translations.fa.fas --prefix rev_
  46. PhilosopherDbAnnotate [Work dir: F:\SINTEF\200925_SINTEF_sample-T2-M7_positionB3]
  47. C:\Users\animeshs\GD\fragpipe\tools\philosopher\philosopher.exe database --annotate F:\SINTEF\2020-10-28-decoys-contam-AP-004_translations.fa.fas --prefix rev_
  48. PhilosopherFilter [Work dir: F:\SINTEF\200925_SINTEF_sample-T7-M6_positionA7]
  49. C:\Users\animeshs\GD\fragpipe\tools\philosopher\philosopher.exe filter --sequential --razor --prot 0.01 --mapmods --tag rev_ --pepxml F:\SINTEF\200925_SINTEF_sample-T7-M6_positionA7 --protxml F:\SINTEF\combined.prot.xml
  50. PhilosopherFilter [Work dir: F:\SINTEF\200925_SINTEF_sample-T5-M8_positionB7]
  51. C:\Users\animeshs\GD\fragpipe\tools\philosopher\philosopher.exe filter --sequential --razor --prot 0.01 --mapmods --tag rev_ --pepxml F:\SINTEF\200925_SINTEF_sample-T5-M8_positionB7 --protxml F:\SINTEF\combined.prot.xml
  52. PhilosopherFilter [Work dir: F:\SINTEF\200925_SINTEF_sample-T7-M3_positionA1]
  53. C:\Users\animeshs\GD\fragpipe\tools\philosopher\philosopher.exe filter --sequential --razor --prot 0.01 --mapmods --tag rev_ --pepxml F:\SINTEF\200925_SINTEF_sample-T7-M3_positionA1 --protxml F:\SINTEF\combined.prot.xml
  54. PhilosopherFilter [Work dir: F:\SINTEF\200925_SINTEF_sample-T2-M3_positionA8]
  55. C:\Users\animeshs\GD\fragpipe\tools\philosopher\philosopher.exe filter --sequential --razor --prot 0.01 --mapmods --tag rev_ --pepxml F:\SINTEF\200925_SINTEF_sample-T2-M3_positionA8 --protxml F:\SINTEF\combined.prot.xml
  56. PhilosopherFilter [Work dir: F:\SINTEF\200925_SINTEF_sample-T6-M7_positionB2]
  57. C:\Users\animeshs\GD\fragpipe\tools\philosopher\philosopher.exe filter --sequential --razor --prot 0.01 --mapmods --tag rev_ --pepxml F:\SINTEF\200925_SINTEF_sample-T6-M7_positionB2 --protxml F:\SINTEF\combined.prot.xml
  58. PhilosopherFilter [Work dir: F:\SINTEF\200925_SINTEF_sample-T5-M5_positionA3]
  59. C:\Users\animeshs\GD\fragpipe\tools\philosopher\philosopher.exe filter --sequential --razor --prot 0.01 --mapmods --tag rev_ --pepxml F:\SINTEF\200925_SINTEF_sample-T5-M5_positionA3 --protxml F:\SINTEF\combined.prot.xml
  60. PhilosopherFilter [Work dir: F:\SINTEF\200925_SINTEF_sample-T6-M8_positionA5]
  61. C:\Users\animeshs\GD\fragpipe\tools\philosopher\philosopher.exe filter --sequential --razor --prot 0.01 --mapmods --tag rev_ --pepxml F:\SINTEF\200925_SINTEF_sample-T6-M8_positionA5 --protxml F:\SINTEF\combined.prot.xml
  62. PhilosopherFilter [Work dir: F:\SINTEF\200925_SINTEF_sample-T5-M4_positionC1]
  63. C:\Users\animeshs\GD\fragpipe\tools\philosopher\philosopher.exe filter --sequential --razor --prot 0.01 --mapmods --tag rev_ --pepxml F:\SINTEF\200925_SINTEF_sample-T5-M4_positionC1 --protxml F:\SINTEF\combined.prot.xml
  64. PhilosopherFilter [Work dir: F:\SINTEF\200925_SINTEF_sample-T5-M3_positionB1]
  65. C:\Users\animeshs\GD\fragpipe\tools\philosopher\philosopher.exe filter --sequential --razor --prot 0.01 --mapmods --tag rev_ --pepxml F:\SINTEF\200925_SINTEF_sample-T5-M3_positionB1 --protxml F:\SINTEF\combined.prot.xml
  66. PhilosopherFilter [Work dir: F:\SINTEF\200925_SINTEF_sample-T2-M8_positionB8]
  67. C:\Users\animeshs\GD\fragpipe\tools\philosopher\philosopher.exe filter --sequential --razor --prot 0.01 --mapmods --tag rev_ --pepxml F:\SINTEF\200925_SINTEF_sample-T2-M8_positionB8 --protxml F:\SINTEF\combined.prot.xml
  68. PhilosopherFilter [Work dir: F:\SINTEF\200925_SINTEF_sample-T2-M6_positionB6]
  69. C:\Users\animeshs\GD\fragpipe\tools\philosopher\philosopher.exe filter --sequential --razor --prot 0.01 --mapmods --tag rev_ --pepxml F:\SINTEF\200925_SINTEF_sample-T2-M6_positionB6 --protxml F:\SINTEF\combined.prot.xml
  70. PhilosopherFilter [Work dir: F:\SINTEF\200925_SINTEF_sample-T5-M6_positionA2]
  71. C:\Users\animeshs\GD\fragpipe\tools\philosopher\philosopher.exe filter --sequential --razor --prot 0.01 --mapmods --tag rev_ --pepxml F:\SINTEF\200925_SINTEF_sample-T5-M6_positionA2 --protxml F:\SINTEF\combined.prot.xml
  72. PhilosopherFilter [Work dir: F:\SINTEF\200925_SINTEF_sample-T2-M5_positionA6]
  73. C:\Users\animeshs\GD\fragpipe\tools\philosopher\philosopher.exe filter --sequential --razor --prot 0.01 --mapmods --tag rev_ --pepxml F:\SINTEF\200925_SINTEF_sample-T2-M5_positionA6 --protxml F:\SINTEF\combined.prot.xml
  74. PhilosopherFilter [Work dir: F:\SINTEF\200925_SINTEF_sample-T5-M7_positionA4]
  75. C:\Users\animeshs\GD\fragpipe\tools\philosopher\philosopher.exe filter --sequential --razor --prot 0.01 --mapmods --tag rev_ --pepxml F:\SINTEF\200925_SINTEF_sample-T5-M7_positionA4 --protxml F:\SINTEF\combined.prot.xml
  76. PhilosopherFilter [Work dir: F:\SINTEF\200925_SINTEF_sample-T7-M4_positionC2]
  77. C:\Users\animeshs\GD\fragpipe\tools\philosopher\philosopher.exe filter --sequential --razor --prot 0.01 --mapmods --tag rev_ --pepxml F:\SINTEF\200925_SINTEF_sample-T7-M4_positionC2 --protxml F:\SINTEF\combined.prot.xml
  78. PhilosopherFilter [Work dir: F:\SINTEF\200925_SINTEF_sample-T2-M4_positionB5]
  79. C:\Users\animeshs\GD\fragpipe\tools\philosopher\philosopher.exe filter --sequential --razor --prot 0.01 --mapmods --tag rev_ --pepxml F:\SINTEF\200925_SINTEF_sample-T2-M4_positionB5 --protxml F:\SINTEF\combined.prot.xml
  80. PhilosopherFilter [Work dir: F:\SINTEF\200925_SINTEF_sample-T7-M5_positionB4]
  81. C:\Users\animeshs\GD\fragpipe\tools\philosopher\philosopher.exe filter --sequential --razor --prot 0.01 --mapmods --tag rev_ --pepxml F:\SINTEF\200925_SINTEF_sample-T7-M5_positionB4 --protxml F:\SINTEF\combined.prot.xml
  82. PhilosopherFilter [Work dir: F:\SINTEF\200925_SINTEF_sample-T2-M7_positionB3]
  83. C:\Users\animeshs\GD\fragpipe\tools\philosopher\philosopher.exe filter --sequential --razor --prot 0.01 --mapmods --tag rev_ --pepxml F:\SINTEF\200925_SINTEF_sample-T2-M7_positionB3 --protxml F:\SINTEF\combined.prot.xml
  84. PhilosopherReport [Work dir: F:\SINTEF\200925_SINTEF_sample-T5-M8_positionB7]
  85. C:\Users\animeshs\GD\fragpipe\tools\philosopher\philosopher.exe report
  86. PhilosopherReport [Work dir: F:\SINTEF\200925_SINTEF_sample-T7-M5_positionB4]
  87. C:\Users\animeshs\GD\fragpipe\tools\philosopher\philosopher.exe report
  88. PhilosopherReport [Work dir: F:\SINTEF\200925_SINTEF_sample-T5-M6_positionA2]
  89. C:\Users\animeshs\GD\fragpipe\tools\philosopher\philosopher.exe report
  90. PhilosopherReport [Work dir: F:\SINTEF\200925_SINTEF_sample-T7-M3_positionA1]
  91. C:\Users\animeshs\GD\fragpipe\tools\philosopher\philosopher.exe report
  92. PhilosopherReport [Work dir: F:\SINTEF\200925_SINTEF_sample-T6-M8_positionA5]
  93. C:\Users\animeshs\GD\fragpipe\tools\philosopher\philosopher.exe report
  94. PhilosopherReport [Work dir: F:\SINTEF\200925_SINTEF_sample-T2-M4_positionB5]
  95. C:\Users\animeshs\GD\fragpipe\tools\philosopher\philosopher.exe report
  96. PhilosopherReport [Work dir: F:\SINTEF\200925_SINTEF_sample-T5-M3_positionB1]
  97. C:\Users\animeshs\GD\fragpipe\tools\philosopher\philosopher.exe report
  98. PhilosopherReport [Work dir: F:\SINTEF\200925_SINTEF_sample-T6-M7_positionB2]
  99. C:\Users\animeshs\GD\fragpipe\tools\philosopher\philosopher.exe report
  100. PhilosopherReport [Work dir: F:\SINTEF\200925_SINTEF_sample-T2-M8_positionB8]
  101. C:\Users\animeshs\GD\fragpipe\tools\philosopher\philosopher.exe report
  102. PhilosopherReport [Work dir: F:\SINTEF\200925_SINTEF_sample-T7-M4_positionC2]
  103. C:\Users\animeshs\GD\fragpipe\tools\philosopher\philosopher.exe report
  104. PhilosopherReport [Work dir: F:\SINTEF\200925_SINTEF_sample-T2-M3_positionA8]
  105. C:\Users\animeshs\GD\fragpipe\tools\philosopher\philosopher.exe report
  106. PhilosopherReport [Work dir: F:\SINTEF\200925_SINTEF_sample-T7-M6_positionA7]
  107. C:\Users\animeshs\GD\fragpipe\tools\philosopher\philosopher.exe report
  108. PhilosopherReport [Work dir: F:\SINTEF\200925_SINTEF_sample-T2-M6_positionB6]
  109. C:\Users\animeshs\GD\fragpipe\tools\philosopher\philosopher.exe report
  110. PhilosopherReport [Work dir: F:\SINTEF\200925_SINTEF_sample-T5-M5_positionA3]
  111. C:\Users\animeshs\GD\fragpipe\tools\philosopher\philosopher.exe report
  112. PhilosopherReport [Work dir: F:\SINTEF\200925_SINTEF_sample-T5-M7_positionA4]
  113. C:\Users\animeshs\GD\fragpipe\tools\philosopher\philosopher.exe report
  114. PhilosopherReport [Work dir: F:\SINTEF\200925_SINTEF_sample-T2-M5_positionA6]
  115. C:\Users\animeshs\GD\fragpipe\tools\philosopher\philosopher.exe report
  116. PhilosopherReport [Work dir: F:\SINTEF\200925_SINTEF_sample-T5-M4_positionC1]
  117. C:\Users\animeshs\GD\fragpipe\tools\philosopher\philosopher.exe report
  118. PhilosopherReport [Work dir: F:\SINTEF\200925_SINTEF_sample-T2-M7_positionB3]
  119. C:\Users\animeshs\GD\fragpipe\tools\philosopher\philosopher.exe report
  120. PhilosopherAbacus [Work dir: F:\SINTEF]
  121. C:\Users\animeshs\GD\fragpipe\tools\philosopher\philosopher.exe abacus --razor --reprint --tag rev_ --protein 200925_SINTEF_sample-T7-M6_positionA7 200925_SINTEF_sample-T5-M8_positionB7 200925_SINTEF_sample-T7-M3_positionA1 200925_SINTEF_sample-T2-M3_positionA8 200925_SINTEF_sample-T6-M7_positionB2 200925_SINTEF_sample-T5-M5_positionA3 200925_SINTEF_sample-T6-M8_positionA5 200925_SINTEF_sample-T5-M4_positionC1 200925_SINTEF_sample-T5-M3_positionB1 200925_SINTEF_sample-T2-M8_positionB8 200925_SINTEF_sample-T2-M6_positionB6 200925_SINTEF_sample-T5-M6_positionA2 200925_SINTEF_sample-T2-M5_positionA6 200925_SINTEF_sample-T5-M7_positionA4 200925_SINTEF_sample-T7-M4_positionC2 200925_SINTEF_sample-T2-M4_positionB5 200925_SINTEF_sample-T7-M5_positionB4 200925_SINTEF_sample-T2-M7_positionB3
  122. WorkspaceClean [Work dir: F:\SINTEF\200925_SINTEF_sample-T5-M8_positionB7]
  123. C:\Users\animeshs\GD\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck
  124. WorkspaceClean [Work dir: F:\SINTEF\200925_SINTEF_sample-T7-M5_positionB4]
  125. C:\Users\animeshs\GD\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck
  126. WorkspaceClean [Work dir: F:\SINTEF\200925_SINTEF_sample-T5-M6_positionA2]
  127. C:\Users\animeshs\GD\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck
  128. WorkspaceClean [Work dir: F:\SINTEF\200925_SINTEF_sample-T7-M3_positionA1]
  129. C:\Users\animeshs\GD\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck
  130. WorkspaceClean [Work dir: F:\SINTEF\200925_SINTEF_sample-T6-M8_positionA5]
  131. C:\Users\animeshs\GD\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck
  132. WorkspaceClean [Work dir: F:\SINTEF]
  133. C:\Users\animeshs\GD\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck
  134. WorkspaceClean [Work dir: F:\SINTEF\200925_SINTEF_sample-T2-M4_positionB5]
  135. C:\Users\animeshs\GD\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck
  136. WorkspaceClean [Work dir: F:\SINTEF\200925_SINTEF_sample-T5-M3_positionB1]
  137. C:\Users\animeshs\GD\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck
  138. WorkspaceClean [Work dir: F:\SINTEF\200925_SINTEF_sample-T6-M7_positionB2]
  139. C:\Users\animeshs\GD\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck
  140. WorkspaceClean [Work dir: F:\SINTEF\200925_SINTEF_sample-T2-M8_positionB8]
  141. C:\Users\animeshs\GD\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck
  142. WorkspaceClean [Work dir: F:\SINTEF\200925_SINTEF_sample-T7-M4_positionC2]
  143. C:\Users\animeshs\GD\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck
  144. WorkspaceClean [Work dir: F:\SINTEF\200925_SINTEF_sample-T2-M3_positionA8]
  145. C:\Users\animeshs\GD\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck
  146. WorkspaceClean [Work dir: F:\SINTEF\200925_SINTEF_sample-T7-M6_positionA7]
  147. C:\Users\animeshs\GD\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck
  148. WorkspaceClean [Work dir: F:\SINTEF\200925_SINTEF_sample-T2-M6_positionB6]
  149. C:\Users\animeshs\GD\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck
  150. WorkspaceClean [Work dir: F:\SINTEF\200925_SINTEF_sample-T5-M5_positionA3]
  151. C:\Users\animeshs\GD\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck
  152. WorkspaceClean [Work dir: F:\SINTEF\200925_SINTEF_sample-T5-M7_positionA4]
  153. C:\Users\animeshs\GD\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck
  154. WorkspaceClean [Work dir: F:\SINTEF\200925_SINTEF_sample-T2-M5_positionA6]
  155. C:\Users\animeshs\GD\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck
  156. WorkspaceClean [Work dir: F:\SINTEF\200925_SINTEF_sample-T5-M4_positionC1]
  157. C:\Users\animeshs\GD\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck
  158. WorkspaceClean [Work dir: F:\SINTEF\200925_SINTEF_sample-T2-M7_positionB3]
  159. C:\Users\animeshs\GD\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck
  160. PTMShepherd [Work dir: F:\SINTEF]
  161. java -Dbatmass.io.libs.thermo.dir="C:\Users\animeshs\GD\fragpipe\tools\MSFragger-3.1\ext\thermo" -cp "C:\Users\animeshs\GD\fragpipe\tools\ptmshepherd-0.4.0.jar;C:\Users\animeshs\GD\fragpipe\tools\batmass-io-1.19.5.jar;C:\Users\animeshs\GD\fragpipe\tools\commons-math3-3.6.1.jar" edu.umich.andykong.ptmshepherd.PTMShepherd "F:\SINTEF\shepherd.config"
  162. ~~~~~~~~~~~~~~~~~~~~~~
  164. Execution order:
  166. Cmd: [START], Work dir: [F:\SINTEF]
  167. Cmd: [WorkspaceCleanInit], Work dir: [F:\SINTEF\200925_SINTEF_sample-T5-M8_positionB7]
  168. Cmd: [WorkspaceCleanInit], Work dir: [F:\SINTEF\200925_SINTEF_sample-T7-M5_positionB4]
  169. Cmd: [WorkspaceCleanInit], Work dir: [F:\SINTEF\200925_SINTEF_sample-T5-M6_positionA2]
  170. Cmd: [WorkspaceCleanInit], Work dir: [F:\SINTEF\200925_SINTEF_sample-T7-M3_positionA1]
  171. Cmd: [WorkspaceCleanInit], Work dir: [F:\SINTEF\200925_SINTEF_sample-T6-M8_positionA5]
  172. Cmd: [WorkspaceCleanInit], Work dir: [F:\SINTEF]
  173. Cmd: [WorkspaceCleanInit], Work dir: [F:\SINTEF\200925_SINTEF_sample-T2-M4_positionB5]
  174. Cmd: [WorkspaceCleanInit], Work dir: [F:\SINTEF\200925_SINTEF_sample-T5-M3_positionB1]
  175. Cmd: [WorkspaceCleanInit], Work dir: [F:\SINTEF\200925_SINTEF_sample-T6-M7_positionB2]
  176. Cmd: [WorkspaceCleanInit], Work dir: [F:\SINTEF\200925_SINTEF_sample-T2-M8_positionB8]
  177. Cmd: [WorkspaceCleanInit], Work dir: [F:\SINTEF\200925_SINTEF_sample-T7-M4_positionC2]
  178. Cmd: [WorkspaceCleanInit], Work dir: [F:\SINTEF\200925_SINTEF_sample-T2-M3_positionA8]
  179. Cmd: [WorkspaceCleanInit], Work dir: [F:\SINTEF\200925_SINTEF_sample-T7-M6_positionA7]
  180. Cmd: [WorkspaceCleanInit], Work dir: [F:\SINTEF\200925_SINTEF_sample-T2-M6_positionB6]
  181. Cmd: [WorkspaceCleanInit], Work dir: [F:\SINTEF\200925_SINTEF_sample-T5-M5_positionA3]
  182. Cmd: [WorkspaceCleanInit], Work dir: [F:\SINTEF\200925_SINTEF_sample-T5-M7_positionA4]
  183. Cmd: [WorkspaceCleanInit], Work dir: [F:\SINTEF\200925_SINTEF_sample-T2-M5_positionA6]
  184. Cmd: [WorkspaceCleanInit], Work dir: [F:\SINTEF\200925_SINTEF_sample-T5-M4_positionC1]
  185. Cmd: [WorkspaceCleanInit], Work dir: [F:\SINTEF\200925_SINTEF_sample-T2-M7_positionB3]
  186. Cmd: [MsFragger], Work dir: [F:\SINTEF]
  187. Cmd: [Crystal-C], Work dir: [F:\SINTEF]
  188. Cmd: [PeptideProphet], Work dir: [F:\SINTEF]
  189. Cmd: [ProteinProphet], Work dir: [F:\SINTEF]
  190. Cmd: [PhilosopherDbAnnotate], Work dir: [F:\SINTEF]
  191. Cmd: [PhilosopherFilter], Work dir: [F:\SINTEF]
  192. Cmd: [PhilosopherReport], Work dir: [F:\SINTEF]
  193. Cmd: [PhilosopherAbacus], Work dir: [F:\SINTEF]
  194. Cmd: [WorkspaceClean], Work dir: [F:\SINTEF\200925_SINTEF_sample-T5-M8_positionB7]
  195. Cmd: [WorkspaceClean], Work dir: [F:\SINTEF\200925_SINTEF_sample-T7-M5_positionB4]
  196. Cmd: [WorkspaceClean], Work dir: [F:\SINTEF\200925_SINTEF_sample-T5-M6_positionA2]
  197. Cmd: [WorkspaceClean], Work dir: [F:\SINTEF\200925_SINTEF_sample-T7-M3_positionA1]
  198. Cmd: [WorkspaceClean], Work dir: [F:\SINTEF\200925_SINTEF_sample-T6-M8_positionA5]
  199. Cmd: [WorkspaceClean], Work dir: [F:\SINTEF]
  200. Cmd: [WorkspaceClean], Work dir: [F:\SINTEF\200925_SINTEF_sample-T2-M4_positionB5]
  201. Cmd: [WorkspaceClean], Work dir: [F:\SINTEF\200925_SINTEF_sample-T5-M3_positionB1]
  202. Cmd: [WorkspaceClean], Work dir: [F:\SINTEF\200925_SINTEF_sample-T6-M7_positionB2]
  203. Cmd: [WorkspaceClean], Work dir: [F:\SINTEF\200925_SINTEF_sample-T2-M8_positionB8]
  204. Cmd: [WorkspaceClean], Work dir: [F:\SINTEF\200925_SINTEF_sample-T7-M4_positionC2]
  205. Cmd: [WorkspaceClean], Work dir: [F:\SINTEF\200925_SINTEF_sample-T2-M3_positionA8]
  206. Cmd: [WorkspaceClean], Work dir: [F:\SINTEF\200925_SINTEF_sample-T7-M6_positionA7]
  207. Cmd: [WorkspaceClean], Work dir: [F:\SINTEF\200925_SINTEF_sample-T2-M6_positionB6]
  208. Cmd: [WorkspaceClean], Work dir: [F:\SINTEF\200925_SINTEF_sample-T5-M5_positionA3]
  209. Cmd: [WorkspaceClean], Work dir: [F:\SINTEF\200925_SINTEF_sample-T5-M7_positionA4]
  210. Cmd: [WorkspaceClean], Work dir: [F:\SINTEF\200925_SINTEF_sample-T2-M5_positionA6]
  211. Cmd: [WorkspaceClean], Work dir: [F:\SINTEF\200925_SINTEF_sample-T5-M4_positionC1]
  212. Cmd: [WorkspaceClean], Work dir: [F:\SINTEF\200925_SINTEF_sample-T2-M7_positionB3]
  213. Cmd: [PTMShepherd], Work dir: [F:\SINTEF]
  215. ~~~~~~~~~~~~~~~~~~~~~~
  217. It's a dry-run, not running the commands.
  220. Please cite:
  221. (Regular searches) MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry–based proteomics. Nat Methods 14:513 (2017)
  222. (Open search) Identification of modified peptides using localization-aware open search. Nat Commun. 11:4065 (2020)
  223. (Open search) Crystal-C: A Computational Tool for Refinement of Open Search Results. J. Proteome Res. 19.6:2511 (2020)
  224. (Open search) PTM-Shepherd: analysis and summarization of post-translational and chemical modifications from open search results. bioRxiv. DOI: 10.1101/2020.07.08.192583 (2020)
  225. (Glyco/labile search) Fast and comprehensive N- and O-glycoproteomics analysis with MSFragger-Glyco. Nat Methods DOI: 10.1101/2020.05.18.10266 (2020)
  226. (timsTOF PASEF) Fast quantitative analysis of timsTOF PASEF data with MSFragger and IonQuant. Mol Cell Proteomics 19: 1575 (2020)
  227. (PeptideProphet/ProteinProphet/PTMProphet/Filtering) Philosopher: a versatile toolkit for shotgun proteomics data analysis. Nat Methods 17:869 (2020)
  228. (TMT-Integrator) Quantitative proteomic landscape of metaplastic breast carcinoma pathological subtypes and their relationship to triple-negative tumors. Nat Commun. 11:1723 (2020)
  229. (DIA-Umpire) DIA-Umpire: comprehensive computational framework for data-independent acquisition proteomics. Nat Methods 12:258 (2015)
  231. #https://github.com/Nesvilab/philosopher/wiki/Simple-Data-Analysis
  232. #FragPipe version 13.0
  233. #MSFragger version 3.0
  234. #Philosopher version 3.2.9 (build 1593192429)
  235. #Pseudomonas project
  236. ln -s /mnt/z/PA
  237. cd PA
  238. $HOME/GD/fragpipe/philosopher workspace --clean --nocheck
  239. $HOME/GD/fragpipe/philosopher workspace --init --nocheck
  240. $HOME/GD/fragpipe/philosopher database --reviewed --contam --id UP000002438
  241. #java -jar $HOME/GD/fragpipe/MSFragger-3.0.jar fragger.open.params 140605_Pseudomonas_O1_K0K6.raw
  242. #for in in *.raw ; do echo $i ; java -Xmx64G -jar $HOME/GD/fragpipe/MSFragger-3.0.jar fragger.open.params $i ; done
  243. #sudo apt -y install parallel
  244. find ./ -name "*.raw" | parallel -j 1 "java -jar $HOME/GD/fragpipe/MSFragger-3.0.jar fragger.open.params {}"
  245. #java -jar -Dfile.encoding=UTF-8 -Xmx64G MSFragger-3.0.jar
  246. for in in *.pepXML ; do echo $i; j=$(basename $i); echo $j ; k=${j%%.*} ; echo $k; mkdir $k ; mv $i $k/. ;mv $k.tsv $k/. ; done
  247. for in in *.tsv ; do echo $i; j=$(basename $i); echo $j ; k=${j%%.*} ; echo $k; mkdir $k ; cp $i $k/. ; done
  248. #java -cp fragpipe/lib/fragpipe-13.0.jar com.github.chhh.utils.FileMove PA/140605_Pseudomonas_O1_K0K6_T2.pepXML GD/Raw/140605_Pseudomonas_O1_K0K6_T2.pepXML
  249. java -Dbatmass.io.libs.thermo.dir="GD/MSFragger-3.0/ext/thermo" -Xmx64G -cp "GD/fragpipe/tools/original-crystalc-1.2.1.jar;GD/fragpipe/tools/batmass-io-1.17.4.jar;GD/fragpipe/tools/grppr-0.3.23.jar" crystalc.Run GD/Raw/crystalc-0-140605_Pseudomonas_O1_K0K6_T2.pepXML.params GD/Raw/140605_Pseudomonas_O1_K0K6_T2.pepXML
  250. PeptideProphet [Work dir: GD/Raw]
  251. GD/philosopher peptideprophet --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --decoy rev_ --database Z:/PA/2020-07-19-decoys-reviewed-contam-UP000002438.fas --combine 140605_Pseudomonas_O1_K0K6_T2_c.pepXML
  252. ProteinProphet [Work dir: GD/Raw]
  253. GD/philosopher proteinprophet --maxppmdiff 2000000 --output combined GD/Raw/interact.pep.xml
  254. PhilosopherDbAnnotate [Work dir: GD/Raw]
  255. GD/philosopher database --annotate Z:/PA/2020-07-19-decoys-reviewed-contam-UP000002438.fas --prefix rev_
  256. PhilosopherFilter [Work dir: GD/Raw]
  257. GD/philosopher filter --sequential --razor --mapmods --prot 0.01 --tag rev_ --pepxml GD/Raw --protxml GD/Raw/combined.prot.xml
  258. PhilosopherReport [Work dir: GD/Raw]
  259. GD/philosopher report --mzid
  260. IonQuant [Work dir: GD/Raw]
  261. GD/fragpipe/jre/bin/java -Xmx64G -Dlibs.bruker.dir="GD/MSFragger-3.0/ext/bruker" -Dlibs.thermo.dir="GD/MSFragger-3.0/ext/thermo" -cp "GD/fragpipe/tools/ionquant-1.3.6.jar;GD/fragpipe/tools/batmass-io-1.17.4.jar" ionquant.IonQuant --threads 23 --ionmobility 0 --mbr 0 --proteinquant 1 --requantify 0 --mztol 10 --imtol 0.05 --rttol 0.4 --mbrmincorr 0.5 --mbrrttol 1 --mbrimtol 0.05 --mbrtoprun 3 --ionfdr 0.01 --proteinfdr 0.01 --peptidefdr 0.01 --normalization 1 --minisotopes 2 --tp 3 --minfreq 0.5 --minions 2 --psm GD/Raw/psm.tsv Z:/PA/140605_Pseudomonas_O1_K0K6_T2.raw 140605_Pseudomonas_O1_K0K6_T2.pepXML
  262. WorkspaceClean [Work dir: GD/Raw]
  263. GD/philosopher workspace --clean --nocheck
  264. PTMShepherd [Work dir: GD/Raw]
  265. GD/fragpipe/jre/bin/java -Dbatmass.io.libs.thermo.dir="GD/MSFragger-3.0/ext/thermo" -cp "GD/fragpipe/tools/ptmshepherd-0.3.4.jar;GD/fragpipe/tools/batmass-io-1.17.4.jar;GD/fragpipe/tools/commons-math3-3.6.1.jar" edu.umich.andykong.ptmshepherd.PTMShepherd "GD/Raw/shepherd.config"
  266. #EL
  267. for i in /mnt/promec-ns9036k/NORSTORE_OSL_DISK/NS9036K/promec/Data/Elite/*.raw ; do echo $i; j=$(basename $i); echo $j ; k=${j%%.*} ; echo $k; java -Xmx64g -jar ./MSFragger-3.0.jar ./open_fragger.params $i ; mkdir ./$k ; mv /mnt/promec-ns9036k/NORSTORE_OSL_DISK/NS9036K/promec/Data/Elite/*.mgf ./$k/. ; mv /mnt/promec-ns9036k/NORSTORE_OSL_DISK/NS9036K/promec/Data/Elite/*.tsv ./$k/. ; mv /mnt/promec-ns9036k/NORSTORE_OSL_DISK/NS9036K/promec/Data/Elite/*.pepXML ./$k/. ; cp -rf ./.meta ./$k/. ; ls -ltrh ./$k ; done
  269. __fragger.open.params__
  270. database_name = 2020-07-22-decoys-reviewed-contam-UP000002438.fas
  271. num_threads = 12 # 0=poll CPU to set num threads; else specify num threads directly (max 64)
  272. precursor_mass_lower = -150
  273. precursor_mass_upper = 500
  274. precursor_mass_units = 0 # 0=Daltons, 1=ppm, 3=DIA, 2=DIA_MS1
  275. precursor_true_tolerance = 10
  276. precursor_true_units = 1 # 0=Daltons, 1=ppm
  277. fragment_mass_tolerance = 0.5
  278. fragment_mass_units = 0 # 0=Daltons, 1=ppm
  279. calibrate_mass = 2 # 0=Off, 1=On, 2=On and find optimal parameters
  280. decoy_prefix = rev_
  282. deisotope = 1
  283. isotope_error = 0 # 0=off, -1/0/1/2/3 (standard C13 error)
  284. mass_offsets = 0 # allow for additional precursor mass window shifts. Multiplexed with isotope_error. mass_offsets = 0/79.966 can be used as a restricted ‘open’ search that looks for unmodified and phosphorylated peptides (on any residue)
  285. precursor_mass_mode = selected
  287. remove_precursor_peak = 0 # 0 = not remove, 1 = only remove the peak with the precursor charge, 2 = remove all peaks with all charge states. Default: 0
  288. remove_precursor_range = -1.50,1.50 # Unit: Da. Default: -1.5,1.5
  289. intensity_transform = 0 # 0 = none, 1 = sqrt root. Default: 0
  291. write_calibrated_mgf = 1 # Write calibrated MS2 scan to a MGF file (0 for No, 1 for Yes).
  292. mass_diff_to_variable_mod = 0 # Put mass diff as a variable modification. 0 for no; 1 for yes and change the original mass diff and the calculated mass accordingly; 2 for yes but not change the original mass diff and the calculated mass.
  294. localize_delta_mass = 1
  295. delta_mass_exclude_ranges = (-1.5,3.5)
  296. fragment_ion_series = b,y
  297. ion_series_definitions =
  299. labile_search_mode = off # options: "off", "nglycan", "labile" (default: off)
  300. deltamass_allowed_residues = ST # aminoacids that are allowed to be modified in Glyco mode. E.g. "ST"
  301. diagnostic_intensity_filter = 0 # possible values are 0 <= x <= 1
  302. Y_type_masses = 0/203.07937/406.15874/568.21156/730.26438/892.3172/349.137279
  303. diagnostic_fragments = 204.086646/186.076086/168.065526/366.139466/144.0656/138.055/126.055/163.060096/512.197375/292.1026925/274.0921325/657.2349/243.026426/405.079246/485.045576/308.09761
  305. search_enzyme_name = trypsin
  306. search_enzyme_cutafter = KR
  307. search_enzyme_butnotafter = P
  309. num_enzyme_termini = 2 # 2 for enzymatic, 1 for semi-enzymatic, 0 for nonspecific digestion
  310. allowed_missed_cleavage = 1 # maximum value is 5
  312. clip_nTerm_M = 1
  314. #maximum of 7 mods - amino acid codes, * for any amino acid, [ and ] specifies protein termini, n and c specifies peptide termini
  315. variable_mod_01 = 15.99490 M 3
  316. variable_mod_02 = 42.01060 [^ 1
  317. # variable_mod_03 = 79.96633 STY 3
  318. # variable_mod_04 = -17.02650 nQnC 1
  319. # variable_mod_05 = -18.01060 nE 1
  320. # variable_mod_06 = 0.00000 site_06 1
  321. # variable_mod_07 = 0.00000 site_07 1
  322. # variable_mod_08 = 0.00000 site_08 1
  323. # variable_mod_09 = 0.00000 site_09 1
  324. # variable_mod_10 = 0.00000 site_10 1
  325. # variable_mod_11 = 0.00000 site_11 1
  326. # variable_mod_12 = 0.00000 site_12 1
  327. # variable_mod_13 = 0.00000 site_13 1
  328. # variable_mod_14 = 0.00000 site_14 1
  329. # variable_mod_15 = 0.00000 site_15 1
  330. # variable_mod_16 = 0.00000 site_16 1
  332. allow_multiple_variable_mods_on_residue = 0 # static mods are not considered
  333. max_variable_mods_per_mod = 3
  334. max_variable_mods_per_peptide = 3 # maximum 5
  335. max_variable_mods_combinations = 5000 # maximum 65534, limits number of modified peptides generated from sequence
  337. output_file_extension = pepXML
  338. output_format = pepXML
  339. output_report_topN = 1
  340. output_max_expect = 50
  341. report_alternative_proteins = 1 # 0=no, 1=yes
  343. precursor_charge = 1 4 # precursor charge range to analyze; does not override any existing charge; 0 as 1st entry ignores parameter
  344. override_charge = 0 # 0=no, 1=yes to override existing precursor charge states with precursor_charge parameter
  346. digest_min_length = 7
  347. digest_max_length = 50
  348. digest_mass_range = 500.0 5000.0 # MH+ peptide mass range to analyze
  349. max_fragment_charge = 2 # set maximum fragment charge state to analyze (allowed max 5)
  351. #open search parameters
  352. track_zero_topN = 0 # in addition to topN results, keep track of top results in zero bin
  353. zero_bin_accept_expect = 0.00 # boost top zero bin entry to top if it has expect under 0.01 - set to 0 to disable
  354. zero_bin_mult_expect = 1.00 # disabled if above passes - multiply expect of zero bin for ordering purposes (does not affect reported expect)
  355. add_topN_complementary = 0
  357. # spectral processing
  359. minimum_peaks = 15 # required minimum number of peaks in spectrum to search (default 10)
  360. use_topN_peaks = 100
  361. min_fragments_modelling = 2
  362. min_matched_fragments = 4
  363. minimum_ratio = 0.01 # filter peaks below this fraction of strongest peak
  364. clear_mz_range = 0.0 0.0 # for iTRAQ/TMT type data; will clear out all peaks in the specified m/z range
  366. # additional modifications
  368. add_Cterm_peptide = 0.000000
  369. add_Nterm_peptide = 0.000000
  370. add_Cterm_protein = 0.000000
  371. add_Nterm_protein = 0.000000
  373. add_G_glycine = 0.000000
  374. add_A_alanine = 0.000000
  375. add_S_serine = 0.000000
  376. add_P_proline = 0.000000
  377. add_V_valine = 0.000000
  378. add_T_threonine = 0.000000
  379. add_C_cysteine = 57.021464
  380. add_L_leucine = 0.000000
  381. add_I_isoleucine = 0.000000
  382. add_N_asparagine = 0.000000
  383. add_D_aspartic_acid = 0.000000
  384. add_Q_glutamine = 0.000000
  385. add_K_lysine = 0.000000
  386. add_E_glutamic_acid = 0.000000
  387. add_M_methionine = 0.000000
  388. add_H_histidine = 0.000000
  389. add_F_phenylalanine = 0.000000
  390. add_R_arginine = 0.000000
  391. add_Y_tyrosine = 0.000000
  392. add_W_tryptophan = 0.000000
  393. add_B_user_amino_acid = 0.000000
  394. add_J_user_amino_acid = 0.000000
  395. add_O_user_amino_acid = 0.000000
  396. add_U_user_amino_acid = 0.000000
  397. add_X_user_amino_acid = 0.000000
  398. add_Z_user_amino_acid = 0.000000

fragger.sh at commit 45f16b9, under GPL-2.0 · at the source

Overview

Authors: Raghumoy Ghosh1,2, Inyoung Jeong3, Preethi Rajamannar3, Nathalie Jurisch-Yaksi3,4, Bernett Teck Kwong Lee1, Suresh Jesuthasan2
ORCID iDs: Nathalie Jurisch-Yaksi, Bernett Teck Kwong Lee, Suresh Jesuthasan
  1. Lee Kong Chian School of Medicine, Nanyang Technological University,Singapore, Singapore
  2. Department of Molecular Biology, Umeå University,Umeå, Sweden
  3. Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology,Trondheim, Norway
  4. Department of Biology, Norwegian University of Science and Technology,Trondheim, Norway
Institutions: Nanyang Technological University (Singapore); Umeå University (Sweden); Norwegian University of Science and Technology (Norway)
Journal: Communications biology, volume 9, issue 1, article 1205
Dates: received 23 November 2025; accepted 3 September 2026; published online 16 September 2026
Type: Research article · Language: English
License: CC BY
Identifiers: DOI 10.1038/s42003-026-10957-8 · PMID 42749783 · PMCID PMC13582957 · OpenAlex W7213253457
Open access: gold, a free copy (OpenAlex)
Status: code verified
Categories: human (organism), mouse (organism), zebrafish (organism), cellular / molecular (subfield)
Methods: Statistics, Smoothing, state filtering, decompositions, Machine learning
Keywords: Neuroimmunology, Infection
MeSH: Brain*, Extracellular Matrix Proteins*, Animals, Humans, Mice, Mycobacterium marinum, Zebrafish, Zebrafish Proteins (* major topic)
Topic: Neurogenesis and neuroplasticity mechanisms (Developmental Neuroscience, Neuroscience), according to OpenAlex
Funding: Ministry of Education - Singapore (MOE) (RG34/20); National Research Foundation Singapore (NRF2017-NRF-ISF002-2676); Nanyang Technological University (Research Scholarship); Norges Forskningsråd (Forskningsrådet) (FRIPRO 353348, 295721)
Citations: not cited yet (Europe PMC); 58 references in the paper

Abstract

The vertebrate brain is protected from infection by tight barriers. However, several barrier structures, including circumventricular organs, can be breached by pathogens. Here, we show that Cochlin, an extracellular matrix-binding protein with anti-bacterial properties, is produced in barrier structures and contributes to immune defence. Transcriptome analysis and in situ hybridisation indicate that cochlin is expressed in the pineal gland, area postrema, choroid plexus and discrete regions of the meninges of zebrafish, mice and humans. The protein is present in the cerebrospinal fluid, and on the surface of ventricle and meninges. Cochlin expression increases in the brain of infected animals and patients, and delivery of recombinant Cochlin reduces bacterial load in zebrafish infected with Mycobacterium marinum. Mutation of cochlin inhibits clearance of bacteria from the brain of zebrafish, and this is reversed by supplying the domain of Cochlin that is implicated in immunity. Barrier tissues thus contribute to brain defence by secreting Cochlin.

Reproduced under the paper's license (CC BY), from the paper cited above.

Repositories

Its files are read in the Code ↔ Paper reader above, with 9 matches between paragraphs and lines of code.

animesh/scripts

License: GPL-2.0
State: the link answers, verified on 26 September 2026
Evidence: files inventoried
Commit: 45f16b9f8493f70d9026045817d91f44bd616a71, 26 September 2026
Languages: Perl (584), R (179), Python (173), MATLAB (96), Shell (88), C (11), Julia (5), Quarto (4), Mathematica (4), JavaScript (3), Java (2), C++ (2), Stan (2), Go (1), Scala (1)
Size: 1,244 files, 1,155 scripts
Software Heritage: archived
Found in: the text, “Extraction and proteomics of adult zebrafish cer”
Holds: README, environment (Dockerfile, Manifest.toml, Project.toml, pyproject.toml, renv.lock), continuous integration, 45 notebooks
Not found: license file, CITATION.cff, tests, documentation
Tools: pandas (95 files), NumPy (82 files), Matplotlib (55 files), ggplot2 (49 files), pheatmap (40 files), limma (33 files), Statistics and Machine Learning Toolbox (24 files), SciPy (21 files), tidyverse (21 files), randomForest (16 files), seaborn (16 files), TensorFlow (16 files), scikit-learn (13 files), Plotly (11 files), survival (9 files), edgeR (8 files), PyTorch (8 files), clusterProfiler (7 files), Signal Processing Toolbox (7 files), Keras (6 files), NEST Simulator (6 files), SPM (5 files), caret (4 files), glmnet (4 files), igraph (4 files), Optimization Toolbox (4 files), NetworkX (4 files), nlme (4 files), Plots.jl (4 files), SAMtools (4 files), statsmodels (4 files), ComplexHeatmap (3 files), DataFrames.jl (3 files), OpenCV (3 files), Stan (3 files), UMAP (3 files), WGCNA (3 files), Biopython (2 files), broom (2 files), data.table (2 files), DESeq2 (2 files), DifferentialEquations.jl (2 files), JAX (2 files), Pillow (2 files), pydicom (2 files), PyMC (2 files), reshape2 (2 files), scikit-image (2 files), Hugging Face Transformers (2 files), XGBoost (2 files), ArviZ (1 file), BCFtools (1 file), brms (1 file), circlize (1 file), CuPy (1 file), Distributions.jl (1 file), Flux.jl (1 file), ggpubr (1 file), imbalanced-learn (1 file), PyTorch Lightning (1 file), lme4 (1 file), Monocle 3 (1 file), Numba (1 file), patchwork (1 file), RDKit (1 file), reticulate (1 file), Seurat (1 file), SHAP (1 file), Subread (featureCounts) (1 file), Turing.jl (1 file), WFDB Python (1 file)
Availability: 1 check, the latest on 26 September 2026: the link answers
  • 26 September 2026: the link answers
1,156 files
At the source: raw.githubusercontent.com/animesh/scripts/ccc63e663e0cd905a4325327292ae8f15c1d5885/geneGroupsQC.r

Raghumoy/Cochlin_manuscript

License: none: the authors keep all their rights
State: the link answers, verified on 26 September 2026
Evidence: files inventoried
Commit: c25d9d751a9be080a7ea0ca4824f1094f3273607, 12 December 2025
Size: 6 files, 0 scripts
Software Heritage: not archived
Found in: “Code availability”
Not found: README, license file, CITATION.cff, environment file, tests, continuous integration, documentation
Availability: 1 check, the latest on 26 September 2026: the link answers
  • 26 September 2026: the link answers
At the source: github.com/Raghumoy/Cochlin_manuscript.git

Code availability

All associated codes are available at https://github.com/Raghumoy/Cochlin_manuscript.git (https://eur01.safelinks.protection.outlook.com/?url=https://github.com/Raghumoy/Cochlin_manuscript.git&data=05|02||2b10fb77f27d40e67bc308dee67c8a39|5a4ba6f9f5314f329467398f19e69de4|0|0|639201619771760121|Unknown|TWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ==|0|||&sdata=r4qd7uFyjN5vVBaUqXbrmxOTt8SP31nWTPrhRmalLGQ=&reserved=0).

Reproduced under the paper's license (CC BY), from the paper cited above.

Tracing map

Proposed by the machine: these links were found in the paper and verified at the source, without human review. The map will receive a Zenodo DOI once one of the paper's authors has validated it with their ORCID.

What the map holds:

  • 2 repositories of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
  • 1,155 scripts, each with its path and the digest of its content;
  • 9 matches between paragraphs of the paper and lines of the code (method lexical-v1);
  • neither the text of the paper nor the code itself.

Its JSON (tracing-map.json) is deposited on Zenodo with its DOI once the map is validated.

Data

Datasets cited

Other data links

Data availability

This paper uses imaging, transcriptomic and mass spec data. Image datasets are available at the NTU Data Repository (https://doi.org/10.21979/N9/VMUBLF). The source data for the charts in Figs. 5 and 6 are available on Figshare (https://doi.org/10.6084/m9.figshare.32447016). We used the following publicly available datasets for transcriptome analysis: GSM3511192 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi), GSE115723 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE115723), GSE221678 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE221678), GSE168704 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE168704), and GSE159812 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE159812). Proteomics data are available on PRIDE Archive via accession ID PXD081626 (https://www.ebi.ac.uk/pride/archive/projects/PXD081626).

Reproduced under the paper's license (CC BY), from the paper cited above.

Versions

The history of this record: each version stored by the harvester or made by a correction of its authors or of the maintainers of its code, and what changed in its facts. The texts of the paper (its abstract, its availability statements) are not part of it; versions that changed only those are not listed.

Version 1, 27 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 6 authors, 2 keywords, 8 MeSH terms, 4 funders, 51 references.

Cite

This paper

Ghosh, R., Jeong, I., Rajamannar, P., Jurisch-Yaksi, N., Lee, B. T. K., & Jesuthasan, S. (2026). Brain defence by the extracellular matrix protein Cochlin. Communications biology, 9(1), 1205. https://doi.org/10.1038/s42003-026-10957-8

BibTeX

@article{ghosh2026brain,
author = {Ghosh, Raghumoy and Jeong, Inyoung and Rajamannar, Preethi and Jurisch-Yaksi, Nathalie and Lee, Bernett Teck Kwong and Jesuthasan, Suresh},
title = {{Brain defence by the extracellular matrix protein Cochlin}},
journal = {Communications biology},
year = {2026},
month = sep,
volume = {9},
number = {1},
pages = {1205},
publisher = {Nature Publishing Group},
issn = {2399-3642},
doi = {10.1038/s42003-026-10957-8},
url = {https://doi.org/10.1038/s42003-026-10957-8},
pmid = {42749783},
pmcid = {PMC13582957}
}

RIS

TY - JOUR
AU - Ghosh, Raghumoy
AU - Jeong, Inyoung
AU - Rajamannar, Preethi
AU - Jurisch-Yaksi, Nathalie
AU - Lee, Bernett Teck Kwong
AU - Jesuthasan, Suresh
TI - Brain defence by the extracellular matrix protein Cochlin
T2 - Communications biology
J2 - Commun Biol
PY - 2026
DA - 2026/09/16
VL - 9
IS - 1
SP - 1205
SN - 2399-3642
PB - Nature Publishing Group
DO - 10.1038/s42003-026-10957-8
UR - https://doi.org/10.1038/s42003-026-10957-8
LA - en
ER -

CSL-JSON

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