Hi Everyone, I'm quite new to Percolator and now I am practicing with data, that has already been published to have crosslinks using Hekate ( https://www.ncbi.nlm.nih.gov/pubmed/24010795). I am trying to validate the crosslinked results found by Kojak 1.6.1 using Percolator 3.02. However, the program stopped working, and I got no results. It says "Warning: No target-decoy protein pairs found for the picked protein strategy. Check if the correct decoy pattern was specified with the -P flag; if the target protein is called "protA" and the decoy protein "decoy_protA", use the option "-P decoy_"." But the settings for the decoy pattern were correct. What do you think can be the problem for this?
Thank you for your help in advance, Gabriella -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
PolIII.fasta
Description: Binary data
SpecId Label scannr Score dScore NormRank PPScoreDiff Charge Mass PPM LenShort LenLong LenSum Peptide Proteins T-2035-25.09 1 2035 3.85 3.85 5 0.5 3 1869.0017 -3.0461 9 5 14 -.DLIKR(4)--LKDMHPTER(2).- PolIII PolIII T-2046-25.18 1 2046 3.275 3.275 26 0.315 3 1864.9817 -0.3292 9 5 14 -.DLIKR(4)--LKDMHPTER(2).- PolIII PolIII T-1718-22.34 1 1718 2.89 2.89 26 1.135 2 1815.0414 -4.2203 7 8 15 -.KKPEEMAK(1)--TAPLVKK(6).- PolIII PolIII T-1718-22.34-2 1 1718 2.89 2.89 26 1.135 2 1815.0414 -4.2203 7 8 15 -.KKPEEMAK(2)--TAPLVKK(6).- PolIII PolIII T-1462-20.15 1 1462 2.665 0.125 26 0.4 2 1464.7555 -4.1295 7 5 12 -.AMGKK(4)--KPEEMAK(1).- PolIII PolIII T-1994-24.75 1 1994 2.38 2.015 26 0.815 4 2251.2709 -2.5749 6 15 21 -.NAGKHAGGVVIAPTK(4)--VMVTKR(5).- PolIII PolIII T-1670-21.92 1 1670 2.115 0.135 4 0.6 3 1811.0214 -0.4854 7 8 15 -.KKPEEMAK(1)--TAPLVKK(6).- PolIII PolIII T-1731-22.44 1 1731 2.015 0.08 26 0.855 2 1811.0214 -0.8762 7 8 15 -.KKPEEMAK(1)--TAPLVKK(6).- PolIII PolIII D-3504-38.43 -1 3504 2.005 2.005 26 0.1 4 2513.2167 4.7306 9 13 22 -.GGVEDDPAEKHTR(10)--RMKAGNAEK(3).- DECOY_ DECOY_ T-1616-21.48 1 1616 1.89 1.89 26 0.435 2 1388.83 -4.3999 7 5 12 -.AMGKK(4)--TAPLVKK(6).- PolIII PolIII T-1648-21.74 1 1648 1.81 0.11 26 0.79 3 1815.0414 -3.0624 7 8 15 -.KKPEEMAK(2)--TAPLVKK(6).- PolIII PolIII T-1729-22.43 1 1729 1.76 0.215 4 0.77 3 1811.0214 -1.5657 7 8 15 -.KKPEEMAK(2)--TAPLVKK(6).- PolIII PolIII D-3204-35.57 -1 3204 1.675 1.675 3 0.46 5 2980.5284 1.1184 10 15 25 -.FSLGMMALIAAKLMR(12)--TDTDRKVDQR(6).- DECOY_ DECOY_ T-4076-43.77 1 4076 1.625 0.98 7 0.415 4 2933.4978 -3.0787 18 7 25 -.GMKDLIK(3)--KPEEMAKQRSVFAEGAEK(1).- PolIII PolIII T-1635-21.65 1 1635 1.615 1.615 26 0.295 2 1384.81 -0.6139 7 5 12 -.AMGKK(4)--TAPLVKK(6).- PolIII PolIII T-1755-22.69 1 1755 1.515 1.515 26 0.39 2 1527.767 -1.0496 5 7 12 -.NKGGYFR(2)--TDTKK(4).- PolIII PolIII T-3236-35.85 1 3236 1.46 0.695 26 0.165 4 2964.5009 -0.7622 18 5 23 -.KLNRR(1)--MTAREVMDIDEAREKYAR(15).- PolIII PolIII D-4477-47.91 -1 4477 1.45 1.45 3 0.345 4 2624.3554 0.0352 9 12 21 -.IVRKCGNELIGR(4)--QTYPKMYGK(5).- DECOY_ DECOY_ D-2912-33.06 -1 2912 1.42 1.42 2 0.445 4 2520.2821 -4.7329 9 13 22 -.GQSQPFAQHAKLR(11)--TGTTAKDHK(6).- DECOY_ DECOY_ T-3875-41.95 1 3875 1.42 0.41 26 0.195 4 3164.601 -2.9108 19 9 28 -.RAKEGLEER(3)--SVFAEGAEKNGINAELAMK(9).- PolIII PolIII D-637-7.14 -1 637 1.39 0.32 26 0.265 3 1937.0102 2.7536 8 8 16 -.MKAGNAEK(2)--TMNKFILK(4).- DECOY_ DECOY_ T-3930-42.45 1 3930 1.385 0.75 4 0.59 4 2933.4978 -3.513 18 7 25 -.GMKDLIK(3)--KPEEMAKQRSVFAEGAEK(1).- PolIII PolIII D-4770-52.38 -1 4770 1.325 1.325 2 0.65 5 2697.5424 -0.4495 12 10 22 -.IVIHDALLKR(9)--VRGVKYICMPAK(5).- DECOY_ DECOY_ D-3993-42.99 -1 3993 1.305 1.305 2 0.595 3 2346.1836 0.3936 15 5 20 -.KVDQR(1)--QKMGANEAVPSEVSR(2).- DECOY_ DECOY_ T-1717-22.33 1 1717 1.29 0.035 4 0.52 4 1811.0214 -0.6554 7 8 15 -.KKPEEMAK(2)--TAPLVKK(6).- PolIII PolIII T-3583-39.24 1 3583 1.25 0.185 26 0.37 3 2094.0879 -2.1482 8 8 16 -.KSFDMLQR(1)--TDTKKLNR(4).- PolIII PolIII T-2403-28.68 1 2403 1.18 0.595 3 0.475 4 2271.1927 3.4753 9 9 18 -.KPEEMAKQR(1)--VMVTKRGNR(5).- PolIII PolIII D-3026-34.07 -1 3026 1.18 1.18 2 0.355 5 2939.5088 0.628 11 13 24 -.GGVEDDPAEKHTR(10)--KRYVEPRLVDR(1).- DECOY_ DECOY_ T-1771-22.85 1 1771 1.16 0.015 7 0.435 5 2256.2182 0.8995 4 14 18 -.AMGKKKPEEMAKQR(4)--KLNR(1).- PolIII PolIII T-3551-38.85 1 3551 1.16 1.16 26 0.49 3 1939.996 -0.903 11 5 16 -.AMGKK(4)--LKDMHPTERGK(2).- PolIII PolIII T-4021-43.24 1 4021 1.14 0.79 3 0.505 3 2934.5247 4.5118 17 8 25 -.AKEGLEER(2)--NGINAELAMKIFDLVEK(10).- PolIII PolIII T-3436-37.82 1 3436 1.005 0.59 6 0.08 3 2881.4784 -1.8287 14 8 22 -.KSFDMLQR(1)--LAFLFPDEEERLKR(13).- PolIII PolIII T-1633-21.64 1 1633 1 1 26 0.205 3 1384.81 -0.5888 7 5 12 -.AMGKK(4)--TAPLVKK(6).- PolIII PolIII D-3572-39.14 -1 3572 1 1 2 0.25 3 2263.1289 -4.7853 8 9 17 -.PMYMTDERK(1)--TMNKFILK(4).- DECOY_ DECOY_ D-3225-35.75 -1 3225 0.965 0.11 26 0.38 4 2836.3506 -4.9357 13 9 22 -.PMYMTDERK(1)--PMYMTDERKIVGK(1).- DECOY_ DECOY_ T-1646-21.73 1 1646 0.95 0.025 2 0.45 4 1815.0414 -3.3086 7 8 15 -.KKPEEMAK(2)--TAPLVKK(6).- PolIII PolIII T-4177-44.81 1 4177 0.945 0.945 26 0.27 3 2076.0661 4.0685 11 5 16 -.EKYAR(2)--LKDMHPTERGK(2).- PolIII PolIII T-3519-38.58 1 3519 0.94 0.395 3 0.405 3 2126.1107 1.0721 10 5 15 -.EKYAR(2)--LKRRPEYDER(2).- PolIII PolIII D-2570-30.06 -1 2570 0.89 0.89 26 0.21 3 1816.9565 3.3464 6 9 15 -.RMKAGNAEK(3)--SQSKIR(4).- DECOY_ DECOY_ D-3180-35.37 -1 3180 0.875 0.875 26 0.135 3 2375.2077 3.5736 12 8 20 -.AEKSDGPR(3)--VRGVKYICMPAK(5).- DECOY_ DECOY_ D-4740-51.88 -1 4740 0.875 0.21 5 0.21 4 2641.4328 4.5243 13 10 23 -.FILKTGTTAK(4)--GQSQPFAQHAKLR(11).- DECOY_ DECOY_ D-2603-30.32 -1 2603 0.805 0.805 3 0.185 3 3757.9199 -4.6718 13 18 31 -.KTPAFNFIELGDFISLQR(1)--PMYMTDERKIVGK(1).- DECOY_ DECOY_ T-1710-22.26 1 1710 0.8 0.03 4 0.365 4 1811.0214 -0.4499 7 8 15 -.KKPEEMAK(2)--TAPLVKK(6).- PolIII PolIII T-4837-53.81 1 4837 0.78 0.78 3 0.3 5 3225.8581 0.8929 9 20 29 -.GKVITAAGLVVAARVMVTKR(2)--RAKEGLEER(3).- PolIII PolIII D-4634-49.96 -1 4634 0.775 0.775 3 0.285 3 2120.1764 -2.27 8 10 18 -.IVIHDALLKR(9)--MKAGNAEK(2).- DECOY_ DECOY_ D-3031-34.10 -1 3031 0.77 0.77 2 0.205 6 2939.5088 0.5685 11 13 24 -.GGVEDDPAEKHTR(10)--KRYVEPRLVDR(1).- DECOY_ DECOY_ D-3170-35.28 -1 3170 0.765 0.265 3 0.355 3 2777.3578 3.6893 9 13 22 -.PMYMTDERKIVGK(9)--QTYPKMYGK(5).- DECOY_ DECOY_ D-4791-52.68 -1 4791 0.765 0.765 26 0.1 5 2801.6056 -3.2086 11 10 21 -.IPLYKLFVQR(5)--KRYVEPRLVDR(1).- DECOY_ DECOY_ D-2887-32.87 -1 2887 0.755 0.755 2 0.27 3 1927.9814 -2.2674 6 9 15 -.QTYPKMYGK(5)--SQSKIR(4).- DECOY_ DECOY_ T-3929-42.44 1 3929 0.74 0.74 5 0.345 3 2933.5161 2.6514 9 15 24 -.IFDLVEKFAGYGFNK(7)--RAKEGLEER(3).- PolIII PolIII T-4161-44.65 1 4161 0.735 0.25 6 0.235 4 2933.5161 3.3343 9 15 24 -.IFDLVEKFAGYGFNK(7)--RAKEGLEER(3).- PolIII PolIII D-4209-45.16 -1 4209 0.725 0.725 26 0.19 2 2053.0679 -3.0496 5 13 18 -.GGVEDDPAEKHTR(10)--KIVGK(1).- DECOY_ DECOY_ D-2810-32.24 -1 2810 0.72 0.72 26 0.135 4 2710.4502 2.1239 6 17 23 -.GSKQALHIAAERQTYPK(3)--SQSKIR(4).- DECOY_ DECOY_ T-1390-19.53 1 1390 0.715 0.16 2 0.32 3 2367.2277 -0.9903 8 10 18 -.KKPEEMAKQR(1)--KSFDMLQR(1).- PolIII PolIII T-1996-24.76 1 1996 0.71 0.71 26 0.145 5 2246.2581 4.2617 8 11 19 -.KLEGVTRNAGK(1)--TDTKKLNR(4).- PolIII PolIII D-3161-35.20 -1 3161 0.7 0.165 2 0.285 4 3284.7174 1.5826 16 13 29 -.FILKTGTTAKDHK(4)--QKMGANEAVPSEVSRK(2).- DECOY_ DECOY_ D-4270-45.74 -1 4270 0.69 0.69 2 0.22 3 2605.3171 3.5135 5 16 21 -.CGNELIGRYPAFKQGR(13)--KVDQR(1).- DECOY_ DECOY_ D-4582-49.31 -1 4582 0.69 0.69 2 0.155 3 2003.0634 -4.808 9 10 19 -.SVGRAGKGSK(7)--TGTTAKDHK(6).- DECOY_ DECOY_ D-3219-35.72 -1 3219 0.66 0.66 26 0.33 3 2083.9807 -0.55 8 7 15 -.KRYVEPR(1)--PMYMTDER(1).- DECOY_ DECOY_ D-4000-43.06 -1 4000 0.655 0.655 2 0.11 3 2069.0715 1.933 8 9 17 -.RMKAGNAEK(3)--YPAFKQGR(5).- DECOY_ DECOY_ D-3795-41.16 -1 3795 0.65 0.155 3 0.32 3 2899.4406 3.9905 10 13 23 -.PMYMTDERKIVGK(9)--TDTDRKVDQR(6).- DECOY_ DECOY_ T-4315-46.16 1 4315 0.65 0.65 4 0.025 3 3882.9397 -2.5756 17 15 32 -.NKGGYFRELFDLCAR(2)--YVGGVRLKDMHPTERGK(8).- PolIII PolIII D-2836-32.43 -1 2836 0.645 0.645 26 0.305 4 1667.8401 -3.6251 6 8 14 -.MKAGNAEK(2)--VHGEKR(5).- DECOY_ DECOY_ D-2860-32.62 -1 2860 0.645 0.645 26 0.17 3 2060.0963 -4.6468 7 9 16 -.QTYPKMYGK(5)--SQSKIRK(4).- DECOY_ DECOY_ D-2664-30.96 -1 2664 0.635 0.635 2 0.12 3 2545.3383 2.0189 10 12 22 -.GSKQALHIAAER(3)--GVKYICMPAK(3).- DECOY_ DECOY_ D-4043-43.50 -1 4043 0.635 0.635 2 0.105 3 2346.1836 -0.2406 15 5 20 -.KVDQR(1)--QKMGANEAVPSEVSR(2).- DECOY_ DECOY_ D-2854-32.59 -1 2854 0.625 0.625 26 0.31 3 2124.0582 4.3432 10 8 18 -.AEKSDGPR(3)--GVKYICMPAK(3).- DECOY_ DECOY_ T-4672-50.57 1 4672 0.615 0.615 5 0.065 4 2252.255 -2.2702 7 14 21 -.GKVITAAGLVVAAR(2)--KPEEMAK(1).- PolIII PolIII T-3210-35.64 1 3210 0.605 0.605 26 0.215 3 2721.3631 0.7986 5 18 23 -.KPEEMAKQRSVFAEGAEK(7)--TDTKK(4).- PolIII PolIII T-3857-41.75 1 3857 0.59 0.05 5 0.25 3 3093.6455 -0.9093 18 8 26 -.KKPEEMAK(2)--VLEKLIMSGAFDRLGPHR(4).- PolIII PolIII T-3426-37.73 1 3426 0.585 0.585 5 0.12 4 2881.4784 -1.6915 14 8 22 -.KSFDMLQR(1)--LAFLFPDEEERLKR(13).- PolIII PolIII D-4388-46.88 -1 4388 0.585 0.585 26 0.265 3 2917.522 3.6211 6 18 24 -.QALHIAAERQTYPKMYGK(14)--SQSKIR(4).- DECOY_ DECOY_ D-4729-51.71 -1 4729 0.585 0.585 3 0.125 4 2476.4014 -2.3309 12 8 20 -.KLSAAVTK(1)--LWRHIKEDVRGR(6).- DECOY_ DECOY_ D-4211-45.17 -1 4211 0.58 0.58 4 0.055 3 2805.414 0.1695 9 15 24 -.AGKGSKQALHIAAER(3)--PMYMTDERK(1).- DECOY_ DECOY_ T-2793-32.08 1 2793 0.56 0.56 2 0.125 3 1625.8448 -1.0418 6 7 13 -.NKGGYFR(2)--RAMGKK(5).- PolIII PolIII T-2247-27.37 1 2247 0.55 0.55 3 0.24 4 1851.9687 3.0342 6 8 14 -.KSFDMLQR(1)--VMVTKR(5).- PolIII PolIII D-3297-36.50 -1 3297 0.545 0.545 2 0.15 4 2308.2751 -1.2217 12 5 17 -.KVDQR(1)--LWRHIKEDVRGR(6).- DECOY_ DECOY_ T-3752-40.75 1 3752 0.535 0.535 7 0.22 4 3463.7718 4.3672 8 22 30 -.ILIVSGQVSFDDFSGGLKMTAR(18)--KSFDMLQR(1).- PolIII PolIII D-4547-48.74 -1 4547 0.53 0.53 26 0.245 4 2624.3554 0.7321 9 12 21 -.IVRKCGNELIGR(4)--QTYPKMYGK(5).- DECOY_ DECOY_ T-2367-28.40 1 2367 0.525 0.525 2 0.17 3 1871.9987 0.0492 6 9 15 -.RAKEGLEER(3)--RAMGKK(5).- PolIII PolIII D-2465-29.19 -1 2465 0.515 0.515 2 0.06 4 2248.1985 4.8393 12 7 19 -.HIKEDVR(3)--VLATKGANVCPK(5).- DECOY_ DECOY_ T-3554-38.86 1 3554 0.5 0.5 26 0.155 2 1939.996 -0.8522 11 5 16 -.AMGKK(4)--LKDMHPTERGK(2).- PolIII PolIII D-3797-41.17 -1 3797 0.495 0.005 26 0.17 3 1937.0102 2.4378 8 8 16 -.MKAGNAEK(2)--TMNKFILK(4).- DECOY_ DECOY_ D-2949-33.39 -1 2949 0.485 0.485 2 0.095 2 2004.0627 -4.5787 9 7 16 -.KRYVEPR(1)--TGTTAKDHK(6).- DECOY_ DECOY_ D-3556-38.91 -1 3556 0.485 0.485 4 0.075 4 3235.5515 -2.2736 16 13 29 -.GGVEDDPAEKHTR(10)--QKMGANEAVPSEVSRK(2).- DECOY_ DECOY_ D-3133-34.98 -1 3133 0.48 0.48 2 0.205 3 2994.4681 -0.6643 15 10 25 -.GVKYICMPAK(3)--YGFYTVGLDPKTMNK(11).- DECOY_ DECOY_ D-3396-37.39 -1 3396 0.475 0.065 4 0.23 3 2864.484 2.9385 10 15 25 -.AGKGSKQALHIAAER(6)--TDTDRKVDQR(6).- DECOY_ DECOY_ D-2994-33.77 -1 2994 0.47 0.47 2 0.23 3 2102.9542 2.2524 8 8 16 -.PMYMTDER(1)--YPAFKQGR(5).- DECOY_ DECOY_ D-3448-37.92 -1 3448 0.465 0.465 26 0.19 3 2811.5304 2.9473 12 13 25 -.FILKTGTTAKDHK(10)--VLATKGANVCPK(5).- DECOY_ DECOY_ D-2658-30.93 -1 2658 0.46 0.46 26 0.23 3 2319.1781 4.6711 9 9 18 -.HIKEDVRGR(3)--QTYPKMYGK(5).- DECOY_ DECOY_ D-3212-35.65 -1 3212 0.455 0.455 2 0.1 3 2088.0007 -3.3469 8 7 15 -.KRYVEPR(1)--PMYMTDER(1).- DECOY_ DECOY_ D-4805-53.07 -1 4805 0.455 0.455 2 0.07 5 2872.6334 -3.7001 10 14 24 -.EMEKIVIHDALLKR(4)--FILKTGTTAK(4).- DECOY_ DECOY_ D-4383-46.86 -1 4383 0.45 0.45 26 0.155 3 2421.2137 -1.4599 13 8 21 -.AEKSDGPR(3)--GQSQPFAQHAKLR(11).- DECOY_ DECOY_ D-1969-24.55 -1 1969 0.445 0.445 2 0.155 3 2791.4063 4.63 8 16 24 -.QKMGANEAVPSEVSRK(2)--YPAFKQGR(5).- DECOY_ DECOY_ T-2886-32.86 1 2886 0.435 0.025 3 0.215 5 2937.5178 -1.1809 18 7 25 -.GMKDLIK(3)--KPEEMAKQRSVFAEGAEK(7).- PolIII PolIII D-4157-44.63 -1 4157 0.435 0.435 26 0.12 2 2053.0679 -3.7239 5 13 18 -.GGVEDDPAEKHTR(10)--KIVGK(1).- DECOY_ DECOY_ T-2911-33.06 1 2911 0.415 0.055 4 0.155 3 1986.0556 -2.421 9 7 16 -.GMKDLIK(3)--RAKEGLEER(3).- PolIII PolIII T-4075-43.77 1 4075 0.41 0.05 6 0.1 3 2933.4978 -3.1305 18 7 25 -.GMKDLIK(3)--KPEEMAKQRSVFAEGAEK(7).- PolIII PolIII T-1944-24.32 1 1944 0.385 0.385 2 0.085 4 1851.9687 4.9973 6 8 14 -.KSFDMLQR(1)--VMVTKR(5).- PolIII PolIII T-4699-51.11 1 4699 0.385 0.385 26 0.165 4 2361.3439 -4.4871 9 9 18 -.TDTKKLNRR(4)--TDTKKLNRR(5).- PolIII PolIII T-4699-51.11-2 1 4699 0.385 0.385 4 0.165 4 2361.3439 -4.4871 9 9 18 -.TDTKKLNRR(4)--TDTKKLNRR(5).- PolIII PolIII T-3682-40.15 1 3682 0.375 0.13 5 0.165 3 2975.5373 -0.4991 5 19 24 -.EIERYVGGVRLKDMHPTER(12)--TDTKK(4).- PolIII PolIII D-4396-46.96 -1 4396 0.375 0.125 27 0.165 4 2624.3554 0.7977 9 12 21 -.IVRKCGNELIGR(4)--QTYPKMYGK(5).- DECOY_ DECOY_ D-3500-38.41 -1 3500 0.37 0.37 2 0.05 3 2513.2167 4.3768 9 13 22 -.GGVEDDPAEKHTR(10)--RMKAGNAEK(3).- DECOY_ DECOY_ D-1975-24.58 -1 1975 0.365 0.365 2 0.115 3 2698.3621 2.4832 14 8 22 -.AEKSDGPR(3)--THIRTDTDRKVDQR(10).- DECOY_ DECOY_ D-4719-51.50 -1 4719 0.35 0.35 5 0.07 4 2555.3821 3.8769 10 9 19 -.HIKEDVRGR(3)--LWRHIKEDVR(6).- DECOY_ DECOY_ D-3224-35.75 -1 3224 0.335 0.335 2 0.085 4 2083.9807 -0.7185 8 7 15 -.KRYVEPR(1)--PMYMTDER(1).- DECOY_ DECOY_ T-3222-35.74 1 3222 0.33 0.33 2 0.05 3 1972.0586 2.2003 4 12 16 -.AMGKKKPEEMAK(4)--KLNR(1).- PolIII PolIII T-2306-27.88 1 2306 0.325 0.325 26 0.1 4 1570.8377 0.9598 7 5 12 -.DLIKR(4)--KPEEMAK(1).- PolIII PolIII D-2953-33.45 -1 2953 0.325 0.325 2 0.13 3 2004.0627 -3.8629 9 7 16 -.KRYVEPR(1)--TGTTAKDHK(6).- DECOY_ DECOY_ D-4636-49.97 -1 4636 0.32 0.32 2 0.08 3 1937.0102 2.0911 8 8 16 -.MKAGNAEK(2)--TMNKFILK(4).- DECOY_ DECOY_ T-2922-33.15 1 2922 0.3 0.3 2 0.015 4 2994.5544 3.8736 8 19 27 -.AALMNSLGDALKAADQHAK(12)--TDTKKLNR(4).- PolIII PolIII D-946-15.60 -1 946 0.285 0.285 2 0.025 3 2380.0889 2.2293 9 9 18 -.PMYMTDERK(1)--QTYPKMYGK(5).- DECOY_ DECOY_ D-2497-29.45 -1 2497 0.28 0.28 9 0.025 4 4519.1031 0.0024 14 22 36 -.GVKYICMPAKDLVGETFWRGMR(3)--MYGKCSDQYQIFDR(4).- DECOY_ DECOY_ T-3352-36.97 1 3352 0.28 0.045 2 0.1 5 2634.3497 2.6414 9 12 21 -.AMGKKKPEEMAK(6)--YQQLLEKDR(7).- PolIII PolIII T-4757-52.17 1 4757 0.28 0.28 2 0.13 4 2669.544 1.1329 15 9 24 -.KLNRRVLEK(1)--NAGKHAGGVVIAPTK(4).- PolIII PolIII D-3678-40.13 -1 3678 0.255 0.255 2 0.075 3 1937.0102 2.5279 8 8 16 -.MKAGNAEK(2)--TMNKFILK(4).- DECOY_ DECOY_ D-2346-28.22 -1 2346 0.235 0.235 2 0.1 4 1671.8601 -2.6946 6 8 14 -.MKAGNAEK(2)--VHGEKR(5).- DECOY_ DECOY_ T-3913-42.24 1 3913 0.23 0.23 2 0.08 2 2043.0117 -4.4632 9 7 16 -.KPEEMAK(1)--KPEEMAKQR(1).- PolIII PolIII D-4159-44.64 -1 4159 0.225 0.065 27 0.105 3 2624.3482 -1.5794 16 5 21 -.KIVGK(1)--YICMPAKDLVGETFWR(7).- DECOY_ DECOY_ D-4269-45.73 -1 4269 0.22 0.055 4 0.09 3 2624.3482 -2.1053 16 5 21 -.KIVGK(1)--YICMPAKDLVGETFWR(7).- DECOY_ DECOY_ D-1911-24.04 -1 1911 0.205 0.205 2 0.025 3 2698.3621 2.6234 14 8 22 -.AEKSDGPR(3)--THIRTDTDRKVDQR(10).- DECOY_ DECOY_ T-2198-26.84 1 2198 0.2 0.2 4 0.015 3 3671.9379 2.5638 17 14 31 -.RVLEKLIMSGAFDR(5)--YVGGVRLKDMHPTERGK(8).- PolIII PolIII D-2342-28.20 -1 2342 0.185 0.185 3 0.065 3 1671.8601 -2.7581 6 8 14 -.MKAGNAEK(2)--VHGEKR(5).- DECOY_ DECOY_ T-2518-29.63 1 2518 0.185 0.185 4 0.03 4 1878.9675 -1.1895 9 5 14 -.TDTKK(4)--YQQLLEKDR(7).- PolIII PolIII T-3346-36.94 1 3346 0.175 0.175 2 0.07 3 2918.4471 -2.0722 19 7 26 -.NKGGYFR(2)--SVFAEGAEKNGINAELAMK(9).- PolIII PolIII T-2660-30.94 1 2660 0.14 0.14 2 0.04 5 3151.6323 -1.1169 19 8 27 -.KSFDMLQR(1)--RAKNGEPPLDIAAIPLDDK(3).- PolIII PolIII D-4590-49.39 -1 4590 0.14 0.075 4 0.01 3 2624.3554 1.4615 9 12 21 -.IVRKCGNELIGR(4)--QTYPKMYGK(5).- DECOY_ DECOY_
c:\>c:/gabi_xlms/percolator-v3-02/bin/percolator c:/gabi_xlms/kojak/ANH_JENN_Tryp_scx_gluc_4b.perc.intra.txt -X c:/gabi_xlms/Kojak/pol_III4b_intra_percval2.xml -Y -f c:/gabi_xlms/kojak/polIII.fasta -P DECOY -t 0.1 -F 0.1 Percolator version 3.02.1, Build Date Aug 14 2018 02:47:48 Copyright (c) 2006-9 University of Washington. All rights reserved. Written by Lukas Käll ([email protected]) in the Department of Genome Sciences at the University of Washington. Issued command: c:/gabi_xlms/percolator-v3-02/bin/percolator c:/gabi_xlms/kojak/ANH_JENN_Tryp_sc x_gluc_4b.perc.intra.txt -X c:/gabi_xlms/Kojak/pol_III4b_intra_percval2.xml -Y - f c:/gabi_xlms/kojak/polIII.fasta -P DECOY -t 0.1 -F 0.1 Started Mon Nov 5 14:39:16 2018 Hyperparameters: selectionFdr=0.1, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile c:/gabi_xlms/kojak/ANH_JENN_Tryp_scx_g luc_4b.perc.intra.txt Features: Score dScore NormRank PPScoreDiff Charge Mass PPM LenShort LenLong LenSum Found 128 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 61 positives and 67 negatives, size ratio=0.910448 and p i0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 1 as initial direction. Could separate 13 train ing set positives with q<0.1 in that direction. Split 2: Selected feature 1 as initial direction. Could separate 6 traini ng set positives with q<0.1 in that direction. Split 3: Selected feature 8 as initial direction. Could separate 9 traini ng set positives with q<0.1 in that direction. Found 0 test set positives with q<0.1 in initial direction Reading in data and feature calculation took 0.031 cpu seconds or 0 seconds wall clock time. ---Training with Cpos selected by cross validation, Cneg selected by cross valid ation, initial_fdr=0.1, fdr=0.1 Iteration 1: Estimated 20 PSMs with q<0.1 Iteration 2: Estimated 23 PSMs with q<0.1 Iteration 3: Estimated 26 PSMs with q<0.1 Iteration 4: Estimated 26 PSMs with q<0.1 Iteration 5: Estimated 26 PSMs with q<0.1 Iteration 6: Estimated 26 PSMs with q<0.1 Iteration 7: Estimated 26 PSMs with q<0.1 Iteration 8: Estimated 26 PSMs with q<0.1 Iteration 9: Estimated 26 PSMs with q<0.1 Iteration 10: Estimated 26 PSMs with q<0.1 Learned normalized SVM weights for the 3 cross-validation splits: Split1 Split2 Split3 FeatureName 0.4853 0.3668 0.7026 Score -0.0389 -0.0209 -0.5131 dScore 0.0751 0.0023 0.1092 NormRank 0.0083 0.2588 0.1331 PPScoreDiff -0.0915 -0.1208 -0.0971 Charge -0.0184 -0.2473 0.1113 Mass -0.0633 -0.0793 -0.0519 PPM 0.0395 0.1128 0.0358 LenShort -0.0165 -0.1770 -0.1890 LenLong 0.0170 -0.0541 -0.1222 LenSum -0.9488 -1.0448 -0.7780 m0 Found 0 test set PSMs with q<0.1. No targets found with q<0.1 Resetting score vector, using default vector. Use --override flag to prevent thi s. Split 1: Selected feature 1 as initial direction. Could separate 13 train ing set positives with q<0.1 in that direction. Split 2: Selected feature 1 as initial direction. Could separate 6 traini ng set positives with q<0.1 in that direction. Split 3: Selected feature 8 as initial direction. Could separate 9 traini ng set positives with q<0.1 in that direction. Selected best-scoring PSM per scan+expMass (target-decoy competition): 59 target PSMs and 67 decoy PSMs. Tossing out "redundant" PSMs keeping only the best scoring PSM for each unique p eptide. Calculating q values. Final list yields 0 target peptides with q<0.1. Calculating posterior error probabilities (PEPs). Processing took 0.298 cpu seconds or 1 seconds wall clock time. PSMId score q-value posterior_error_prob peptide proteinIds T-2035-25.09 0 0.4 0.44268 -.DLIKR(4)--LKDMHPTER(2).- PolIII PolIII T-1731-22.44 0 0.4 0.44268 -.KKPEEMAK(1)--TAPLVKK(6).- PolIII PolIII T-1616-21.48 -0.0874126 0.4 0.499052 -.AMGKK(4)--TAPLVKK(6).- PolIII PolIII T-1648-21.74 -0.143357 0.4 0.538826 -.KKPEEMAK(2)--TAPLVKK(6 ).- PolIII PolIII T-1462-20.15 -0.219424 0.4 0.597728 -.AMGKK(4)--KPEEMAK(1).- PolIII PolIII T-1994-24.75 -0.321942 0.5 0.685212 -.NAGKHAGGVVIAPTK(4)--VM VTKR(5).- PolIII PolIII T-3930-42.45 -0.440559 0.571429 0.795857 -.GMKDLIK(3)--KP EEMAKQRSVFAEGAEK(1).- PolIII PolIII T-3551-38.85 -0.597902 0.571429 0.950298 -.AMGKK(4)--LKDM HPTERGK(2).- PolIII PolIII T-1755-22.69 -0.633094 0.571429 0.985039 -.NKGGYFR(2)--TD TKK(4).- PolIII PolIII T-3436-37.82 -0.706294 0.571429 1 -.KSFDMLQR(1)--LAFLFPDEE ERLKR(13).- PolIII PolIII T-3583-39.24 -0.728417 0.571429 1 -.KSFDMLQR(1)--TDTKKLNR( 4).- PolIII PolIII T-2403-28.68 -0.753597 0.571429 1 -.KPEEMAKQR(1)--VMVTKRGN R(5).- PolIII PolIII T-3236-35.85 -0.75873 0.571429 1 -.KLNRR(1)--MTAREVMDIDEA REKYAR(15).- PolIII PolIII T-3875-41.95 -0.771429 0.571429 1 -.RAKEGLEER(3)--SVFAEGAE KNGINAELAMK(9).- PolIII PolIII T-1771-22.85 -0.853968 0.647059 1 -.AMGKKKPEEMAKQR(4)--KLN R(1).- PolIII PolIII T-4021-43.24 -0.860317 0.647059 1 -.AKEGLEER(2)--NGINAELAM KIFDLVEK(10).- PolIII PolIII T-4837-53.81 -0.863636 0.647059 1 -.GKVITAAGLVVAARVMVTKR(2 )--RAKEGLEER(3).- PolIII PolIII T-4161-44.65 -0.895105 0.666667 1 -.IFDLVEKFAGYGFNK(7)--RA KEGLEER(3).- PolIII PolIII T-1996-24.76 -0.912587 0.761905 1 -.KLEGVTRNAGK(1)--TDTKKL NR(4).- PolIII PolIII T-4177-44.81 -0.922222 0.761905 1 -.EKYAR(2)--LKDMHPTERGK( 2).- PolIII PolIII T-3519-38.58 -0.92381 0.761905 1 -.EKYAR(2)--LKRRPEYDER(2 ).- PolIII PolIII T-4315-46.16 -0.944245 0.909091 1 -.NKGGYFRELFDLCAR(2)--YV GGVRLKDMHPTERGK(8).- PolIII PolIII T-3210-35.64 -0.960432 1 1 -.KPEEMAKQRSVFAEGAEK(7)--TDTKK(4 ).- PolIII PolIII T-4672-50.57 -0.979021 1 1 -.GKVITAAGLVVAAR(2)--KPEEMAK(1). - PolIII PolIII T-2247-27.37 -0.980216 1 1 -.KSFDMLQR(1)--VMVTKR(5).- PolIII PolIII T-1390-19.53 -0.995238 1 1 -.KKPEEMAKQR(1)--KSFDMLQR(1).- PolIII PolIII T-2886-32.86 -1.02158 1 1 -.GMKDLIK(3)--KPEEMAKQRSVFAEGAEK (7).- PolIII PolIII T-3857-41.75 -1.03492 1 1 -.KKPEEMAK(2)--VLEKLIMSGAFDRLGPH R(4).- PolIII PolIII T-2793-32.08 -1.04444 1 1 -.NKGGYFR(2)--RAMGKK(5).- PolIII PolIII T-3752-40.75 -1.05238 1 1 -.ILIVSGQVSFDDFSGGLKMTAR(18)--KS FDMLQR(1).- PolIII PolIII T-2367-28.40 -1.05556 1 1 -.RAKEGLEER(3)--RAMGKK(5).- PolIII PolIII T-3222-35.74 -1.05935 1 1 -.AMGKKKPEEMAK(4)--KLNR(1).- PolIII PolIII T-2306-27.88 -1.06115 1 1 -.DLIKR(4)--KPEEMAK(1).- PolIII PolIII T-4699-51.11-2 -1.1 1 1 -.TDTKKLNRR(4)--TDTKKLNRR(5).- PolIII PolIII T-2518-29.63 -1.11151 1 1 -.TDTKK(4)--YQQLLEKDR(7).- PolIII PolIII T-2911-33.06 -1.11888 1 1 -.GMKDLIK(3)--RAKEGLEER(3).- PolIII PolIII T-3682-40.15 -1.14685 1 1 -.EIERYVGGVRLKDMHPTER(12)--TDTKK (4).- PolIII PolIII T-3913-42.24 -1.14921 1 1 -.KPEEMAK(1)--KPEEMAKQR(1).- PolIII PolIII T-2198-26.84 -1.15873 1 1 -.RVLEKLIMSGAFDR(5)--YVGGVRLKDMH PTERGK(8).- PolIII PolIII T-3346-36.94 -1.16667 1 1 -.NKGGYFR(2)--SVFAEGAEKNGINAELAM K(9).- PolIII PolIII T-2660-30.94 -1.17778 1 1 -.KSFDMLQR(1)--RAKNGEPPLDIAAIPLD DK(3).- PolIII PolIII T-2922-33.15 -1.1993 1 1 -.AALMNSLGDALKAADQHAK(12)--TDTKKLNR(4).- PolIII PolIII T-4757-52.17 -1.21329 1 1 -.KLNRRVLEK(1)--NAGKHAGGVVIAPTK( 4).- PolIII PolIII T-3352-36.97 -1.21329 1 1 -.AMGKKKPEEMAK(6)--YQQLLEKDR(7). - PolIII PolIII Calculating protein level probabilities. Miscleavage detected: -.DLIKR(4)--LKDMHPTER(2).- Miscleavage detected: -.GGVEDDPAEKHTR(10)--RMKAGNAEK(3).- Miscleavage detected: -.GGVEDDPAEKHTR(10)--KRYVEPRLVDR(1).- Miscleavage detected: -.KLNRR(1)--MTAREVMDIDEAREKYAR(15).- Miscleavage detected: -.TDTKKLNRR(4)--TDTKKLNRR(5).- Protein digestion parameters for duplicate/fragment detection (detected from PSM input): enzyme=trypsin, digestion=full, min-pept-length=20, max-pept-length=44, max-mis cleavages=11 Detecting protein fragments/duplicates in target database Detecting protein fragments/duplicates in decoy database Initialized protein inference engine. Computing protein probabilities. Performing picked protein strategy Warning: No target-decoy protein pairs found for the picked protein strategy. Check if the correct decoy pattern was specified with the -P flag; if the target protein is called "protA" and the decoy protein "decoy_protA", u se the option "-P decoy_". Eliminated lower-scoring target-decoy protein: 1 target proteins and 1 decoy pro teins remaining. Logit transforming all scores prior to PEP calculation c:\>
