mspire 0.5.0 → 0.6.1

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Files changed (107) hide show
  1. data/README.rdoc +24 -0
  2. data/Rakefile +51 -0
  3. data/VERSION +1 -0
  4. data/lib/cv/description.rb +18 -0
  5. data/lib/cv/param.rb +33 -0
  6. data/lib/cv.rb +3 -0
  7. data/lib/io/bookmark.rb +13 -0
  8. data/lib/merge.rb +7 -0
  9. data/lib/ms/cvlist.rb +76 -0
  10. data/lib/ms/digester.rb +245 -0
  11. data/lib/ms/fasta.rb +86 -0
  12. data/lib/ms/ident/peptide/db.rb +243 -0
  13. data/lib/ms/ident/peptide.rb +72 -0
  14. data/lib/ms/ident/peptide_hit/qvalue.rb +56 -0
  15. data/lib/ms/ident/peptide_hit.rb +26 -0
  16. data/lib/ms/ident/pepxml/modifications.rb +83 -0
  17. data/lib/ms/ident/pepxml/msms_pipeline_analysis.rb +70 -0
  18. data/lib/ms/ident/pepxml/msms_run_summary.rb +82 -0
  19. data/lib/ms/ident/pepxml/parameters.rb +14 -0
  20. data/lib/ms/ident/pepxml/sample_enzyme.rb +165 -0
  21. data/lib/ms/ident/pepxml/search_database.rb +49 -0
  22. data/lib/ms/ident/pepxml/search_hit/modification_info.rb +79 -0
  23. data/lib/ms/ident/pepxml/search_hit.rb +144 -0
  24. data/lib/ms/ident/pepxml/search_result.rb +35 -0
  25. data/lib/ms/ident/pepxml/search_summary.rb +92 -0
  26. data/lib/ms/ident/pepxml/spectrum_query.rb +85 -0
  27. data/lib/ms/ident/pepxml.rb +112 -0
  28. data/lib/ms/ident/protein.rb +33 -0
  29. data/lib/ms/ident/protein_group.rb +80 -0
  30. data/lib/ms/ident/search.rb +114 -0
  31. data/lib/ms/ident.rb +37 -0
  32. data/lib/ms/isotope/aa.rb +59 -0
  33. data/lib/ms/mascot.rb +6 -0
  34. data/lib/ms/mass/aa.rb +79 -0
  35. data/lib/ms/mass.rb +55 -0
  36. data/lib/ms/mzml/index_list.rb +98 -0
  37. data/lib/ms/mzml/plms1.rb +34 -0
  38. data/lib/ms/mzml.rb +197 -0
  39. data/lib/ms/obo.rb +38 -0
  40. data/lib/ms/plms1.rb +156 -0
  41. data/lib/ms/quant/qspec/protein_group_comparison.rb +22 -0
  42. data/lib/ms/quant/qspec.rb +112 -0
  43. data/lib/ms/spectrum.rb +154 -8
  44. data/lib/ms.rb +3 -10
  45. data/lib/msplat.rb +2 -0
  46. data/lib/obo/ims.rb +5 -0
  47. data/lib/obo/ms.rb +7 -0
  48. data/lib/obo/ontology.rb +41 -0
  49. data/lib/obo/unit.rb +5 -0
  50. data/lib/openany.rb +23 -0
  51. data/lib/write_file_or_string.rb +18 -0
  52. data/obo/ims.obo +562 -0
  53. data/obo/ms.obo +11677 -0
  54. data/obo/unit.obo +2563 -0
  55. data/spec/ms/cvlist_spec.rb +60 -0
  56. data/spec/ms/digester_spec.rb +351 -0
  57. data/spec/ms/fasta_spec.rb +100 -0
  58. data/spec/ms/ident/peptide/db_spec.rb +108 -0
  59. data/spec/ms/ident/pepxml/sample_enzyme_spec.rb +181 -0
  60. data/spec/ms/ident/pepxml/search_hit/modification_info_spec.rb +37 -0
  61. data/spec/ms/ident/pepxml_spec.rb +442 -0
  62. data/spec/ms/ident/protein_group_spec.rb +68 -0
  63. data/spec/ms/mass_spec.rb +8 -0
  64. data/spec/ms/mzml/index_list_spec.rb +122 -0
  65. data/spec/ms/mzml/plms1_spec.rb +62 -0
  66. data/spec/ms/mzml_spec.rb +50 -0
  67. data/spec/ms/plms1_spec.rb +38 -0
  68. data/spec/ms/quant/qspec_spec.rb +25 -0
  69. data/spec/msplat_spec.rb +24 -0
  70. data/spec/obo_spec.rb +25 -0
  71. data/spec/spec_helper.rb +25 -0
  72. data/spec/testfiles/ms/ident/peptide/db/uni_11_sp_tr.fasta +69 -0
  73. data/spec/testfiles/ms/ident/peptide/db/uni_11_sp_tr.msd_clvg2.min_aaseq4.yml +728 -0
  74. data/spec/testfiles/ms/mzml/j24z.idx_comp.3.mzML +271 -0
  75. data/spec/testfiles/ms/mzml/openms.noidx_nocomp.12.mzML +330 -0
  76. data/spec/testfiles/ms/quant/kill_extra_tabs.rb +13 -0
  77. data/spec/testfiles/ms/quant/max_quant_output.provenance.txt +15 -0
  78. data/spec/testfiles/ms/quant/max_quant_output.txt +199 -0
  79. data/spec/testfiles/ms/quant/pdcd5_final.killedextratabs.tsv +199 -0
  80. data/spec/testfiles/ms/quant/pdcd5_final.killedextratabs.tsv_qspecgp +199 -0
  81. data/spec/testfiles/ms/quant/pdcd5_final.killedextratabs.tsv_qspecgp.csv +199 -0
  82. data/spec/testfiles/ms/quant/pdcd5_final.txt +199 -0
  83. data/spec/testfiles/ms/quant/pdcd5_final.txt_qspecgp +0 -0
  84. data/spec/testfiles/ms/quant/pdcd5_lfq_qspec.CSV.csv +199 -0
  85. data/spec/testfiles/ms/quant/pdcd5_lfq_qspec.csv +199 -0
  86. data/spec/testfiles/ms/quant/pdcd5_lfq_qspec.oneprot.csv +199 -0
  87. data/spec/testfiles/ms/quant/pdcd5_lfq_qspec.oneprot.tsv +199 -0
  88. data/spec/testfiles/ms/quant/pdcd5_lfq_qspec.oneprot.tsv_qspecgp +199 -0
  89. data/spec/testfiles/ms/quant/pdcd5_lfq_qspec.oneprot.tsv_qspecgp.csv +199 -0
  90. data/spec/testfiles/ms/quant/pdcd5_lfq_qspec.txt +199 -0
  91. data/spec/testfiles/ms/quant/pdcd5_lfq_tabdel.txt +134 -0
  92. data/spec/testfiles/ms/quant/pdcd5_lfq_tabdel.txt_qspecgp +134 -0
  93. data/spec/testfiles/ms/quant/remove_rest_of_proteins.rb +13 -0
  94. data/spec/testfiles/ms/quant/unlog_transform.rb +13 -0
  95. data/spec/testfiles/plms1/output.key +0 -0
  96. metadata +157 -40
  97. data/README +0 -77
  98. data/changelog.txt +0 -196
  99. data/lib/ms/calc.rb +0 -32
  100. data/lib/ms/data/interleaved.rb +0 -60
  101. data/lib/ms/data/lazy_io.rb +0 -73
  102. data/lib/ms/data/lazy_string.rb +0 -15
  103. data/lib/ms/data/simple.rb +0 -59
  104. data/lib/ms/data/transposed.rb +0 -41
  105. data/lib/ms/data.rb +0 -57
  106. data/lib/ms/format/format_error.rb +0 -12
  107. data/lib/ms/support/binary_search.rb +0 -126
data/spec/testfiles/ms/quant/pdcd5_lfq_qspec.CSV.csv ADDED
@@ -0,0 +1,199 @@
1
+ "protid" "protLen" 0 0 0 1 1 1
2
+ "P16104;Q96QV6;A4FTV9;B2R5B3;P04908;P0C0S8;P20671;Q08AJ9;Q6FI13;Q7L7L0;Q93077;Q16777;Q9BTM1;A3KPC7;Q96KK5;Q99878;C9JE22;Q9BTM1-2;B2R5B6;Q8IUE6;P0C0S5;Q71UI9;C9J0D1;A6NN01;B4E0B3;A6NKY0;A6NFA8;C9J386;A8MQC5" 1 -10.1748 21.57658 -11.79741 21.6756 -13.53891 21.91554
3
+ "P04406;Q2TSD0;E7EUT4;E7EUT5;Q0QET7;A4UCT1;E7EPW1;Q5ZEY3" 1 20.84445 20.82648 20.52258 20.91634 21.22588 20.78532
4
+ "P29590;P29590-7;Q9BZY1;P29590-11;P29590-8;P29590-3;P29590-6;Q15156;P29590-13;P29590-9;P29590-5;E9PG00;P29590-2;P29590-12;Q59H09;P29590-4;A4VCI9;E9PBR7;P29590-10;P29590-14;Q59GQ8;Q05835" 1 -10.73202 -11.98464 -10.42344 -7.477787 -14.00278 -11.96467
5
+ "A5JHP3;P81605;Q53YJ2" 1 21.5695 21.77989 -12.43826 21.44081 21.40561 20.8966
6
+ "Q92794;A5PKX7;A5PLL3" 1 -9.716413 -3.583641 -17.64762 -8.342788 -10.27187 -16.43587
7
+ "A5YM50;Q15907;Q5U0I1;Q6FHR0;B4DMK0;B4DMN1;Q6FI42;P62491;B4DT13;B4DQU5" 1 22.25381 22.27523 22.3938 20.48886 20.20729 20.32608
8
+ "Q14315;Q14315-2;E9KL45;P21333;P21333-2;B2ZZ83;Q60FE5;Q60FE6;Q5HY54;O75369;Q60FE7;O75369-2;O75369-3;O75369-6;A6NDY9;B2ZZ80;O75369-4;O75369-5" 1 17.14967 -13.14418 -10.14975 -9.094846 -11.56903 -9.011176
9
+ "A6NE09;P08865;C9J9K3;Q96RS2;C9JQR9" 1 19.60259 20.11426 19.26591 19.04354 18.54808 -15.37007
10
+ "B4DUT8;Q53GK7;Q6FHC3;Q6FHE4;Q99439;B4DDF4;A6NFI4" 1 -11.94525 -10.09451 -13.05105 -8.697504 -3.733516 -15.28478
11
+ "P30044;A6NG06;B7ZLJ4;P30044-2;A6NC19;B7ZVW3" 1 19.97519 20.10917 19.06863 18.47908 18.01149 18.66837
12
+ "A6NHL2;A6NHL2-2" 1 -12.56135 -7.988067 -13.00901 -9.405752 -14.37151 16.64005
13
+ "Q8NI27;Q8NI27-2;E9PHG2;Q5JZ13;A6PVD0" 1 -18.3428 -5.515328 -11.6108 -14.80355 -7.519837 -10.10585
14
+ "A8K0T9;P52907" 1 -8.070804 19.27394 18.9881 -16.03139 -4.297441 -12.72701
15
+ "B2R8N1;Q53QS9;Q99627;E9PGT6;A8K1H6" 1 -6.645485 -3.159239 -6.579911 -7.806178 -10.67114 16.4076
16
+ "A8K220;A8K486;P62937;B2RE56;B4DM82;C9J5S7;Q71V99;Q567Q0;E5RIZ5" 1 22.1986 22.38929 22.38087 21.16944 21.32592 21.29418
17
+ "A8K2X8;E7ENZ3;B4DYC8;B4DE30;B4DYD8;Q96GI1;B4DZY9;Q9HB74;D6RIZ7" 1 21.44294 21.35676 21.02439 27.51676 27.83744 27.34908
18
+ "A8K3K1;P68032;P68133;B7Z6P1;D2JYH4;P62736;P63267;A6NL76;Q5T8M8;B3KW67;B3KUD3;Q5T8M7;B4DUI8;Q13707;E7EQV5;Q7Z7J6;B4E315;E9PG30;B7Z6I1;Q5T9N7;C9JFL5;B8ZZJ2;C9JZR7;C9JUM1;B3KPP5;C9JTX5;Q562L3;Q562M3;Q562M5;Q562N2;Q562P8;Q562Q0;Q562Q2;Q562Q4;Q562Q6;Q562Q8;Q562Q9;Q562R0;Q562R5;Q562R6;Q562T0;Q562T3;Q562T4;Q562T5;Q562T6;Q562T8;Q562U0;Q562U1;Q562W2;Q562X0;Q562X1;Q562X2;Q562X4;Q562X6;Q562X7;Q562Y4;Q562Y8;A0AUL6" 1 -8.780886 -17.22744 -11.99804 -11.46239 -9.619148 -16.34999
19
+ "A8K4I2;P16403;P16402;A3R0T7;A3R0T8;B2R984;P10412;Q4VB24;Q02539;A1L407;P22492" 1 20.76418 20.74993 21.21561 21.25678 21.20574 20.81245
20
+ "Q99615;A8K4T2;Q59EH7;B7Z9W6;Q7Z784;B4DKK3" 1 -10.2706 18.26467 -12.02999 -12.49216 -4.80777 -9.250307
21
+ "B4DSZ4;E7EWS7;A8K4W8;P68036;B4DDG1" 1 19.52338 19.43561 19.70301 18.72341 19.21295 19.45617
22
+ "A8K4Z4;P05388;Q53HW2;Q8NHW5;B4E3D5;Q3B7A4;Q6NSF2;Q53HK9" 1 17.82607 -15.11839 -13.71657 -9.695791 -14.91231 -20.01069
23
+ "Q59EJ3;A8K5I0;P08107;B4DNT8;B4DWK5;B4DI39;B4E3B6;B4DFN9;E7EP94;B4E388;B4E1S9;B4DVU9;B4DNV4;C9JCM4;E7EP11;B2R6X5;B3KSM6;P17066;Q53FC7;B3KTT5;Q5SP16;B4DNX1;B4E1T6;P48741;B4DHP5" 1 20.3722 19.70376 20.21916 19.89714 19.99175 20.05457
24
+ "A8K5T7;Q9Y2Z0;A8K7W3;Q9Y2Z0-2;B4DYC6" 1 -11.04554 -8.394851 -12.22395 -12.15968 -9.030668 -9.055989
25
+ "Q59EM9;Q66K58;P0CG48;A8K674;Q96H31;Q96MH4;Q96C32;Q9UFQ0;P0CG47;Q5PY61;Q5U5U6;B2RDW1;P62979;Q5RKT7;B4DV12;Q5UGI3;P62987;Q3MIH3;Q49A90;Q8WYN9" 1 25.01933 25.02817 25.25324 24.37498 24.61352 24.12123
26
+ "Q3ZCU9;A8K690;P31948;B4DM70" 1 -15.79622 -12.4429 -8.251936 -14.61531 -6.618255 -11.69185
27
+ "Q05D08;Q9UQ80;Q6PIN5;A8K6Y1" 1 19.58187 19.67385 19.48418 -9.563393 -9.759739 -13.90931
28
+ "Q14240-2;Q14240;A8K7F6;P60842;E7EQG2;Q9NZE6;B4DNH2;A8K088;Q96B07;Q59F68;B4DJX6;B4DKP9" 1 20.29019 -3.275673 18.7028 -9.760659 -11.02793 -8.931159
29
+ "Q59HD4;A8K7X6;Q68Y55;B4DLC0;Q6IPF4;Q15366;Q32Q82;B4DXP5;B4DRD7;P57721;P57721-4;A8MX33;E9PFP8;Q5MJP6;P57721-5;P57721-3;P57721-2" 1 22.9206 23.02955 22.65014 21.91368 21.96141 22.22335
30
+ "Q9UBL6;B7Z1M3;Q9HCH3;B7Z370;Q96A23-2;Q86YQ8;Q9UBL6-2;O95741;Q96A23;Q8IYJ1;A8K8A4;Q96FN4;O75131;B2RD40;Q719H8;B3KWK1;Q7Z6C8;Q86VY2;Q4G168" 1 -7.090923 -13.03055 17.60074 -15.48375 -7.483465 -9.849869
31
+ "Q13561-2;Q53H88;Q13561-3;Q13561;B3KTX4;A8K8J9" 1 -13.29258 -11.61868 -16.22564 -11.85453 -13.5876 -8.071517
32
+ "A8K9C4;P68104;Q53G85;Q53GE9;Q53HM9;Q53HQ7;Q53HR5;Q5VTE0;Q6IPN6;Q6IPS9;Q6IPT9;E7EUM7;Q6IQ15;B4DNE0;Q96RE1;Q53GA1;Q9NZS6;B4DV42;Q53G89;Q9H2I7;Q16577;Q53HR1;Q8IUB0;Q504Z0;Q6P4C9;Q96CD8;Q6P082;Q8TBL1;Q96C29;B4E2C5;Q05639;Q59GP5;Q14222;Q5JR01;A9X7H1;A6PW80;Q96EB3;E7EPH7;Q6NSH7;Q2F837;Q6NS35" 1 25.19363 25.12912 24.41125 24.75903 24.928 24.59087
33
+ "A8KAH7;P13861;Q9BUB1" 1 -12.12438 -16.2057 -10.1214 -15.34898 -9.445698 -12.16657
34
+ "A8KAY2;Q75N90;E7EP57;Q6ZNB8;B3KU56" 1 -14.53446 -13.40562 -9.063076 -17.21276 -9.328329 -8.495333
35
+ "Q9H2G2;Q9H2G2-2;REV__Q9P2R3-2;REV__Q9P2R3;REV__B3KPZ0;Q5M775;B4DZC9;A8MV89;B4E2A4;Q5M775-4;REV__Q5H9P4;Q5M775-2;Q5M775-3;Q5M775-5" 1 19.92454 -8.690648 -6.982073 -12.38774 -12.12938 -12.40572
36
+ "A8MVA2" 1 -10.62001 -14.80463 -5.787057 -11.14217 -9.217167 -13.77398
37
+ "C9JS35;Q92890-1;B4E3I3;Q541A5;Q92890;A8MW31;C9J6N9;B7Z9N3;A6NJ11;C9IZG3;C9JNP9" 1 19.71 19.57119 19.18175 18.66716 18.48562 18.95311
38
+ "A8MXP9;P43243;Q68D11;D6REM6;D6R991" 1 -10.82731 -4.6525 -5.913542 -11.42858 -14.86205 -13.279
39
+ "C9JE52;A8MZ76;Q2TNB3;Q6FHK9;Q86SZ7;Q9UL46" 1 21.74755 21.54628 21.21804 20.50048 20.27537 20.84805
40
+ "E7EX29;D0PNI1;P63104;B0AZS6;B7Z465;E7EX24;B7Z2E6;Q2F831;E7ESK7" 1 19.81649 19.99811 19.79994 18.96002 18.55981 19.11802
41
+ "Q13148-2;Q13148;B4DRW3;B1AKP7" 1 -9.201861 -8.547015 -12.34555 -4.826214 -13.71331 -14.84832
42
+ "P10599;B1ALW1;O60744" 1 -10.34632 -10.56697 -11.52899 -7.476205 -12.8407 -10.40727
43
+ "B2R4M6;P06702" 1 -12.68759 -14.11326 -8.289717 -8.96431 -9.109454 -6.145557
44
+ "B2R4P2;Q06830;Q13162;E9PEN3" 1 21.84219 21.74086 20.95865 21.18707 -9.354398 20.667
45
+ "E9PAV3;B2R4P8;Q13765;B4DDI8" 1 19.63336 19.85194 19.99189 19.41607 19.86116 -11.03913
46
+ "B2R4R0;P62805;Q0VAS5;Q6B823" 1 -9.551398 20.73513 20.94528 20.9234 21.9374 20.9102
47
+ "B2R4R9;P62857" 1 21.36335 21.36608 21.48094 21.57768 20.64262 21.08868
48
+ "B2R4U3;O00762;Q5TZN3;E1P5N7;A6NP33" 1 19.57873 19.47781 18.81994 17.99722 17.64934 -9.015995
49
+ "B2R679;Q5SQT9;Q6FID4;Q9NR31;Q8NG23;B4DQ19;D6RDB2;Q5SQT8;E9PBN0;Q5SQU0;D6RAA2" 1 23.11618 22.90564 22.8795 22.50913 22.308 22.55194
50
+ "B2R9K8;P40227;Q59ET3;B4DPJ8;A1JUI8;A6NCD2;B4DN39;Q92526;B4DYB0;B4DX20" 1 20.17597 19.99272 19.95603 27.8846 27.92388 27.62659
51
+ "B2R9U2;Q02790" 1 -9.570673 -6.285736 -13.28069 -15.74234 -14.50727 -8.327213
52
+ "B2RBR9;Q14974;B7Z752;B7ZAV6;B7Z5M1" 1 18.6568 18.27653 -14.11772 17.96002 17.45282 -8.417989
53
+ "P10809;B3GQS7;B7Z597;B7Z5E7;B7Z4F6;E7ESH4;Q53SE2;E7EXB4;B7Z532;C9JL25;B7Z712;C9JCQ4;C9JL19;C9J0S9;Q53QD5" 1 23.93454 23.96402 23.99136 23.44468 23.2764 23.46376
54
+ "B3KM68;Q9Y6E2;E7ETZ4;B7Z4K8;B5MCH7;B5MCE7;Q05D83;B4DLZ8;Q53FN7;B4DWF7;Q7L1Q6;E9PRN2;Q7L1Q6-2;Q75MG1;D3DN77" 1 19.31358 19.20125 18.97396 -10.97263 -12.16192 -8.993392
55
+ "B3KNA8;Q07352;B4E1N3;B4DG15" 1 -10.32378 -6.598993 -9.45362 -9.234979 -9.904229 -11.74547
56
+ "B3KUH0;Q8WUX9;E5RJI3;B3KRZ9;E5RIU9;B4DKJ6" 1 17.05801 17.9016 -8.524639 -8.500674 -3.22365 -6.724072
57
+ "B3KW39;Q5H9R6;Q8WXH5" 1 -11.1052 -5.320193 -13.60777 -17.3987 -9.64648 -16.14916
58
+ "E9PDP1;B3KXM2;Q07161;P36873-2;P62136;P36873;Q9UPN1;E9PMD7;P62140;B4DJ75;B7ZB67;B4E163;E7ETD8;C9JP48;C9J9S3;A6NNR3" 1 19.56744 19.48564 19.48156 18.37105 18.27362 18.7264
59
+ "P04350;B4DE77;B4DJ43;B4DFH6;E7EM46" 1 -7.801593 18.33136 19.15247 -12.86542 -12.8622 -7.263447
60
+ "P32119;B4DF70;A6NIW5" 1 -12.16686 -14.48203 -12.85298 -9.178046 -6.847968 -9.206059
61
+ "Q15417;Q6FHA7;B4DFK6;B4DP09;E7ENQ7;E9PDU6;Q9BWY6" 1 19.49717 19.00306 18.5068 -14.06474 18.66171 19.17767
62
+ "P08238;B4DGL0;B4DMA2;Q6PK50;Q58FF7;Q58FF8;A8K3W9;Q9H6X9;Q14568;Q86SX1;B4DTA5;O14942;P14625;Q5CAQ5;Q12931;Q53FS6;Q53G55;Q9BV61;B4DR68;Q8N9Z3;Q59FC6;Q96HX7;Q58FG1;Q96GW1;E9PHH7;Q5T9W4;Q5T9W8;B4DQX3;E9PHI1;E9PHI2;Q5T9W5;Q5T9W6" 1 21.50896 21.49892 21.6747 20.74041 19.85345 20.78987
63
+ "D3DPU2;B4DI38;B2RDY9;Q01518;B4DNW7;B4DNY3;Q01518-2;Q5T0R1;Q5T0R2;Q5T0R3;Q5T0R4;Q5T0R5;Q5T0R6;Q5T0R7;B4DNA3;B4DUZ8;Q5T0R9;E7ENY9" 1 21.6832 21.56025 21.57261 21.13871 20.94027 21.01004
64
+ "Q53FR9;Q9P000;E9PJ95;B4DQW0;E9PAN2;B4DIH0" 1 -9.596016 18.24776 -7.699231 -10.7063 -10.17703 -13.45574
65
+ "P61086;C9JGP1;B4DIZ2;D6RDM7" 1 -8.994216 -12.62541 -5.835931 -8.976171 -7.628281 18.02702
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+ "P17812;B4DMB5;B4E1E0;B4DR64;B7Z9C4" 1 -9.063957 -10.08892 -11.26493 -11.47813 -11.13477 -11.11889
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+ "B5ME63;Q92835;Q92835-2;Q92835-3;B4DQ61" 1 -5.391627 -9.045222 -8.187441 -9.703869 -6.676554 -10.21431
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+ "Q53G16;Q7Z4W5;Q9UMR2;Q9HBZ9;Q9NUU7;B4DXS6;E7EMK4;Q2NL95;Q9UMR2-2;B4DS24;E7EPY4" 1 18.80146 -7.213804 -17.52335 -18.3976 -7.410078 -11.72704
70
+ "E9PCF5;B4DT31;E9PEB5;C9JT73;Q96AE4-2;E7EMK0;Q96AE4;B4DWL1;B4E0X8;Q6PJY1;Q59FU3;C9JSZ1;A3KFK8;Q96I24;A6NJ37;Q96I24-2" 1 21.01536 20.88487 20.59596 20.02188 20.60991 19.93848
71
+ "Q14103;Q14103-2;Q14103-3;B4DTC3;Q14103-4;Q12771;B9ZVU1;D6RAF8;B4E0W4;D6RF44;D6RBQ9;O14979;O14979-2;B4DTA2;O14979-3;D6RD83" 1 20.51768 20.62819 20.17207 19.77349 19.95844 20.11032
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+ "P25685;Q6FHS4;Q6FI51;B4DX52;B4DKK9" 1 -11.34094 -5.602256 -9.866002 18.82448 -9.522322 -15.38411
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+ "B4DZF2;Q59G42;D3DQV9;P78344;P78344-2;Q2TU89;E9PCV8;Q3LIE0" 1 -8.065076 17.53374 -10.82608 -12.04515 -10.95889 -7.42203
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+ "Q9Y371-2;Q9Y371;B4E182" 1 -2.551314 -7.276527 -7.441837 -14.31029 -7.28746 -5.179357
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+ "P28066;Q5U0A0;B4E2V4" 1 -12.5564 -11.23456 16.1719 -2.304186 -14.18422 -8.240927
81
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+ "B5BU32;B5BUF9;P04183" 1 -9.703285 -11.10878 -5.453605 -10.84511 -14.27154 -10.94397
83
+ "B5BU38;P04083;Q5TZZ9;Q5T3N1;Q5T3N0;B4DL19;Q05BR2" 1 21.04059 20.88502 20.86439 18.36158 18.94135 -5.979648
84
+ "Q8N6T3-2;Q8N6T3;B7ZBI2;Q8N6T3-3;B7Z3U0;E7EV62;B7Z8H8;E5RHH7" 1 -13.99549 -8.407551 -16.42668 -19.41523 -9.075064 -11.88774
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88
+ "Q9NVD7;B7Z952;E9PS97;Q9NVD7-2" 1 -9.460929 -11.15873 -13.67356 -9.492962 -9.836108 -10.73004
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90
+ "B7ZLS9;Q15431;Q9H2G7;Q5VXJ5" 1 -10.23098 -7.656287 -15.66482 -7.089435 -11.6862 -11.56794
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+ "C7DJS2" 1 -9.09039 -9.746332 -8.25273 -8.557491 -10.93754 -12.68969
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+ "Q15942;C9IZ41" 1 -5.137085 -16.57598 -10.65647 -10.01639 -11.41379 -9.139287
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+ "Q9BUL8;C9J5C3;C9J6F3;C9J363;C9JND6;C9JSA3" 1 -12.56861 -10.74126 -15.59777 -9.194325 -18.0781 -12.45802
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+ "E9PC16;C9JEQ5" 1 -8.375236 -13.61158 -13.66537 -13.72985 -15.36838 -10.02013
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98
+ "D3DQ70;D3DQ69;Q8NC51;Q8NC51-2;Q8NC51-3;Q5VU21;Q63HR1;Q8NC51-4" 1 -12.37386 -7.763814 -17.1609 -5.07688 -8.629203 17.46786
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100
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101
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+ "E5KN55;E5KN59;Q08752;Q6FGM6;Q05DH6" 1 -9.400893 -15.53695 -13.06128 -7.844266 -9.440896 -12.51987
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105
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106
+ "Q9H0U4;Q9H1C9;E7EWA5;Q6FIG4;Q92927" 1 23.89208 23.98198 23.74273 22.67282 22.63962 22.37263
107
+ "E9KL23;P01009;P01009-2;P01009-3;Q13747;Q9P173;C1KH65;A7L8C5;A7L8C6;B2D098" 1 20.19039 -9.17988 -6.633758 19.48016 -15.74496 -9.44243
108
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110
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114
+ "Q9UHX1;Q9UHX1-2;Q9UHX1-5;Q9UHX1-3;Q9UHX1-6;Q9UHX1-4;E9PQ56;E9PN18;E9PMU7;E9PL19" 1 -15.87114 -10.66053 -9.407564 15.60574 -18.49609 -22.69006
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+ "O43175;B3KSC3;Q5SZU1;Q9UMY2;Q8N5M8;Q9UMY3;Q96RV6;Q96RV7" 1 21.11108 20.84751 20.54425 19.98607 19.97533 19.86478
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119
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125
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126
+ "P06733;P06733-2;E2DRY6;Q9BT62;Q96GV1;D3DTL2;P09104;P13929;Q6FHV6;E7ERT6;P13929-2;B7Z2X9;P13929-3;D3DTL4;Q9NPL4;A4QMW8" 1 20.06894 19.9805 20.20275 -9.30103 19.39897 19.33723
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+ "P07355-2;P07355;A6NMY6;B4DNH8;B3KRQ1" 1 25.34996 25.25158 25.17976 24.09184 23.9968 24.0441
128
+ "P07384;B2RDI5;A8MSM1;B4DWH5;E9PRM1;E9PQB3;E9PLQ6;E9PSA6;E9PJA6;E9PMC6;E9PLC9;E9PJJ3;E9PLX0;E9PIA9" 1 21.46508 21.429 21.70771 19.9959 19.90806 19.46408
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+ "P07437;Q5SU16;Q5JP53;B4DY90;B7ZAF0;Q6LC01;Q5ST81;B7ZAK1;B4DQN9;E7EX69;B4E052;Q9BUU9;B4DMU8;E9PBJ4;B4DMJ5;B4DXZ5;E7ENH1;Q96B85;Q1KSF8;A5D906;A5D907;A1L195;Q6P602;A4UCT2;A6NNZ2;Q5SQY0;C9JAA5;CON__ENSEMBL:ENSBTAP00000025008;Q9H4B7;A6NKZ8;Q5SQY1;A1L196;A4UCU2" 1 24.5093 24.59024 24.54646 22.91379 22.79198 23.11634
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+ "P08758;E7ENQ5;D6RBL5;D6RBE9;E9PHT9;B4DNG6" 1 19.69729 19.32854 19.04817 18.29212 18.16315 19.23916
133
+ "P09211;A8MX94;C7DJS1;B2C310" 1 22.56888 22.45493 22.36209 22.41568 22.29765 21.92401
134
+ "P09382" 1 25.12017 25.13739 24.96354 24.19024 23.97044 24.05961
135
+ "P09651;P09651-2;Q0VAC0;Q32P51;Q6IPF2;P09651-3;Q9BSM5;B4E0B5;B4DP35" 1 19.90721 19.9045 19.93934 19.30425 19.05261 19.30828
136
+ "P11142;Q53GZ6;E9PKE3;B3KTV0;E7ET08;P11142-2;Q53HF2;Q96IS6;E9PNE6;B4DTX2;E9PLF4;E9PN89;E9PK54;E9PQK7;E9PQQ4;B4E1Q1;E9PI65;E9PPY6;E9PN25;P54652;A8K7Q2;B3KUS2;Q96BE0;E9PS65;Q96H53;Q9NWW3;Q9NZ87;P11021;B4DEF7;C9IYE6;A4D111;E9PM13;E9PSH5" 1 23.61358 23.56023 24.01171 23.54097 23.31769 23.14404
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+ "P11586;B7Z809" 1 19.62578 20.54501 20.32608 -7.156656 19.10991 -13.73077
138
+ "P12273" 1 -10.83245 -10.53748 -10.03411 -13.35282 -12.67365 -10.41932
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+ "P13639;B4DPU3;Q8TA90;Q6PK56;B4DRE8;B4DMC6;Q6W6M8" 1 23.80902 23.84 23.60162 22.4743 22.20774 22.27481
140
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+ "P14618;P14618-2;B4DUU6;E7EUQ8;E9PF79;B4DNK4;B4DRT3;Q8WUW7;E7EUJ4;Q504U3;Q9UKK4;Q9UK31;Q9NYI7;Q9UN47" 1 22.23248 22.28729 21.86359 21.69562 21.39037 21.54581
142
+ "P17987;E7EQR6" 1 17.85392 17.0281 18.56309 27.4677 27.4964 27.33048
143
+ "P18206;P18206-2;B3KXA2;B4E3Q9;P18206-3;Q5JQ13;B4DKC9;B4DTM7" 1 21.10534 21.0001 19.93531 18.44273 19.34953 19.23079
144
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146
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148
+ "P30050;P30050-2;Q59FI9" 1 19.5282 19.22771 19.76158 19.58602 19.40674 19.05608
149
+ "P31151" 1 21.41101 20.94049 -5.475178 -13.97814 -14.54195 -11.57172
150
+ "P31949" 1 -6.616476 -17.54778 -14.59551 -8.167336 -10.0172 -9.259502
151
+ "P35754" 1 -9.601591 -9.607951 -13.12461 -14.6505 -6.372745 -8.536594
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+ "P46060;B4DY16;B0QYT4;B0QYT5;B4E0U0;Q9BSK3;B0QYT6" 1 -7.518831 -13.19537 -8.816086 -10.24924 -10.07651 -16.03507
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+ "P48643;Q9BU08;E7EWW2;B4DZT5;B4DXI1;E9PCA1;B7ZAR1;B4DDU6;B4DX08;D6RHV5" 1 -10.50235 -9.97741 -13.23022 -13.70337 -9.895056 -8.993415
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+ "Q59H77;P49368;E9PAQ6;B3KX11;Q5SZY0;Q2TU64;B4DUR8;A6NE14;Q5SZX6;E9PRC8;Q5SZW8;Q5SZX9;E9PM09;E9PQ35;Q5SZX8;Q16878;Q16857" 1 19.61184 19.67721 19.23673 27.72175 27.93568 27.5947
155
+ "P50990;Q53HU0;B4DEM7;Q7Z759;B4DQH4" 1 22.38743 22.56686 22.1832 27.88052 28.13256 27.85863
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+ "P50991;A8K3C3;B7Z8B1;B7Z9L0;B7Z2Z8;B7Z2F4" 1 18.2702 19.35316 18.61924 27.32071 27.30583 27.11088
157
+ "P51148;P20339;P61020;Q6FI44;Q6FI54;B4DJA5;B4DKD7" 1 22.42401 22.49931 22.80075 21.62582 21.73723 21.4171
158
+ "P51149;B4DPH9;C9J592;C9J8S3;C9J4V0;C9J4S4;C9J7D1;C9IZZ0" 1 21.89807 21.86948 21.64777 20.35681 20.17121 20.69702
159
+ "P61026;Q53T70" 1 21.11388 22.00717 -10.0114 20.01209 20.61746 20.56104
160
+ "P61088" 1 21.85935 21.72226 21.87376 20.92832 20.85681 20.85711
161
+ "P61106" 1 -13.46907 -14.33496 -7.414689 -12.04448 -11.67296 -10.06022
162
+ "P61204;P84077;B4DEB9;B4DLJ3;A4D0Z3;P84085;B4DN70;B4DJC8;C9J1Z8;B4E190;B7ZB63" 1 21.42992 21.4289 21.03113 21.60603 21.18041 21.39603
163
+ "P61289-2;P61289;Q6FHK7;B3KQ25;B7Z8D3" 1 22.46214 22.42846 22.45651 21.61553 21.28444 21.46523
164
+ "Q5VXS0;P61960" 1 -5.901867 -11.14697 -7.353172 -9.288275 -9.663898 -14.19445
165
+ "P62258;P62258-2;B7ZA86;B4DJB0;C9JAV0;B4DJF2" 1 -9.879312 -9.866565 -16.13984 -19.80651 15.69759 -12.41216
166
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167
+ "Q01995;Q5U0D2;Q6FI52;Q53GC9;E9PC82;Q59FA5;E9PJ32" 1 21.99186 21.96116 22.44831 21.29905 21.51831 21.04414
168
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169
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data/spec/testfiles/ms/quant/pdcd5_lfq_qspec.csv ADDED
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