OSCR

Disruption of the LRRK2 substrate RAB12 facilitates neurotransmission and causes hyperactivity in mice.

Code ↔ Paper

2 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 2 matches
  1. [1] § Methods › Proteomic data analysis ↔ JUMPg/programs/params/jump_params.pl, lines 229–288 · score 0.72 · amino acids, database search, static, dynamic, modifications, cysteine
  2. [2] § Methods › Whole-proteome profiling using 18-plex TMTpro coupled with LC/LC-MS/MS ↔ JUMPg/programs/params/jump_params.pl, lines 82–167 · score 0.66 · isolation offset, isolation window, MS1, TMT, dynamic, MS2

Paper

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

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The authors' code

Perl · 905 lines · 50 KB · no license · 2 matches

  1. #!/bin/env perl
  3. use strict;
  4. use warnings;
  5. use Cwd;
  6. use File::Basename;
  8. ## Directory information
  9. my $currDir = getcwd()."/ParameterFiles";
  10. if (!-e $currDir) {
  11. system ("mkdir $currDir");
  12. }
  14. ## Version information
  15. my $version = "12.0.0";
  16. my $releaseDate = "05/01/2015";
  18. ## Search engines/Conditions
  19. my @searchEngines = ("JUMP", "SEQUEST");
  20. my @conditions = ("HH", "HL", "TMThh", "TMThhpho");
  22. ##################################################
  23. ## Search parameter file generation (jump -s) ##
  24. ##################################################
  25. foreach my $searchEngine (@searchEngines) {
  26. foreach my $condition (@conditions) {
  27. ##############################################################
  28. ## Search engine- and condition-dependent parameter setting ##
  29. ##############################################################
  30. my $databaseName;
  31. my $pitFile;
  32. my $isolationWindow = 1.6;
  33. my $isolationOffset = 0.25;
  34. my $isolationVariation = 0.25;
  35. my $percentagePPI = 10;
  36. my $massCorrection = 2;
  37. my $ms2Deisotope = 1;
  38. my $ms2Consolidation = 10;
  39. my $TMTdata = 0;
  40. my $tagGeneration = 0;
  41. my $tagTolerance = 10;
  42. my $tagToleranceUnit = 2;
  43. my $ionSeries = "1 1 0 0 0 0 0 1 0";
  44. my $fragMassTolerance;
  45. my $fragMassToleranceUnit;
  46. my $ionLossesMS2 = "0 0 0 0";
  47. my $ionLossesMS1 = 0;
  48. my $secondSearch = 0;
  49. my $addNtermPeptide = "0.0000";
  50. my $addKLysine = "0.0000";
  51. my ($dynamicS, $dynamicT, $dynamicY);
  52. my $paramsDir;
  53. my $paramsName;
  54. ## Database name and pit file
  55. if ($searchEngine eq "JUMP") {
  56. if ($condition eq "HH" || $condition eq "HL") {
  57. $databaseName = "/data1/database/20150201/human_ft_mc2_c0.fasta.mdx";
  58. $pitFile = "/data1/database/20150201/human_ft_mc2_c0.pit";
  59. } elsif ($condition eq "TMThh") {
  60. $databaseName = "/data1/database/20150201/human_ft_mc2_c0_TMT_K229.fasta.mdx";
  61. $pitFile = "/data1/database/20150201/human_ft_mc2_c0_TMT_K229.pit";
  62. } elsif ($condition eq "TMThhpho") {
  63. $databaseName = "/data1/database/20150201/human_ft_mc2_c0_pho_TMT_K229.fasta.mdx";
  64. $pitFile = "/data1/database/20150201/human_ft_mc2_c0_pho_TMT_K229.pit";
  65. }
  66. } else {
  67. if ($condition eq "HH" || $condition eq "HL") {
  68. $databaseName = "/data1/database/20150201/human_ft_mc2_c0.fasta.hdr";
  69. $pitFile = "/data1/database/20150201/human_ft_mc2_c0.pit";
  70. } elsif ($condition eq "TMThh") {
  71. $databaseName = "/data1/database/20150201/human_ft_mc2_c0_TMT_K229.fasta.hdr";
  72. $pitFile = "/data1/database/20150201/human_ft_mc2_c0_TMT_K229.pit";
  73. } elsif ($condition eq "TMThhpho") {
  74. $databaseName = "/data1/database/20150201/human_ft_mc2_c0_TMT_K229.fasta.hdr";
  75. $pitFile = "/data1/database/20150201/human_ft_mc2_c0_TMT_K229.pit";
  76. }
  77. }
  78. ## Isolation window
  79. if ($condition eq "TMThh") {
  80. $isolationWindow = 1.0;
  81. $isolationOffset = 0.2;
  82. $isolationVariation = 0.2;
  83. } elsif ($condition eq "TMThhpho") {
  84. $isolationWindow = 1.4;
  85. $isolationOffset = 0;
  86. $isolationVariation = 0.2;
  87. }
  88. ## PPI percentage
  89. if ($condition eq "TMThh" || $condition eq "TMThhpho") {
  90. $percentagePPI = 50;
  91. }
  92. ## Mass correction and MS2-deisotope
  93. if ($condition eq "HL") {
  94. $massCorrection = 1;
  95. $ms2Deisotope = 0;
  96. }
  97. ## MS2-consolidation
  98. if ($condition eq "TMThhpho") {
  99. $ms2Consolidation = 30;
  100. } elsif ($searchEngine eq "SEQUEST" && $condition eq "HL") {
  101. $ms2Consolidation = 20;
  102. }
  103. ## SEQUEST-phospho-search
  104. if ($searchEngine eq "SEQUEST" && $condition eq "TMThhpho") {
  105. $ms2Deisotope = 0;
  106. $ms2Consolidation = 10000;
  107. }
  108. ## TMT-data
  109. if ($condition eq "TMThh" || $condition eq "TMThhpho") {
  110. $TMTdata = 1;
  111. }
  112. ## Tag generation
  113. if ($searchEngine eq "JUMP") {
  114. $tagGeneration = 1;
  115. }
  116. ## Tag tolerance and ion series
  117. if ($condition eq "HL") {
  118. $tagTolerance = 0.4;
  119. $tagToleranceUnit = 1;
  120. $ionSeries = "0 1 0 0 0 0 0 1 0";
  121. }
  122. ## Fragment ion mass tolerance
  123. if ($condition eq "HL") {
  124. $fragMassTolerance = 0.5;
  125. $fragMassToleranceUnit = 1;
  126. } else {
  127. if ($searchEngine eq "JUMP") {
  128. $fragMassTolerance = 15;
  129. $fragMassToleranceUnit = 2;
  130. } else {
  131. $fragMassTolerance = 0.015;
  132. $fragMassToleranceUnit = 1;
  133. }
  134. }
  135. ## Ion losses and dynamic modifications for phosphoproteome
  136. if ($condition eq "TMThhpho") {
  137. $ionLossesMS2 = "1 1 1 0 ";
  138. $ionLossesMS1 = 1;
  139. $dynamicS = 79.96633;
  140. $dynamicT = 79.96633;
  141. $dynamicY = 79.96633;
  142. }
  143. ## Second search
  144. if ($searchEngine eq "JUMP") {
  145. $secondSearch = 1;
  146. }
  147. ## Static modification
  148. if ($TMTdata == 1) {
  149. $addNtermPeptide = 229.162932;
  150. $addKLysine = 229.162932;
  151. }
  152. ## Params file name
  153. if ($searchEngine eq "JUMP") {
  154. $paramsName = "jump_sj_";
  155. } else {
  156. $paramsName = "jump_ss_";
  157. }
  158. if ($condition eq "HH") {
  159. #$paramsName = $paramsName."HH_human.params";
  160. $paramsName = $paramsName."HH.params";
  161. } elsif ($condition eq "HL") {
  162. $paramsName = $paramsName."HL.params";
  163. } elsif ($condition eq "TMThh") {
  164. $paramsName = $paramsName."TMThh.params";
  165. } elsif ($condition eq "TMThhpho") {
  166. $paramsName = $paramsName."TMThhpho.params";
  167. }
  169. ##########################
  170. ## Print .params files ##
  171. ##########################
  172. if ($condition eq "HH") {
  173. $paramsDir = $currDir."/HH";
  174. if (!-e $paramsDir) {
  175. system("mkdir $paramsDir");
  176. }
  177. $paramsName = $paramsDir."/".$paramsName;
  178. } elsif ($condition eq "HL") {
  179. $paramsDir = $currDir."/HL";
  180. if (!-e $paramsDir) {
  181. system("mkdir $paramsDir");
  182. }
  183. $paramsName = $paramsDir."/".$paramsName;
  184. } elsif ($condition eq "TMThh") {
  185. $paramsDir = $currDir."/TMThh";
  186. if (!-e $paramsDir) {
  187. system("mkdir $paramsDir");
  188. }
  189. $paramsName = $paramsDir."/".$paramsName;
  190. } else {
  191. $paramsDir = $currDir."/TMThhpho";
  192. if (!-e $paramsDir) {
  193. system("mkdir $paramsDir");
  194. }
  195. $paramsName = $paramsDir."/".$paramsName;
  196. }
  197. open (PARAMS, ">", $paramsName) or die "Cannot generate $paramsName\n";
  198. print PARAMS "# JUMP search parameter file (Version: $version, Date: $releaseDate)\n";
  199. print PARAMS "\n";
  200. print PARAMS "search_engine = $searchEngine # use JUMP or SEQUEST for database search\n";
  201. print PARAMS "\n";
  202. print PARAMS "# Database settings\n";
  203. if ($condition eq "TMThh" or $condition eq "TMThhpho") {
  204. print PARAMS "database_name = $databaseName # use .fasta.mdx for JUMP and .fasta.hdr for SEQUEST\n";
  205. print PARAMS "pit_file = $pitFile # protein inference table (pit) for grouping proteins/genes\n";
  206. } else {
  207. print PARAMS "database_name = $databaseName # use .fasta.mdx for JUMP and .fasta.hdr for SEQUEST\n";
  208. print PARAMS "pit_file = $pitFile # protein inference table (pit) for grouping proteins/genes\n";
  209. }
  210. print PARAMS "peptide_tolerance = 6 # precursor mass (MH+) tolerance, default = 6 ppm after mass correction\n";
  211. print PARAMS "peptide_tolerance_units = 2 # 1 = Da; 2 = ppm\n";
  212. print PARAMS "\n";
  213. print PARAMS "# Preprocessing parameters\n";
  214. print PARAMS "first_scan_extraction = 5000 # the first scan number for search\n";
  215. print PARAMS "last_scan_extraction = 10000 # the last scan number for search, use a large number (e.g. 10E6) for full scans\n";
  216. print PARAMS "isolation_window = $isolationWindow # +/- (isolation_window)/2 based on MS2 isolation window (e.g. 1.6 m/z)\n";
  217. print PARAMS "isolation_window_offset = $isolationOffset # +/- isolation_window_offset based on MS2 isolation window offset (e.g. 0.25 m/z)\n";
  218. print PARAMS "isolation_window_variation = $isolationVariation # +/- isolation_window_variation based on MS2 isolation window offset (e.g. 0.25 m/z)\n";
  219. print PARAMS "\n";
  220. print PARAMS "interscanppm = 15 # mass tolerance for interscan precursor identification\n";
  221. print PARAMS "intrascanppm = 10 # mass tolerance for intrascan isotopic decharging\n";
  222. print PARAMS "max_num_ppi = 0 # 0 = disable; 1-0 = max precursor ions selected for mixed MS2 search\n";
  223. print PARAMS "percentage_ppi = $percentagePPI # minimal percentage of precursor peak intensity (ppi) when max_num_ppi = 0\n";
  224. print PARAMS "ppi_charge_0 = 1 # 0 = discard uncharged MS1 (charge = 0); 1 = manual charge assignment (+2 and +3)\n";
  225. print PARAMS "ppi_charge_1 = 1 # 0 = discard MS1 with charge +1; 1 = enable original charge +1\n";
  226. print PARAMS "mass_correction = $massCorrection # 0 = no correction, 1 = MS1-based, 2 = MS1/2-based, 3 = manual correction\n";
  227. print PARAMS "prec_window = 3 # 0 = disable; 1-10 (Da) = mz windows for removing precursor ions\n";
  228. print PARAMS "MS2_deisotope = $ms2Deisotope # 0 = disable; 1 = enable\n";
  229. print PARAMS "ppm = 10 # mass tolerance for MS2 decharging and deisotoping\n";
  230. print PARAMS "charge12_ppm = 15 # mass tolerance for merging different charged ions with the same mass\n";
  231. print PARAMS "ms2_consolidation = $ms2Consolidation # maximal number of peaks retained within each 100-Da window\n";
  232. print PARAMS "TMT_data = $TMTdata # 0 = disable; 1 = enable\n";
  233. print PARAMS "\n";
  234. print PARAMS "# Tagging\n";
  235. print PARAMS "tag_generation = $tagGeneration # 0 = disable; 1 = enable to generate tags\n";
  236. print PARAMS "tag_tolerance = $tagTolerance # mass tolerance for measuring peak distance for generating tags\n";
  237. print PARAMS "tag_tolerance_unit = $tagToleranceUnit # 1 = Da; 2 = ppm\n";
  238. print PARAMS "tag_select_method = comb_p # tag ranking: comb_p, hyper_p or rank_p\n";
  239. print PARAMS "\n";
  240. print PARAMS "# Database searching\n";
  241. print PARAMS "ion_series = $ionSeries # a, b, c, d, v, w, x, y and z ions, respectively\n";
  242. print PARAMS "frag_mass_tolerance = $fragMassTolerance # mass tolerance for MS2 ion matching\n";
  243. print PARAMS "frag_mass_tolerance_unit = $fragMassToleranceUnit # 1 = Da; 2 = ppm\n";
  244. print PARAMS "ion_losses_MS2 = $ionLossesMS2 # 0 = disable; 1 = enable neutral loss of H2O, HPO3, H3PO4 and NH3, respectively\n";
  245. print PARAMS "ion_losses_MS1 = $ionLossesMS1 # 0 = disable; 1 = use precursor ion phosphate neutral loss to estimate #S/T phosphorylation\n";
  246. print PARAMS "ion_scoring = 1 # 1 = scoring product ions simultaneously; 2 = scoring ion series and charge states separately\n";
  247. print PARAMS "\n";
  248. print PARAMS "matching_method = hyper_p # PSM scoring: comb_p, hyper_p, rank_p\n";
  249. print PARAMS "tag_search_method = 2 # 1 = exit when found; 2 = exhaustive search using tags defined by max_number_tag_for_search\n";
  250. print PARAMS "max_number_tags_for_search = 50 # max tags used for search unless the total number of tags is smaller than this defined value\n";
  251. print PARAMS "number_of_selected_result = 5 # maximal tentative PSMs in .spout ranked by Jscore\n";
  252. print PARAMS "number_of_detailed_result = 5 # maximal tentative PSMs in .spout ranked by pattern matching score\n";
  253. print PARAMS "second_search = $secondSearch # 0 = disable; 1 = enable; for PSMs with FDR>0, perform the another round of search\n";
  254. print PARAMS " # by relaxing monoisotopic mass by including M-2, M-1, M, M+1, M+2\n";
  255. print PARAMS "# Dynamic Modifications: SEQUEST requires no new database; but JUMP requires new database\n";
  256. print PARAMS "# C: 57.02146 carbamidomethylation or 71.0371 acrylamide\n";
  257. print PARAMS "# STY: 79.96633; M: 15.99492; GG: 114.04293\n";
  258. print PARAMS "# SILAC: K:4.02511, 6.02013, 8.01420; SILAC: R:6.02013, 10.00827\n";
  259. print PARAMS "# TMT6-10: 229.1629321; TMT2: 225.1558327; TMT0: 224.1524779\n";
  260. print PARAMS "dynamic_M = 15.99492 # add each dynamic modification by one line, starting with dynamic_aa\n";
  261. print PARAMS "# dynamic_C = 57.02146 # add additional dynamic modification by line, starting with dynamic_aa\n";
  262. if (defined $dynamicS) {
  263. print PARAMS "dynamic_S = $dynamicS\n";
  264. print PARAMS "dynamic_T = $dynamicT\n";
  265. print PARAMS "dynamic_Y = $dynamicY\n";
  266. }
  267. print PARAMS "\n";
  268. print PARAMS "# Parameters for creating database (should match with the selected database)\n";
  269. print PARAMS "enzyme_info = Tryptic KR P # LysC K ; ArgC R ; GluC DE ;\n";
  270. print PARAMS "digestion = full # full or partial\n";
  271. print PARAMS "max_mis_cleavage = 2 # maximal miscleavage sites allowed for each peptide\n";
  272. print PARAMS "min_peptide_mass = 400.0000 # minimal mass of peptide database\n";
  273. print PARAMS "max_peptide_mass = 6000.0000 # maximal mass of peptide database\n";
  274. print PARAMS "max_modif_num = 3 # maximal modifications allowed for each peptide\n";
  275. print PARAMS "\n";
  276. print PARAMS "# Static Modification\n";
  277. print PARAMS "add_Nterm_peptide = $addNtermPeptide # TMT modification or other amine labeling\n";
  278. print PARAMS "add_Cterm_peptide = 0.0000\n";
  279. print PARAMS "add_A_Alanine = 0.0000\n";
  280. print PARAMS "add_B_avg_NandD = 0.0000\n";
  281. print PARAMS "add_C_Cysteine = 0.0000 # Cys alkylation\n";
  282. print PARAMS "add_D_Aspartic_Acid = 0.0000\n";
  283. print PARAMS "add_E_Glutamic_Acid = 0.0000\n";
  284. print PARAMS "add_F_Phenylalanine = 0.0000\n";
  285. print PARAMS "add_G_Glycine = 0.0000\n";
  286. print PARAMS "add_H_Histidine = 0.0000\n";
  287. print PARAMS "add_I_Isoleucine = 0.0000\n";
  288. print PARAMS "add_J_user_amino_acid = 0.0000\n";
  289. if ($condition eq "TMThh" or $condition eq "TMThhpho") {
  290. print PARAMS "add_K_Lysine = $addKLysine # TMT modification or other amine labeling\n";
  291. } else {
  292. print PARAMS "add_K_Lysine = $addKLysine # TMT modification or other amine labeling\n";
  293. }
  294. print PARAMS "add_L_Leucine = 0.0000\n";
  295. print PARAMS "add_M_Methionine = 0.0000\n";
  296. print PARAMS "add_N_Asparagine = 0.0000\n";
  297. print PARAMS "add_O_Ornithine = 0.0000\n";
  298. print PARAMS "add_P_Proline = 0.0000\n";
  299. print PARAMS "add_Q_Glutamine = 0.0000\n";
  300. print PARAMS "add_R_Arginine = 0.0000\n";
  301. print PARAMS "add_S_Serine = 0.0000\n";
  302. print PARAMS "add_T_Threonine = 0.0000\n";
  303. print PARAMS "add_U_user_amino_acid = 0.0000\n";
  304. print PARAMS "add_V_Valine = 0.0000\n";
  305. print PARAMS "add_W_Tryptophan = 0.0000\n";
  306. print PARAMS "add_X_LorI = 0.0000\n";
  307. print PARAMS "add_Y_Tyrosine = 0.0000\n";
  308. print PARAMS "add_Z_avg_QandE = 0.0000\n";
  309. print PARAMS "\n";
  310. print PARAMS "# Other parameters\n";
  311. print PARAMS "simulation = 0 # 0 = disable; 1 = enable; this function used for testing the target-decoy strategy\n";
  312. print PARAMS "sim_MS1 = 1000 # ppm addition for MS1 decoys\n";
  313. print PARAMS "sim_MS2 = 5 # Da window for randomized MS2 peaks\n";
  314. print PARAMS "cluster = 1 # 0 = disable; 1 = enable; using master node only or entire cluster\n";
  315. print PARAMS "processors_used = 40 # \n";
  316. print PARAMS "Job_Management_System = SGE # SGE used by current cluster; other systems (e.g. LSF & PBS) may be used\n";
  317. print PARAMS "temp_file_removal = 1 # 0 = disable (keep temporary files); 1 = enable (remove temporary files)\n";
  318. close (PARAMS);
  319. }
  320. }
  322. ##############################################
  323. ## Filtering parameter generation (jump -f) ##
  324. ##############################################
  325. foreach my $searchEngine (@searchEngines) {
  326. foreach my $condition (@conditions) {
  327. ##############################################################
  328. ## Search engine- and condition-dependent parameter setting ##
  329. ##############################################################
  330. my $input;
  331. my $uniqueProteinPeptide = "protein";
  332. my $initialOutfileFDR = 5;
  333. my $FDR = 2;
  334. my $minXCorr;
  335. my $mods = 0;
  336. my $minOutfileNumXcorrFilter = 500;
  337. my ($oneHitMinXCorrZ1, $oneHitMinXCorrZ2, $oneHitMinXCorrZ3);
  338. my $paramsDir;
  339. my $paramsName;
  340. ## Input name
  341. if ($condition eq "HH") {
  342. $input = "HH_human_".lc($searchEngine).":"."/data1/pipeline/release/version$version"."/SampleData/HH/HH_human_".lc($searchEngine)."/HH_human_".lc($searchEngine).".1";
  343. } elsif ($condition eq "HL") {
  344. $input = "HL_human_".lc($searchEngine).":"."/data1/pipeline/release/version$version"."/SampleData/HL/HL_human_".lc($searchEngine)."/HL_human_".lc($searchEngine).".1";
  345. } elsif ($condition eq "TMThh") {
  346. $input = "HH_tmt10_human_".lc($searchEngine).":"."/data1/pipeline/release/version$version"."/SampleData/TMThh/HH_tmt10_human_".lc($searchEngine)."/HH_tmt10_human_".lc($searchEngine).".1";
  347. } else {
  348. $input = "HH_pho_tmt10_human_".lc($searchEngine).":"."/data1/pipeline/release/version$version"."/SampleData/TMThhpho/HH_pho_tmt10_human_".lc($searchEngine)."/HH_pho_tmt10_human_".lc($searchEngine).".1";
  349. }
  350. ## Protein or peptide
  351. if ($condition eq "TMThhpho") {
  352. $uniqueProteinPeptide = "peptide";
  353. }
  354. ## Initial outfile FDR
  355. if ($condition eq "TMThhpho") {
  356. $initialOutfileFDR = 10;
  357. }
  358. ## FDR
  359. if ($condition eq "TMThhpho") {
  360. $FDR = 2;
  361. }
  362. ## minXcorr
  363. if ($searchEngine eq "JUMP") {
  364. $minXCorr = 10;
  365. } else {
  366. $minXCorr = 1;
  367. }
  368. ## Modifications
  369. if ($condition eq "TMThhpho") {
  370. $mods = "STY";
  371. }
  372. ## Minimum outfile number for Xcorr filtering
  373. if ($condition eq "TMThhpho") {
  374. $minOutfileNumXcorrFilter = 200;
  375. }
  376. ## One-hit wonders
  377. if ($searchEngine eq "JUMP") {
  378. $oneHitMinXCorrZ1 = 100;
  379. $oneHitMinXCorrZ2 = 25;
  380. $oneHitMinXCorrZ3 = 35;
  381. } else {
  382. $oneHitMinXCorrZ1 = 10;
  383. $oneHitMinXCorrZ2 = 2.5;
  384. $oneHitMinXCorrZ3 = 3.5;
  385. }
  386. ## Params file name
  387. if ($searchEngine eq "JUMP") {
  388. $paramsName = "jump_fj_";
  389. } else {
  390. $paramsName = "jump_fs_";
  391. }
  392. if ($condition eq "HH") {
  393. $paramsName = $paramsName."HH.params";
  394. } elsif ($condition eq "HL") {
  395. $paramsName = $paramsName."HL.params";
  396. } elsif ($condition eq "TMThh") {
  397. $paramsName = $paramsName."TMThh.params";
  398. } elsif ($condition eq "TMThhpho") {
  399. $paramsName = $paramsName."TMThhpho.params";
  400. }
  402. ##########################
  403. ## Print .params files ##
  404. ##########################
  405. if ($condition eq "HH") {
  406. $paramsDir = $currDir."/HH";
  407. if (!-e $paramsDir) {
  408. system("mkdir $paramsDir");
  409. }
  410. $paramsName = $paramsDir."/".$paramsName;
  411. } elsif ($condition eq "HL") {
  412. $paramsDir = $currDir."/HL";
  413. if (!-e $paramsDir) {
  414. system("mkdir $paramsDir");
  415. }
  416. $paramsName = $paramsDir."/".$paramsName;
  417. } elsif ($condition eq "TMThh") {
  418. $paramsDir = $currDir."/TMThh";
  419. if (!-e $paramsDir) {
  420. system("mkdir $paramsDir");
  421. }
  422. $paramsName = $paramsDir."/".$paramsName;
  423. } else {
  424. $paramsDir = $currDir."/TMThhpho";
  425. if (!-e $paramsDir) {
  426. system("mkdir $paramsDir");
  427. }
  428. $paramsName = $paramsDir."/".$paramsName;
  429. }
  430. open (PARAMS, ">", $paramsName) or die "Cannot generate $paramsName\n";
  431. print PARAMS "# JUMP filtering parameter file (Version: $version, Date: $releaseDate)\n";
  432. print PARAMS "\n";
  433. print PARAMS "# Grouping # Input of the program, using full path of the search result folders (containing dta files and out/spout files)\n";
  434. print PARAMS "# Information (e.g., search engine, pit table) will be directly parsed from jump.params in the input path below\n";
  435. print PARAMS "\n";
  436. print PARAMS "$input\n";
  437. print PARAMS "\n";
  438. print PARAMS "##### commonly adjusted parameters ############################################################################################################\n";
  439. print PARAMS "# PSMs filtered by (i) defined minimum filtering parameters, (ii) mass accuracy, and (iii) scoring\n";
  440. print PARAMS "# For scoring filtering, PSMs filtered by (i) initial FDR, (ii) peptide or protein categorization and mupltistep FDR filtering, and (iii) manual one hit-wonder-removal\n";
  441. print PARAMS "unique_protein_or_peptide = $uniqueProteinPeptide # use protein or peptide FDR as cutoff\n";
  442. print PARAMS "initial_outfile_fdr = $initialOutfileFDR # %initial FDR for score filtering; default = 5 (%)\n";
  443. print PARAMS "multistep_FDR_filtering = 1 # 0 = disabled; 1 = enabled\n";
  444. print PARAMS "FDR = $FDR # %FDR for filtering peptides or one-hit-wonder proteins (fixed <1% FDR for proteins matched by two or more precursors)\n";
  445. print PARAMS "min_protein_SC = 1 # minimum spectral counts requirement for proteins\n";
  446. print PARAMS "one_hit_wonders_removal = 0 # keep or remove one hit wonders (-1: removal all, 0:no filter, 1: partial+fully, 2: fully)\n";
  447. print PARAMS "mods = $mods # Display modified peptides and their unmodified (0:Off, K:Lys, STY: Phosphorylation, ...)\n";
  448. print PARAMS "modpairs = 0 # Show modified peptides pairs or just modified peptides (0:only modified peptides, 1:modified pairs)\n";
  449. print PARAMS "pit_file = 0 # absolute path of pit file: use updated pit file; 0 = using pit file in jump.params in the search folder\n";
  450. print PARAMS "\n";
  451. print PARAMS "# Minimum filtering parameters for removing low quality PSMs during reading process\n";
  452. print PARAMS "min_peptide_length = 7 # peptide length (6 can be used for small database)\n";
  453. print PARAMS "max_peptide_mis = 2 # maximal number of miscleavages allowed for one peptide, default=2\n";
  454. print PARAMS "max_peptide_mod = 3 # maximal number of modifications allowed for one peptide, M = 2, SILAC (KR) = 4, Ub = 3, Pho (STY) = 5\n";
  455. print PARAMS "peptide_mod_removal = 0 # 0: Off, C: Remove all C-modified peptides, STY: Remove all STY-modifed peptides\n";
  456. print PARAMS "peptide_aa_removal = 0 # 0: Off, M: Remove all M-containing peptides\n";
  457. print PARAMS "min_XCorr = $minXCorr # XCorr (default = 1) or Jscore (default = 10)\n";
  458. print PARAMS "min_dCn = 0 # dCn or dJ\n";
  459. print PARAMS "mix_label = 0 # Remove mixed labeled peptides: (0: None, KR: SILAC, C: ICAT, etc...)\n";
  460. print PARAMS "filter_contaminants = 0 # 0: Not used, 1: remove listed contaminants named with \"CON_\"\n";
  461. print PARAMS "12combinations = 1 1 1 1 1 1 1 1 0 0 0 0 # Trypticity and charge => FT1 FT2 FT3 FT4 PT1 PT2 PT3 PT4 NT1 NT2 NT3 NT4 # 1=yes, 0=no\n";
  462. print PARAMS "\n";
  463. print PARAMS "# Filtering PSMs by mass accuracy (no grouping, mass correction for each LC run) and matching scores (grouped)\n";
  464. print PARAMS "bypass_filtering = 0 # 0: NO, 1: YES bypasses all mass accuracy and dCn/XCorr filtering\n";
  465. print PARAMS "mass_accuracy = 1 # Mass accuracy filtering # 1=yes, 0=no\n";
  466. print PARAMS "mass_consideration = 1 # Mass consideration for accuracy filtering => 1:(MH), 2:(MH,MH+1), 3:(MH,MH+1,MH+2), 4:(MH,MH+1,MH+2,MH+3),\n";
  467. print PARAMS " # 5:(MH,MH+1,MH+2,MH+3,MH+4), 6:(MH-1,MH,MH+1,MH+2), 7:(MH-2,MH-1,MH,MH+1,MH+2)\n";
  468. print PARAMS "sd_or_static = sd # Mass accuracy cutoff based on experimental standard deviation (sd_or_static = sd)\n";
  469. print PARAMS "sd = 5 # or static ppm values (sd_or_static = static)\n";
  470. print PARAMS "static_cutoff = 6 # ppm\n";
  471. print PARAMS "static_cutoff_without_mass_calib = 10 # ppm; if not enough good scans, use this threshold for ppm cut without mass calibration\n";
  472. print PARAMS "\n";
  473. print PARAMS "# Filtering PSMs by matching scores (grouping by Peptide length; Trypticity; Mod; Miscleavage; Charge; deltaCn (0.01 step)\n";
  474. print PARAMS "# Sorting outfile into different dynamic groups until each group has sufficient outfiles (e.g. min_outfile_num_for_XCorr_filter = 500)\n";
  475. print PARAMS "# Filtering by assigned scan FDR based on unique peptides or proteins.\n";
  476. print PARAMS "# Removing false outfiles (if no charge state found, assign both +2 and +3 to make two dta files, same SC, same m/z, different charge state)\n";
  477. print PARAMS "# Grouping SC (1000) into unique SC (350), peptides (500), unique peptides (300), proteins (900), unique proteins (150), and protein groups (120)\n";
  478. print PARAMS "# Using SC FDR to predict unique protein/peptide FDR to shorten the filtering process\n";
  479. print PARAMS "FDR_filtering_method = group # LDA or group (select one of the two filtering methods)\n";
  480. print PARAMS "min_outfile_num_for_XCorr_filter = $minOutfileNumXcorrFilter # number of outfiles in each group for XCorr filtering; any number between 500 and 1000 is recomemded\n";
  481. print PARAMS "\n";
  482. print PARAMS "# Applyling additional filtering for one-hit-wonders\n";
  483. print PARAMS "one_hit_wonders_min_XCorr_z1 = $oneHitMinXCorrZ1 # minimum XCorr for peptides with charge state 1\n";
  484. print PARAMS "one_hit_wonders_min_XCorr_z2 = $oneHitMinXCorrZ2 # minimum XCorr for peptides with charge state 2\n";
  485. print PARAMS "one_hit_wonders_min_XCorr_z3 = $oneHitMinXCorrZ3 # minimum XCorr for peptides with charge state 3 or above\n";
  486. print PARAMS "one_hit_wonders_min_dCn = 0.1 # minimum dCn\n";
  487. print PARAMS "one_hit_wonders_mis = 1 # number of miscleavages allowed for one hit wonders\n";
  488. print PARAMS "one_hit_wonders_mods = 1 # number of modifications allowed for hit wonders, M = 1, SILAC (KR) = 3, Ub = 2, Pho (STY) = 4\n";
  489. print PARAMS "######################################################################################################################################################\n";
  490. print PARAMS "\n";
  491. print PARAMS "#################### To turn on pepXML generation ######################\n";
  492. print PARAMS "output_pepXML = 1\n";
  493. close (PARAMS);
  494. }
  495. }
  497. ##########################################################
  498. ## Quantification parameter file generation (jump -q) ##
  499. ##########################################################
  500. foreach my $searchEngine (@searchEngines) {
  501. foreach my $condition (@conditions) {
  502. next if ($condition eq "HH" || $condition eq "HL");
  503. ##############################################################
  504. ## Search engine- and condition-dependent parameter setting ##
  505. ##############################################################
  506. my $paramsDir;
  507. my $paramsName;
  508. my $idTxt;
  509. my $saveDir;
  510. if ($searchEngine eq "JUMP") {
  511. if ($condition eq "TMThh") {
  512. $paramsDir = $currDir."/TMThh";
  513. if (!-e $paramsDir) {
  514. system("mkdir $paramsDir");
  515. }
  516. $paramsName = $paramsDir."/jump_qj_HH_tmt10_human.params";
  517. $idTxt = "/data1/pipeline/release/version$version/SampleData/TMThh/sum_HH_tmt10_human_jump/ID.txt";
  518. $saveDir = "HH_tmt10_human_jump";
  519. } elsif ($condition eq "TMThhpho") {
  520. $paramsDir = $currDir."/TMThhpho";
  521. if (!-e $paramsDir) {
  522. system("mkdir $paramsDir");
  523. }
  524. $paramsName = $paramsDir."/jump_qj_HH_pho_tmt10_human.params";
  525. $idTxt = "/data1/pipeline/release/version$version/SampleData/TMThhpho/sum_HH_pho_tmt10_human_jump_mod/IDmod.txt";
  526. $saveDir = "HH_pho_tmt10_human_jump_mod";
  527. }
  528. } else {
  529. if ($condition eq "TMThh") {
  530. $paramsDir = $currDir."/TMThh";
  531. if (!-e $paramsDir) {
  532. system("mkdir $paramsDir");
  533. }
  534. $paramsName = $paramsDir."/jump_qs_HH_tmt10_human.params";
  535. $idTxt = "/data1/pipeline/release/version$version/SampleData/TMThh/sum_HH_tmt10_human_sequest/ID.txt";
  536. $saveDir = "HH_tmt10_human_sequest";
  537. } elsif ($condition eq "TMThhpho") {
  538. $paramsDir = $currDir."/TMThhpho";
  539. if (!-e $paramsDir) {
  540. system("mkdir $paramsDir");
  541. }
  542. $paramsName = $paramsDir."/jump_qs_HH_pho_tmt10_human.params";
  543. $idTxt = "/data1/pipeline/release/version$version/SampleData/TMThhpho/sum_HH_pho_tmt10_human_sequest_mod/IDmod.txt";
  544. $saveDir = "HH_pho_tmt10_human_sequest_mod";
  545. }
  546. }
  548. ##########################
  549. ## Print .params files ##
  550. ##########################
  551. open (PARAMS, ">", $paramsName) or die "Cannot generate $paramsName\n";
  552. print PARAMS "# JUMP quantification parameter file (Version: $version, Date: $releaseDate)\n";
  553. print PARAMS "\n";
  554. print PARAMS "# Input: ID.txt or IDmod.txt\n";
  555. print PARAMS "idtxt = $idTxt\n";
  556. if ($condition eq "TMThh") {
  557. print PARAMS "save_dir = $saveDir # name of the directory for JUMPq results (prefix \"quan-\" will be added)\n";
  558. } elsif ($condition eq "TMThhpho") {
  559. print PARAMS "save_dir = $saveDir # name of the directory for JUMPq results (prefix \"quan-\" will be added)\n";
  560. }
  561. print PARAMS "ppi_filter = 50 # precursor peak intensity percentage threshold\n";
  562. print PARAMS "quan_method = MS2 # MS2 = reporter ions from MS2; MS3 = reporter ions from MS3\n";
  563. print PARAMS "Top_sel = 1 # only for the MS3 method, to find MS3 scans for peptides assigned by MS2\n";
  564. print PARAMS " # 1 = MS3 (used for quan) immediately after MS2 (used for ID)\n";
  565. print PARAMS " # 5 = 5 MS3 followed by 5 MS2\n";
  566. print PARAMS "min_intensity_method = 2 # 1 = minimum, 2 = maximum, 3 = mean, 4 = median\n";
  567. print PARAMS "min_intensity_value = 5000 # Minimum intensity threshold\n";
  568. print PARAMS "ms2_ms3_tolerance = 0.02 # dalton, only for the MS3 method, to define mass tolerance for finding MS3\n";
  569. print PARAMS "\n";
  570. print PARAMS "# TMT10 reporter ions (126.127726;127.124761;127.131081;128.128116;128.134436;129.131471;129.137790;130.134825;130.141145;131.138180)\n";
  571. print PARAMS "# TMT8 reporter ions (126.127726;127.124761;127.131081;128.134436;129.131471;129.137790;130.141145;131.138180)\n";
  572. print PARAMS "# TMT6 reporter ions (126.127726;127.124761;128.134436;129.131471;130.141145;131.138180)\n";
  573. print PARAMS "# ITRAQ 4-plex reporter ions (114.1112;115.1082;116.1116;117.1149)\n";
  574. print PARAMS "# ITRAQ 8-plex reporter ions (113.1078;114.1112;115.1082;116.1116;117.1149;118.1120;119.1153;121.1220)\n";
  575. print PARAMS "itraq_reporters = 126.127726;127.124761;127.131081;128.128116;128.134436;129.131471;129.137790;130.134825;130.141145;131.138180\n";
  576. print PARAMS "itraq_peak_extraction_first_ppm = 25 # reporter ion initial mass tolerance +/- ppm\n";
  577. print PARAMS "itraq_peak_extraction_second_sd = 8 # SD used for identification of reporter ions\n";
  578. print PARAMS "itraq_peak_extraction_method = 1 # 1 = strongest intensity; 2 = closest to expected report ion mass;\n";
  579. print PARAMS " # only if multiple peaks detected within mass tolerance\n";
  580. print PARAMS "report_impurity = 1 # 1 = Yes; 0 = No;\n";
  581. print PARAMS "impurity_matrix = /data1/pipeline/release/version$version/JUMPq/TMT10.ini # impurity table for correction\n";
  582. print PARAMS "impurity_batch = Batch2 # Batch # of TMT reagents\n";
  583. print PARAMS "\n";
  584. print PARAMS "# The program allows multiple comparisons (e.g. comparison_groups_comp1, do not change the prefix \"comparison_groups_\")\n";
  585. print PARAMS "# For TMT10, input sig126, sig127N, sig127C, sig128N, sig128C, sig129N, sig129C, sig130N, sig130C, and sig131 (sorted by mass)\n";
  586. print PARAMS "# e.g. comparison_groups_twoGroups = sig126, sig127N, sig127C, sig128N, sig128C : sig129N, sig129C, sig130N, sig130C, sig131\n";
  587. print PARAMS "# comparison_groups_threeGroups = sig126, sig127N, sig127C : sig128N, sig128C, sig129N : sig129C, sig130N, sig130C, sig131\n";
  588. print PARAMS "comparison_analysis = 1 # 1 = Yes; 0 = No; for group comparison\n";
  589. print PARAMS "comparison_groups_twoGroups = sig126, sig127N, sig127C, sig128N, sig128C : sig129N, sig129C, sig130N, sig130C, sig131\n";
  590. print PARAMS "\n";
  591. print PARAMS "Loading_Bias_Adjustment = 1 # 1 = Yes; 0 = No;\n";
  592. print PARAMS "min_SN_for_adjustment = 10 # define the minimal signal (SN ratio) used for adjustment\n";
  593. print PARAMS "percentage_outlier_removal = 10 # percenage of scans that are not included for each end\n";
  594. print PARAMS "loading_bias_correction_method = 1 # 1 = average; 2 = median;\n";
  595. print PARAMS "\n";
  596. print PARAMS "# Define variations by moving average\n";
  597. print PARAMS "# If auto_create_window is set as 1, automatically create 100 windows based on the total number of scans\n";
  598. print PARAMS "# If auto_create_window is set as 1, moving_window_size and move_window_step are not used\n";
  599. print PARAMS "auto_create_window = 0 # 1 = Yes; 0 = No; if setting 1, the scan # needs to be >500\n";
  600. print PARAMS "moving_window_size = 100 # A small number setting significantly increase the processing time\n";
  601. print PARAMS "moving_window_step = 20 # A small number setting significantly increase the processing time\n";
  602. print PARAMS "\n";
  603. print PARAMS "# Outlier removal by Dixon's Q test for summing up peptide and proteins\n";
  604. print PARAMS "outlier_threshold = Q95 # Input Q90, Q95 and Q99 (the larger number, the more stringent)\n";
  605. print PARAMS "FDR_method = BH # Nine FDR methods can be used (i.e. \"holm\", \"hochberg\", \"hommel\", \"bonferroni\", \"BH\", \"BY\", \"fdr\", \"none\",\"0\")\n";
  606. print PARAMS "\n";
  607. print PARAMS "publication_table = 1 # 1 = Yes, 0 = NO\n";
  608. print PARAMS "publication_comparison_group = sig126, sig127N, sig127C, sig128N, sig128C, sig129N, sig129C, sig130N, sig130C, sig131\n";
  609. print PARAMS "publication_Loading_Bias_Adjustment = 0 # 1 = Yes, 0 = NO\n";
  610. close (PARAMS);
  611. }
  612. }
  614. ##################################################
  615. ## Database parameter file generation (jump -d) ##
  616. ##################################################
  617. my $paramsDir = $currDir;
  618. if (!-e $paramsDir) {
  619. system ("mkdir $paramsDir");
  620. }
  621. my $paramsName = $paramsDir."/jump_d.params";
  622. open (PARAMS, ">", $paramsName) or die "Cannot generate $paramsName\n";
  623. print PARAMS "# JUMP database generation parameter file (Version: $version, Date: $releaseDate)\n";
  624. print PARAMS "# JUMPd generates a search database and/or a protein inference table (PIT) using the input databases (.fasta files)\n";
  625. print PARAMS "# The type of a database (for JUMP or SEQUEST) solely depends on the search_engine information in \"jump.params\" file below\n";
  626. print PARAMS "# All the modification information for the database also depends on the \"jump.params\" file\n";
  627. print PARAMS "\n";
  628. print PARAMS "# Parameters for generating a new database ######################################################################################################################################\n";
  629. print PARAMS "input_database1 = /data1/database/20150201/HUMAN.fasta # Absolute path of input_database1 (i.e. .fasta file)\n";
  630. print PARAMS "#input_database2 = /data1/database/20150201/MOUSE.fasta # Absolute path of input_database2\n";
  631. print PARAMS " # More databases can be used (e.g. input_database3 = /data1/database/20150201/ECOLI.fasta)\n";
  632. print PARAMS "output_prefix = mouse # Prefix for a new database (and .pit) file\n";
  633. print PARAMS "include_contaminants = 1 # 0 = do not include contaminants; 1 = include contaminants\n";
  634. print PARAMS "input_contaminants = /data1/database/contaminants.fasta # Absolute path of a .fasta file containing contaminants\n";
  635. print PARAMS "decoy_generation = 1 # 0 = do not include decoys; 1 = include decoys\n";
  636. print PARAMS "decoy_generation_method = 1 # 1 = reverse; 2 = reverse and switch every K/R with its preceding AA\n";
  637. print PARAMS "jump.params = /usr/search/jump_search.params # Only search engine and modification information will be obtained from the file\n";
  638. print PARAMS " # \"database_name\" in a jump.params file will be ignored\n";
  639. print PARAMS "bypass_db_generation = 0 # 0 = generate database, 1 = bypass the generation of database (only pit will be generated)\n";
  640. print PARAMS "\n";
  641. print PARAMS "# Parameters for generating a protein inference table (PIT) (keep the prefix \"list_\") ###########################################################################################\n";
  642. #print PARAMS "list_protein_abundance1 = /data1/database/KnowledgeTables/ProteinAbundance/Mouse_Abundance_emPAI.txt # Absolute path of a file containing protein abundance information\n";
  643. print PARAMS "list_protein_abundance1 = /data1/database/KnowledgeTables/ProteinAbundance/Human_Abundance_emPAI.txt # Absolute path of a file containing protein abundance information\n";
  644. print PARAMS " # More abundance information can be used\n";
  645. print PARAMS " # (e.g. list_protein_abundance2 = /data1/database/Rat_Abundance.txt)\n";
  646. print PARAMS "list_TFs = /data1/database/KnowledgeTables/TFs/tfs_from_TRANSFAC.txt # Absolute path of a file containing protein annotation information, TFs (transcription factors)\n";
  647. print PARAMS "list_oncogenes = /data1/database/KnowledgeTables/Oncogenes/oncogenes_from_literatures.txt # Absolute path of a file containing protein annotation information, oncogenes\n";
  648. print PARAMS "list_kinases = /data1/database/KnowledgeTables/Kinases/kinases_from_pkinfam.txt # Absolute path of a file containing protein annotation information, kinases\n";
  649. print PARAMS "list_GPCRs = /data1/database/KnowledgeTables/GPCRs/gpcrs.txt # Absolute path of a file containing protein annotation information, GPCRs\n";
  650. print PARAMS "list_epigenetic_factors = /data1/database/KnowledgeTables/EpigeneticRegulators/epigenetic_regulators.txt\n";
  651. print PARAMS "list_spliceosomal_proteins = /data1/database/KnowledgeTables/SpliceosomalProteins/spliceosomal_proteins.txt\n";
  652. close (PARAMS);
  654. ##################################################################
  655. ## Absolute quantification parameter file generation (jump -aq) ##
  656. ##################################################################
  657. $paramsName = $paramsDir."/jump_aq.params";
  658. open (PARAMS, ">", $paramsName) or die "Cannot generate $paramsName\n";
  659. print PARAMS "# JUMP absolute quantification parameter file (Version: $version, Date: $releaseDate)\n";
  660. print PARAMS "# JUMPaq generates a protein abundance table based on a search/filtering result\n";
  661. print PARAMS "\n";
  662. print PARAMS "# Database (i.e. a fasta file)\n";
  663. print PARAMS "database = /data1/database/20150201/HUMAN.fasta\n";
  664. print PARAMS "\n";
  665. print PARAMS "# The Report file generated by JUMPf\n";
  666. print PARAMS "report_file = /data1/pipeline/release/version$version/SampleData/HH/sum_HH_human_jump/publications/id_all_prot.txt\n";
  667. print PARAMS "\n";
  668. print PARAMS "# Output file name\n";
  669. print PARAMS "output = protein_absolute_abundance.txt\n";
  670. print PARAMS "\n";
  671. print PARAMS "# Parameters used for calculating theoretical peptides\n";
  672. print PARAMS "min_peptide_length = 6\n";
  673. print PARAMS "enzyme = trypsin #types of enzyme: trypsin, chymotrypsin, gluc_nahpo, gluc, lysc, argc, aspc\n";
  674. print PARAMS "max_peptide_length = 30\n";
  675. print PARAMS "max_peptide_hydro = 17\n";
  676. print PARAMS "min_peptide_hydro = -24\n";
  677. close (PARAMS);
  679. ##################################################################
  680. ## Statistical inference parameter file generation (jump -i) ##
  681. ##################################################################
  682. $paramsName = $paramsDir."/jump_i_default.params";
  683. open (PARAMS, ">", $paramsName) or die "Cannot generate $paramsName\n";
  684. print PARAMS "# JUMP statistical inference parameter file (Version: $version, Date: $releaseDate)\n";
  685. print PARAMS "\n";
  686. print PARAMS "#-----------------------------------------------------------------------------------------------------------------------------------\n";
  687. print PARAMS "# Expected results:\n";
  688. print PARAMS "#\n";
  689. print PARAMS "# 1) log 2 ratio distribution for each pair of samples:\n";
  690. print PARAMS "# a) log 2 ratio distributions figure: log2ratio_distributions.pdf\n";
  691. print PARAMS "# b) log 2 ratio distribution mean: log2ratio_mean_matrix.txt (typical mean for replicates is around 0)\n";
  692. print PARAMS "# c) log 2 ratio distribution SD: log2ratio_SD_matrix.txt (typical SD for replicates is 0.2)\n";
  693. print PARAMS "#\n";
  694. print PARAMS "# 2) Heatmap for sample cluster: heatmap_XXpct.pdf (default cutting %: 0.1, 0.5, 1, 5, 10 and 20)\n";
  695. print PARAMS "#\n";
  696. print PARAMS "#-----------------------------------------------------------------------------------------------------------------------------------\n";
  697. print PARAMS "\n";
  698. print PARAMS "# input file (either protein or peptide table from jump -q results in folder 'publications')\n";
  699. print PARAMS "input_table = /data1/pipeline/release/version11.2.0/SampleData/TMThh/quan_HH_tmt10_human_jump/publications/id_uni_prot_quan.txt # absolute path needed;\n";
  700. print PARAMS " # protein file: /home/user/project/quan_test1/publications/id_uni_prot_quan.txt\n";
  701. print PARAMS " # peptide file: /home/user/project/quan_test1/publications/quan_phosphopep_uni_prot.txt\n";
  702. print PARAMS "\n";
  703. print PARAMS "# sample labels\n";
  704. print PARAMS "sig126 = condition1a\n";
  705. print PARAMS "sig127N = condition1b\n";
  706. print PARAMS "sig127C = condition2a\n";
  707. print PARAMS "sig128N = condition2b\n";
  708. print PARAMS "sig128C = condition3a\n";
  709. print PARAMS "sig129N = condition3b\n";
  710. print PARAMS "sig129C = condition4a\n";
  711. print PARAMS "sig130N = condition4b\n";
  712. print PARAMS "sig130C = condition5a\n";
  713. print PARAMS "sig131 = condition5b\n";
  714. print PARAMS "\n";
  715. print PARAMS "# output folder\n";
  716. print PARAMS "output_folder = test1 # output folder suffix name; prefix always 'inf_'\n";
  717. print PARAMS "\n";
  718. print PARAMS "# contaminant removel option\n";
  719. print PARAMS "remove_contaminants = 1 # remove contaminants? 1 = yes; 0 = no\n";
  720. print PARAMS "\n";
  721. print PARAMS "# SD / mean matrix: analysis based on the stable proteins / peptides\n";
  722. print PARAMS "pair_cutoff_percentage = 10 # percentage/2 of data will be ignored on each end of the distribution\n";
  723. print PARAMS "pair_cutoff_intensity = 3000 # median intensity cutoff across samples\n";
  724. print PARAMS "\n";
  725. print PARAMS "# heatmap / sample clustering: analysis based on the most variable proteins / peptides\n";
  726. print PARAMS "cluster_cutoff_percentage = 0.5 # percentage of most variable proteins (defined by RSD of intensity) used for clustering\n";
  727. print PARAMS "cluster_cutoff_intensity = 3000 # median intensity cutoff across samples\n";
  728. close (PARAMS);
  730. $paramsName = $paramsDir."/jump_i_custom.params";
  731. open (PARAMS, ">", $paramsName) or die "Cannot generate $paramsName\n";
  732. print PARAMS "# JUMP statistical inference parameter file (Version: $version, Date: $releaseDate)\n";
  733. print PARAMS "\n";
  734. print PARAMS "#-----------------------------------------------------------------------------------------------------------------------------------\n";
  735. print PARAMS "# Expected results:\n";
  736. print PARAMS "#\n";
  737. print PARAMS "# 1) log 2 ratio distribution for each pair of samples:\n";
  738. print PARAMS "# a) log 2 ratio distributions figure: log2ratio_distributions.pdf\n";
  739. print PARAMS "# b) log 2 ratio distribution mean: log2ratio_mean_matrix.txt (typical mean for replicates is around 0)\n";
  740. print PARAMS "# c) log 2 ratio distribution SD: log2ratio_SD_matrix.txt (typical SD for replicates is 0.2)\n";
  741. print PARAMS "#\n";
  742. print PARAMS "# 2) Heatmap for sample cluster: heatmap_XXpct.pdf (default cutting %: 0.1, 0.5, 1, 5, 10 and 20)\n";
  743. print PARAMS "#\n";
  744. print PARAMS "#-----------------------------------------------------------------------------------------------------------------------------------\n";
  745. print PARAMS "\n";
  746. print PARAMS "# customized input\n";
  747. print PARAMS "# 1) Excel: make an Excel sheet with format below:\n";
  748. print PARAMS "# customID sig126 sig127N ... sig131\n";
  749. print PARAMS "# 2) Excel: save the file as 'Text (Tab delimited)'\n";
  750. print PARAMS "# 3) WinSCP: upload the saved file to cluster using WinSCP\n";
  751. print PARAMS "# 4) JUMPi: turn off all filtering in jump -i parameter file (default)\n";
  752. print PARAMS "input_table = /home/yli4/development/JUMPi/v11.3.042915/cus_prot1.txt # absolute path of customized input file\n";
  753. print PARAMS "\n";
  754. print PARAMS "# sample labels\n";
  755. print PARAMS "sig126 = condition1a\n";
  756. print PARAMS "sig127N = condition1b\n";
  757. print PARAMS "sig127C = condition2a\n";
  758. print PARAMS "sig128N = condition2b\n";
  759. print PARAMS "sig128C = condition3a\n";
  760. print PARAMS "sig129N = condition3b\n";
  761. print PARAMS "sig129C = condition4a\n";
  762. print PARAMS "sig130N = condition4b\n";
  763. print PARAMS "sig130C = condition5a\n";
  764. print PARAMS "sig131 = condition5b\n";
  765. print PARAMS "\n";
  766. print PARAMS "# output folder\n";
  767. print PARAMS "output_folder = cu_test1 # output folder suffix name; prefix always 'inf_'\n";
  768. print PARAMS "\n";
  769. print PARAMS "# contaminant removel option\n";
  770. print PARAMS "remove_contaminants = 0 # remove contaminants? 1 = yes; 0 = no\n";
  771. print PARAMS "\n";
  772. print PARAMS "# SD / mean matrix: analysis based on the stable proteins / peptides\n";
  773. print PARAMS "pair_cutoff_percentage = 0 # percentage/2 of data will be ignored on each end of the distribution\n";
  774. print PARAMS "pair_cutoff_intensity = 0 # median intensity cutoff across samples\n";
  775. print PARAMS "\n";
  776. print PARAMS "# heatmap / sample clustering: analysis based on the most variable proteins / peptides\n";
  777. print PARAMS "cluster_cutoff_percentage = 100 # percentage of most variable proteins (defined by RSD of intensity) used for clustering\n";
  778. print PARAMS "cluster_cutoff_intensity = 0 # median intensity cutoff across samples\n";
  779. close (PARAMS);
  781. ######################################################################
  782. ## Validation of known targets parameter file generation (jump -v) ##
  783. ######################################################################
  784. $paramsName = $paramsDir."/jump_v.params";
  785. open (PARAMS, ">", $paramsName) or die "Cannot generate $paramsName\n";
  786. print PARAMS "# JUMP validation (of known targets) parameter file (Version: $version, Date: $releaseDate)\n";
  787. print PARAMS "# JUMPv extracts the identification/quantification results of input peptides/proteins\n";
  788. print PARAMS "\n";
  789. print PARAMS "# Peptides or proteins to be validated\n";
  790. print PARAMS "peptide_1 = VRHDSPDPSPPR\n";
  791. print PARAMS "peptide_2 = SSDEDATGEPK\n";
  792. print PARAMS "#peptide_3 = VMSSLAPYNSSTSPQK\n";
  793. print PARAMS "protein_1 = sp|Q9BRD0|BUD13_HUMAN\n";
  794. print PARAMS "#protein_2 = tr|B2KFM4|B2KFM4_MOUSE\n";
  795. print PARAMS "\n";
  796. print PARAMS "# The raw quantification file generated by JUMPq\n";
  797. print PARAMS "quan_file = /data1/pipeline/release/version$version/SampleData/TMThhpho/quan_HH_pho_tmt10_human_jump_mod/raw_quan_HH_pho_tmt10_human_jump_mod_scan.txt\n";
  798. print PARAMS "\n";
  799. print PARAMS "# Output file name\n";
  800. print PARAMS "output = validation_quan_HH_pho_tmt10_human_jump_mod.txt\n";
  801. close (PARAMS);
  803. ###################################
  804. ## customized database (jump -c) ##
  805. ###################################
  806. $paramsName = $paramsDir."/jump_c.params";
  807. open (PARAMS, ">", $paramsName) or die "Cannot generate $paramsName\n";
  808. print PARAMS "# JUMP customized database (jump -c)\n";
  809. print PARAMS "mode = junction # mutation, junction, 6FT\n";
  810. print PARAMS "input_file = /home/yli4/development/JUMPg/wrapUp_052915/junction_simple_input.txt # absolute path of input file\n";
  811. print PARAMS "output_folder = correctChr_jun_test12\n";
  812. print PARAMS "species = human # human; required for 'mutation' and 'junction' mode\n";
  813. print PARAMS "read_coverage_cutoff = 2 # minimum number of reads that support a candidate peptide; required for '6FT' mode\n";
  814. close (PARAMS);
  816. ##############################
  817. ## spectrum quality control ##
  818. ##############################
  819. $paramsName = $paramsDir."/jump_qc.params";
  820. open (PARAMS, ">", $paramsName) or die "Cannot generate $paramsName\n";
  821. print PARAMS "# JUMP spectrum quality control (jump -qc)\n";
  822. print PARAMS "run1 = /home/yli4/customizedDB/AD/JUMPsearch_032015/multistage/ad_pl01/ad_pl01.5\n";
  823. print PARAMS "confident_IDtxt = /home/yli4/customizedDB/AD/JUMPsearch_032015/uniPro/sum_10fr_peptide0FDR_ppi1_test2/ID.txt\n";
  824. print PARAMS "accepted_IDtxt = /home/yli4/customizedDB/AD/JUMPsearch_032015/multistage/sum_proNtermAcetyl_test1/ID.txt\n";
  825. print PARAMS "PSM_recoveray_rate = 99\n";
  826. print PARAMS "output_folder = after_proNtermAcetyl_test1\n";
  827. close (PARAMS);
  829. ##################################################
  830. ## Localization of modification sites (jump -l) ##
  831. ##################################################
  833. $paramsName = $paramsDir."/jump_l.params";
  834. open (PARAMS, ">", $paramsName) or die "Cannot generate $paramsName\n";
  835. print PARAMS "# JUMP localization parameter file (Version: $version, Date: $releaseDate)\n";
  836. print PARAMS "# JUMPl identifies (localizes) the modification sites (e.g. phosphorylation)\n";
  837. print PARAMS "\n";
  838. print PARAMS "# Input and output settings\n";
  839. print PARAMS "IDmod = /home/htan/1412Gilbertson/pho/sum_pho_NSC_20150206_mod/IDmod.txt # path for the input IDmod.txt file\n";
  840. print PARAMS "#IDmod = /home/xwang4/JUMPl_testing/test.txt\n";
  841. print PARAMS "Output = ID.lscore # output file name\n";
  842. print PARAMS "\n";
  843. print PARAMS "# Preprocessing parameters\n";
  844. print PARAMS "peptide_score_tolerance = 10 # tolerance for peptide localization score (percentage)\n";
  845. print PARAMS "mass_correction = 2 # 0 = no correction, 1 = MS1-based, 2 = MS2-based, 3 = manual correction\n";
  846. print PARAMS "isolation_window = 1.2 # +/- (isolation_window)/2 based on MS2 isolation window (e.g. 1.2 m/z)\n";
  847. print PARAMS "first_scan_extraction = 0 # the first scan number for search\n";
  848. print PARAMS "last_scan_extraction = 1000000 # the last scan number for search, use a large number (e.g. 10E6) for full scans\n";
  849. print PARAMS "MS2_deisotope = 1 # 0 = disable; 1 = enable\n";
  850. print PARAMS "ppm = 10 # mass tolerance for MS2 decharging and deisotoping\n";
  851. print PARAMS "ms2_consolidation = 10 # maximal number of peaks retained within each 100-Da window\n";
  852. print PARAMS "\n";
  853. print PARAMS "# Peptide selection and scoring options\n";
  854. print PARAMS "ion_series = 0 1 0 0 0 0 0 1 0 # a, b, c, d, v, w, x, y and z ions, respectively\n";
  855. print PARAMS "ion_losses_MS2 = 1 0 0 0 # 0 = disable; 1 = enable neutral loss of H2O, HPO3, H3PO4 and NH3, respectively\n";
  856. print PARAMS "frag_mass_tolerance = 10 # mass tolerance for MS2 ion matching\n";
  857. print PARAMS "frag_mass_tolerance_unit = 2 # 1 = Da; 2 = PPM;\n";
  858. print PARAMS "\n";
  859. print PARAMS "# Dynamic modifications\n";
  860. print PARAMS "dynamic_M = 15.99492 # add each dynamic modification by one line, starting with dynamic_AA\n";
  861. print PARAMS "dynamic_S = 79.96633\n";
  862. print PARAMS "dynamic_T = 79.96633\n";
  863. print PARAMS "dynamic_Y = 79.96633\n";
  864. print PARAMS "max_modif_num = 3\n";
  865. print PARAMS "\n";
  866. print PARAMS "# Static Modification\n";
  867. print PARAMS "add_Nterm_peptide = 229.1629321 # TMT modification or other amine labeling\n";
  868. print PARAMS "add_Cterm_peptide = 0.0000\n";
  869. print PARAMS "add_A_Alanine = 0.0000\n";
  870. print PARAMS "add_B_avg_NandD = 0.0000\n";
  871. print PARAMS "add_C_Cysteine = 0.0000 # Cys alkylation\n";
  872. print PARAMS "add_D_Aspartic_Acid = 0.0000\n";
  873. print PARAMS "add_E_Glutamic_Acid = 0.0000\n";
  874. print PARAMS "add_F_Phenylalanine = 0.0000\n";
  875. print PARAMS "add_G_Glycine = 0.0000\n";
  876. print PARAMS "add_H_Histidine = 0.0000\n";
  877. print PARAMS "add_I_Isoleucine = 0.0000\n";
  878. print PARAMS "add_J_user_amino_acid = 0.0000\n";
  879. print PARAMS "add_K_Lysine = 229.1629321 # TMT modification or other amine labeling\n";
  880. print PARAMS "add_L_Leucine = 0.0000\n";
  881. print PARAMS "add_M_Methionine = 0.0000\n";
  882. print PARAMS "add_N_Asparagine = 0.0000\n";
  883. print PARAMS "add_O_Ornithine = 0.0000\n";
  884. print PARAMS "add_P_Proline = 0.0000\n";
  885. print PARAMS "add_Q_Glutamine = 0.0000\n";
  886. print PARAMS "add_R_Arginine = 0.0000\n";
  887. print PARAMS "add_S_Serine = 0.0000\n";
  888. print PARAMS "add_T_Threonine = 0.0000\n";
  889. print PARAMS "add_U_user_amino_acid = 0.0000\n";
  890. print PARAMS "add_V_Valine = 0.0000\n";
  891. print PARAMS "add_W_Tryptophan = 0.0000\n";
  892. print PARAMS "add_X_LorI = 0.0000\n";
  893. print PARAMS "add_Y_Tyrosine = 0.0000\n";
  894. print PARAMS "add_Z_avg_QandE = 0.0000\n";
  895. close (PARAMS);

jump_params.pl at commit 7064d22, no license · at the source

Overview

Authors: Xingjian Li1, Yuanxin Chen2,3, Huaixing Wang2,3, Xue Zhang4, Noah Guy Lewis Guiberson5, Xianting Li1, Jacqueline Burré5, Junmin Peng4, Hui Zhang2,3, Zhenyu Yue1,6,7
  1. Department of Neurology, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY USA
  2. Department of Physiology & Pharmacology, College of Veterinary Medicine, The University of Georgia, Athens, GA USA
  3. Department of Neuroscience, Thomas Jefferson University, Philadelphia, PA USA
  4. Departments of Structural Biology and Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN USA
  5. Brain and Mind Research Institute, Appel Alzheimer’s Disease Research Institute, Weill Cornell Medicine, New York, NY USA
  6. Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY USA
  7. Center for Parkinson’s Disease Neurobiology, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY USA
Institutions: Icahn School of Medicine at Mount Sinai (United States); Thomas Jefferson University (United States); University of Georgia (United States); St. Jude Children's Research Hospital (United States); Weill Cornell Medicine (United States)
Journal: NPJ Parkinson's disease, volume 12, issue 1, article 159
Dates: received 24 September 2025; accepted 1 April 2026; published online 24 April 2026
Type: Research article · Language: English
License: CC BY
Identifiers: DOI 10.1038/s41531-026-01353-4 · PMID 42031745 · PMCID PMC13319756 · OpenAlex W7155550725
Open access: gold, a free copy (OpenAlex)
Status: code verified
Categories: mouse (organism), Parkinson's (population), cellular / molecular (subfield)
Methods: Spectral & time-frequency, Statistics, Smoothing, state filtering, decompositions, Preprocessing, Evoked potentials, Connectivity
Keywords: Cell biology, Neuroscience
Topic: Cellular transport and secretion (Cell Biology, Biochemistry, Genetics and Molecular Biology), according to OpenAlex
Funding: NIH HHS (R01NS113960); NINDS NIH HHS (P20NS123320, NS097530); New York Community Trust (P23-000586)
Citations: not cited yet (Europe PMC); 45 references in the paper

Abstract

RAB12 is a small GTPase and a validated substrate of LRRK2, a kinase genetically linked to Parkinson’s disease (PD). While RAB12–LRRK2 signaling has been implicated in ciliogenesis and immune regulation, the neuronal function of RAB12 remains largely unexplored. Here, we investigated the role of RAB12 in synaptic physiology using Rab12 knockout (KO) mice. Rab12 KO mice developed normally but exhibited increased locomotor activity in adulthood. Electrophysiological recordings from striatal slices revealed enhanced presynaptic release probability and increased excitatory drive onto medium spiny neurons. Consistently, live-cell imaging of cultured cortical neurons revealed that Rab12 deletion facilitated, while Rab12 overexpression inhibited, synaptic vesicle exocytosis. Biochemical fractionation showed enrichment of RAB12 in synaptic vesicle–associated fractions containing presynaptic components. Proteomic analysis of Rab12 KO striatal synaptosomes further identified alterations in proteins involved in synaptic membrane trafficking pathways. Together, these findings establish RAB12 as a negative regulator of synaptic vesicle exocytosis and excitatory neurotransmission in vivo. Our study defines a physiological role for RAB12 in synaptic function and provides a basis for future investigation into how LRRK2-dependent RAB12 signaling may contribute to neuronal dysfunction in PD.

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

Repository

Its files are read in the Code ↔ Paper reader above, with 2 matches between paragraphs and lines of code.

JUMPSuite/JUMP

License: none: the authors keep all their rights
State: the link answers, verified on 30 September 2026
Evidence: files inventoried
Commit: 7064d224b155c7dafb5e3495b041e9e9ad886067, 5 August 2022
Languages: Perl (103), Shell (8), R (6), Python (2)
Size: 296 files, 119 scripts
Software Heritage: not archived
Found in: “Code availability”
Holds: README, documentation
Not found: license file, CITATION.cff, environment file, tests, continuous integration
Tools: limma (3 files)
Availability: 1 check, the latest on 30 September 2026: the link answers
  • 30 September 2026: the link answers
120 files
At the source: github.com/JUMPSuite/JUMP

Code availability

JUMPSuite (https://github.com/JUMPSuite/JUMP) was applied to analyze the proteomic data.

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:

  • 1 repository of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
  • 119 scripts, each with its path and the digest of its content;
  • 2 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

No dataset and no data link were found in the paper.

Data availability

The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD075183. All other data of this study are indicated in the article and its Supplementary Information and supplementary files.

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, 30 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 10 authors, 2 keywords, 3 funders, 45 references.

Cite

This paper

Li, X., Chen, Y., Wang, H., Zhang, X., Guiberson, N. G. L., Li, X., Burré, J., Peng, J., Zhang, H., & Yue, Z. (2026). Disruption of the LRRK2 substrate RAB12 facilitates neurotransmission and causes hyperactivity in mice. NPJ Parkinson's disease, 12(1), 159. https://doi.org/10.1038/s41531-026-01353-4

BibTeX

@article{li2026disruption,
author = {Li, Xingjian and Chen, Yuanxin and Wang, Huaixing and Zhang, Xue and Guiberson, Noah Guy Lewis and Li, Xianting and Burré, Jacqueline and Peng, Junmin and Zhang, Hui and Yue, Zhenyu},
title = {{Disruption of the LRRK2 substrate RAB12 facilitates neurotransmission and causes hyperactivity in mice}},
journal = {NPJ Parkinson's disease},
year = {2026},
month = apr,
volume = {12},
number = {1},
pages = {159},
publisher = {Nature Publishing Group},
issn = {2373-8057},
doi = {10.1038/s41531-026-01353-4},
url = {https://doi.org/10.1038/s41531-026-01353-4},
pmid = {42031745},
pmcid = {PMC13319756}
}

RIS

TY - JOUR
AU - Li, Xingjian
AU - Chen, Yuanxin
AU - Wang, Huaixing
AU - Zhang, Xue
AU - Guiberson, Noah Guy Lewis
AU - Li, Xianting
AU - Burré, Jacqueline
AU - Peng, Junmin
AU - Zhang, Hui
AU - Yue, Zhenyu
TI - Disruption of the LRRK2 substrate RAB12 facilitates neurotransmission and causes hyperactivity in mice
T2 - NPJ Parkinson's disease
J2 - NPJ Parkinsons Dis
PY - 2026
DA - 2026/04/24
VL - 12
IS - 1
SP - 159
SN - 2373-8057
PB - Nature Publishing Group
DO - 10.1038/s41531-026-01353-4
UR - https://doi.org/10.1038/s41531-026-01353-4
LA - en
ER -

CSL-JSON

{
"id": "10.1038/s41531-026-01353-4",
"type": "article-journal",
"title": "Disruption of the LRRK2 substrate RAB12 facilitates neurotransmission and causes hyperactivity in mice",
"container-title": "NPJ Parkinson's disease",
"author": [
{
"family": "Li",
"given": "Xingjian"
},
{
"family": "Chen",
"given": "Yuanxin"
},
{
"family": "Wang",
"given": "Huaixing"
},
{
"family": "Zhang",
"given": "Xue"
},
{
"family": "Guiberson",
"given": "Noah Guy Lewis"
},
{
"family": "Li",
"given": "Xianting"
},
{
"family": "Burré",
"given": "Jacqueline"
},
{
"family": "Peng",
"given": "Junmin"
},
{
"family": "Zhang",
"given": "Hui"
},
{
"family": "Yue",
"given": "Zhenyu"
}
],
"container-title-short": "NPJ Parkinsons Dis",
"volume": "12",
"issue": "1",
"page": "159",
"DOI": "10.1038/s41531-026-01353-4",
"PMID": "42031745",
"PMCID": "PMC13319756",
"ISSN": "2373-8057",
"publisher": "Nature Publishing Group",
"URL": "https://doi.org/10.1038/s41531-026-01353-4",
"language": "en",
"issued": {
"date-parts": [
[
2026,
4,
24
]
]
}
}

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