pyopenms 2.3.0__zip

media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/CHEMISTRY/MissedCleavage.model

@@ -0,0 +1,229 @@
+### missed cleavage model for trypsin
+### columns:
+### residue position (0-8, 4|5 being cleavage site), residue type, p[cleaved model], p[missed model]
+0 S 0.00155119425371577 -0.00721584368297066
+0 F 0.0101203450370329 -0.0499143795822267
+0 T 0.00437580160216219 -0.0207404654555115
+0 N 0.00863951037114175 -0.0421668411875381
+0 K -0.0426349905702423 0.155520296424895
+0 x 0 0
+0 Y -0.00523499887692041 0.0233253947565591
+0 E 0.00818034396259026 -0.039797629165997
+0 V 0.00493316169438667 -0.0234703056642569
+0 Z 0.0853437450703708 0
+0 Q -0.00238950679147767 0.0108374287670045
+0 M 0.00754132801219614 -0.0365259139536316
+0 C 0.01095597703868 -0.0543599833494246
+0 L 0.00188686459291307 -0.00879665556808435
+0 A -0.0049122447091631 0.0219309154288239
+0 W 0.00693320815473958 -0.0334395263233619
+0 X -0.011566267937686 0.0496159156380304
+0 P 0.0103237181563291 -0.0509913667336383
+0 Ct 0 0
+0 B 0.0853437450703708 0
+0 H 0.00578955397457641 -0.0277053940254705
+0 D 0.0141624132472289 -0.0719369441334252
+0 I 0.00384378298672882 -0.0181538887728747
+0 R -0.0559191548111558 0.192111114311861
+0 G -0.000318027050528464 0.00146155865238389
+0 Nt 0.0809346261653139 -1.2470492746235
+1 S -0.00188774397621617 0.00858895217038756
+1 F 0.0144613722136596 -0.0736193995313521
+1 T 0.00526322191736816 -0.0250966660897753
+1 N 0.0111926226367841 -0.0556288300737603
+1 K -0.044153635141278 0.159921600947166
+1 x 0 0
+1 Y 0.0152488432689032 -0.0780881261688707
+1 E -0.00222127914039957 0.0100851603709803
+1 V 0.00417320066605687 -0.0197532660165449
+1 Z 0.0853437450703708 0
+1 Q 0.00636975003212183 -0.0306030716008546
+1 M -0.00524147923293532 0.0233533371391882
+1 C 0.0148254346379286 -0.075678654240404
+1 L 0.00508630706016019 -0.0242240132320469
+1 A -0.00626781185306248 0.0277509980548175
+1 W 0.0181272910523906 -0.0948976405530249
+1 X -0.090747513985311 0.271464665254386
+1 P 0.0150543502357306 -0.0769793817145727
+1 Ct 0 0
+1 B 0.0853437450703708 0
+1 H 0.00455527468070269 -0.021617235705912
+1 D 0.0099568688324829 -0.0490509678757512
+1 I 0.00131189125848209 -0.00609311139032893
+1 R -0.0455394380519306 0.163886132848834
+1 G 0.000868058270173546 -0.00402007022809444
+1 Nt 0.0688146873864017 -0.679188613161495
+2 S -0.00179609780733301 0.00817672965188891
+2 F 0.0280184052564126 -0.159199188226274
+2 T -0.0022521384724719 0.0102232743918174
+2 N 0.010514806562435 -0.05200619945784
+2 K -0.0498530534413316 0.175921830105783
+2 x 0 0
+2 Y 0.0194801608035318 -0.103068708688225
+2 E 0.0028442937155881 -0.0133442628224803
+2 V 0.00917321806055152 -0.0449401919765487
+2 Z 0 0
+2 Q 0.012161600167981 -0.0608706268016039
+2 M 0.0057657018440194 -0.0275867644275067
+2 C 0.0219373168460715 -0.118382665495958
+2 L 0.0015271894185259 -0.00710306174657736
+2 A -0.00113516316915836 0.00518962066798522
+2 W 0.0254494100003613 -0.141415693210588
+2 X 0.0183969554397552 -0.0965121200402077
+2 P 0.00487552628651554 -0.0231870591559591
+2 Ct 0 0
+2 H 0.020885755843452 -0.111752086596945
+2 D 0.000929377266564833 -0.00430576272835574
+2 I -0.000352115411225422 0.00161786388127948
+2 R -0.0541455813655727 0.187463071487379
+2 G 0.000330198733098511 -0.00152385762818177
+2 Nt -0.00598639055684963 0.0265506115693381
+3 S 0.00120217171057805 -0.00557951790496735
+3 F 0.0181982754958097 -0.0953219453246492
+3 T 0.00746782714495857 -0.0361514776936105
+3 N 0.000459581898316416 -0.00212273527092521
+3 K -0.0497578863798243 0.175661135601301
+3 x 0 0
+3 Y 0.0168451463172139 -0.0873159356295266
+3 E 0.00491926832574982 -0.0234020070165263
+3 V 0.00952970722162894 -0.0468044755798308
+3 Z 0 0
+3 Q 0.0104019447570531 -0.05140647211982
+3 M -0.0101222284297051 0.0437912585812453
+3 C 0.0112312454730355 -0.055836336165553
+3 L 0.000930249394099852 -0.00430982772116158
+3 A 0.00392961759045261 -0.0185699461081312
+3 W 0.0354451553685568 -0.215820560584245
+3 X 0.0853437450703708 0
+3 P 0.0258005600513561 -0.143797826856209
+3 Ct 0 0
+3 H 0.00594142776223056 -0.0284616589594472
+3 D -0.0162973823115694 0.0680412256217175
+3 I 0.00565904209703786 -0.0270567632506103
+3 R -0.0538609149609292 0.186710603099994
+3 G -0.00346452584212206 0.0156073024880689
+3 Nt -0.190862666868579 0.421226985587719
+4 S 0 0
+4 F 0 0
+4 T 0 0
+4 N 0 0
+4 K -0.0106125875004242 0.045780112741825
+4 x 0 0
+4 Y 0 0
+4 E 0 0
+4 V 0 0
+4 Q 0 0
+4 M 0 0
+4 C 0 0
+4 L 0 0
+4 A 0 0
+4 W 0 0
+4 X 0 0
+4 P 0 0
+4 Ct 0 0
+4 H 0 0
+4 D 0 0
+4 I 0 0
+4 R 0.0112126601842253 -0.0557364696622383
+4 G 0 0
+4 Nt 0 0
+5 S -0.00414728931498034 0.0186037055032237
+5 F 0.0119920426834694 -0.0599479594033155
+5 T 0.0115728837855243 -0.0576769689205623
+5 N 0.0153786428896758 -0.0788299287119621
+5 K 0.00402270759345742 -0.0190217159063933
+5 x 0 0
+5 Y 0.0194284810017644 -0.1027532603019
+5 E -0.0124248587558356 0.053033404763815
+5 V 0.00681194613657833 -0.0328272141698239
+5 Z 0.0853437450703708 0
+5 Q 0.0218723992037776 -0.117969916479998
+5 M 0.0212654895269526 -0.114132974344623
+5 C 0.0173071318266984 -0.0900299925122872
+5 L 0.0147945517930332 -0.0755035242375552
+5 A 0.0186237213392114 -0.0978752075888718
+5 W 0.0306856368818309 -0.178586262592309
+5 X -0.0395949915379296 0.146525928646086
+5 P -1.408135429711 0.734415886060518
+5 Ct 0.0853437450703708 0
+5 H 0.0117663765407453 -0.0587235591508078
+5 D -0.007133815548037 0.0314193812682074
+5 I 0.0199421197114211 -0.105900364403556
+5 R -0.0206030273840874 0.0839923310796518
+5 G -8.20312810020782e-05 0.000377565111733786
+5 Nt 0 0
+6 S -0.00607359115820411 0.026922998856415
+6 F 0.0139395144782525 -0.0706875113660484
+6 T 0.00871709724548706 -0.0425687027718217
+6 N -0.00122862317011291 0.00561354121363955
+6 K -0.0148551046432945 0.0625277225670337
+6 x 0 0
+6 Y 0.0127667737830556 -0.0641827923770768
+6 E -0.0232307606334326 0.0933726218622424
+6 V 0.0173429094275379 -0.0902410077930348
+6 Q 0.0101618904516775 -0.0501341304713985
+6 M -0.0087793419126029 0.0382858518051329
+6 C 0.0182362544270455 -0.0955491607057649
+6 L 0.00748424375471079 -0.0362350755152361
+6 A 0.00420022515410901 -0.0198847901320386
+6 W 0.00282917821310596 -0.0132720175157153
+6 X 0.00616249902274598 -0.0295653304095948
+6 P -0.0151176661385177 0.0635380307218723
+6 Ct -0.0332362471694817 0.126871240649617
+6 B 0.0853437450703708 0
+6 H 0.0184516214958325 -0.0968402609563878
+6 D -0.0118184470690743 0.0506231703962375
+6 I 0.0138750181207925 -0.0703267734771773
+6 R -0.0245971841699276 0.098149568952218
+6 G -0.00290995754241101 0.0131546928606713
+6 Nt 0 0
+7 S 0.00688957312924048 -0.0332190722669007
+7 F 0.00468781345674047 -0.0222660916680952
+7 T 0.00208777500908572 -0.00974617373848127
+7 N 0.00644852823507257 -0.0309983090244586
+7 K -0.0267866580116544 0.105665409640322
+7 x 0 0
+7 Y 0.00498714111480968 -0.0237357867488708
+7 E 0.00181031130741747 -0.00843551965998847
+7 V 0.00479136512294075 -0.0227738520402987
+7 Z 0 0
+7 Q 0.0109962160318145 -0.0545754266914563
+7 M -0.013142656172641 0.0558648649150308
+7 C 0.0058884097224481 -0.0281974726429136
+7 L 0.00219706314393281 -0.0102637359244067
+7 A 3.53002332739628e-05 -0.000162599309729288
+7 W 0.00730387808155344 -0.0353176592986856
+7 X -0.0395949915379296 0.146525928646086
+7 P 0.000582621641907323 -0.00269318400929317
+7 Ct -0.00965307329340537 0.0418777246061289
+7 H 0.0133219958800885 -0.0672480561621474
+7 D 0.00654705296026112 -0.0314932243949499
+7 I 0.00102285937033262 -0.00474174668456256
+7 R -0.0427821442802085 0.15594940772927
+7 G 0.000209352903511755 -0.000965402581785676
+7 Nt 0 0
+8 S -0.00101967408837821 0.00466508103872825
+8 F 0.00297659657226406 -0.0139772319849951
+8 T 3.77150826628033e-06 -1.73687197929421e-05
+8 N 0.0143452805729061 -0.0729651571272533
+8 K -0.043014650796067 0.156626255550412
+8 x 0 0
+8 Y 0.00476543997301542 -0.0226466622914581
+8 E 0.00716014784841427 -0.0345882434083597
+8 V 0.00825865300614361 -0.0402005991445456
+8 Q 0.00779255049091823 -0.0378086424322195
+8 M -0.00273285530984907 0.0123678582184007
+8 C 0.00192544607949062 -0.00897879962781697
+8 L 0.00457080341133138 -0.0216931977051885
+8 A 0.00133092924208546 -0.00618230263814537
+8 W 0.0120257729838156 -0.0601313220751986
+8 X -0.0395949915379296 0.146525928646086
+8 P 0.00559968095391454 -0.0267621290007437
+8 Ct 0.0276120364797184 -0.156330115182119
+8 B 0.0853437450703708 0
+8 H 0.00914181836068942 -0.0447764411487796
+8 D 0.0067050281150376 -0.0322881887450678
+8 I 0.00455976059407499 -0.0216391778358078
+8 R -0.0566332092070675 0.193963194795178
+8 G 0.00371362222983421 -0.0175238898661841
+8 Nt 0 0

media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/CHEMISTRY/NegativeAdducts.tsv

@@ -0,0 +1,15 @@
+M-3H;3-
+M-2H;2-
+M-H2O-H;1-
+M-H;1-
+M+Na-2H;1-
+M+Cl;1-
+M+K-2H;1-
+M+CH2O2-H;1-
+M+C2H4O2-H;1-
+M+Br;1-
+M+C2HO2F3-H;1-
+2M-H;1-
+2M+CH2O2-H;1-
+2M+C2H4O2-H;1-
+3M-H;1-

media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/CHEMISTRY/OMSSA_modification_mapping

@@ -0,0 +1,158 @@
+# OMSSA-internal-number, OMSSA-description, UniMod term
+0,methylation of K,Methyl (K)
+1,oxidation of M,Oxidation (M)
+2,carboxymethyl C,Carboxymethyl (C)
+3,carbamidomethyl C,Carbamidomethyl (C)
+4,deamidation of N and Q, 
+5,propionamide C,Propionamide (C)
+6,phosphorylation of S,Phospho (S)
+7,phosphorylation of T,Phospho (T)
+8,phosphorylation of Y,Phospho (Y)
+9,M cleavage from protein n-term, 
+10,acetylation of protein n-term,Acetyl (N-term)
+11,methylation of protein n-term,Methyl (N-term)
+12,tri-methylation of protein n-term, 
+13,beta methythiolation of D, 
+14,methylation of Q, 
+15,tri-methylation of K, 
+16,methylation of D, 
+17,methylation of E, 
+18,methylation of peptide c-term, 
+19,tri-deuteromethylation of D, 
+20,tri-deuteromethylation of E, 
+21,tri-deuteromethylation of peptide c-term, 
+22,n-formyl met addition, 
+23,2-amino-3-oxo-butanoic acid T, 
+24,acetylation of K, 
+25,amidation of peptide c-term, 
+26,beta-methylthiolation of D, 
+27,carboxyamidomethylation of K, 
+28,carboxyamidomethylation of H, 
+29,carboxyamidomethylation of D, 
+30,carboxyamidomethylation of E, 
+31,carbamylation of K, 
+32,carbamylation of n-term peptide, 
+33,citrullination of R, 
+34,oxidation of C to cysteic acid, 
+35,di-iodination of Y, 
+36,di-methylation of K, 
+37,di-methylation of R, 
+38,di-methylation of peptide n-term, 
+39,oxidation of F to dihydroxyphenylalanine, 
+40,thioacylation of K, 
+41,thioacylation of peptide n-term, 
+42,farnesylation of C, 
+43,formylation of K, 
+44,formylation of peptide n-term, 
+45,oxidation of W to formylkynurenin, 
+46,fluorophenylalanine, 
+47,gamma-carboxylation of D, 
+48,gamma-carboxylation of E, 
+49,geranyl-geranyl, 
+50,glucuronylation of protein n-term, 
+51,glutathione disulfide, 
+52,ubiquitinylation residue, 
+53,guanidination of K,Guanidinyl (K)
+54,oxidation of H to N, 
+55,oxidation of H to D, 
+56,homoserine, 
+57,homoserine lactone, 
+58,oxidation of W to hydroxykynurenin, 
+59,hydroxylation of D, 
+60,hydroxylation of K, 
+61,hydroxylation of N, 
+62,hydroxylation of P, 
+63,hydroxylation of F, 
+64,hydroxylation of  Y, 
+65,iodination of Y, 
+66,oxidation of W to kynurenin, 
+67,lipoyl K, 
+68,methyl ester of peptide c-term, 
+69,methyl ester of D, 
+70,methyl ester of E, 
+71,methyl ester of S, 
+72,methyl ester of Y, 
+73,methyl C, 
+74,methyl H, 
+75,methyl N, 
+76,methylation of peptide n-term, 
+77,methyl R, 
+78,myristoleylation of G, 
+79,myristoyl-4H of G, 
+80,myristoylation of peptide n-term G, 
+81,myristoylation of K, 
+82,formylation of protein n-term, 
+83,NEM C, 
+84,NIPCAM, 
+85,oxidation of W to nitro, 
+86,oxidation of Y to nitro, 
+87,O18 on peptide n-term, 
+88,di-O18 on peptide n-term, 
+89,oxidation of H, 
+90,oxidation of W, 
+91,phosphopantetheine S, 
+92,palmitoylation of C, 
+93,palmitoylation of K, 
+94,palmitoylation of S, 
+95,palmitoylation of T, 
+96,phosphorylation of S with prompt loss, 
+97,phosphorylation of T with prompt loss, 
+98,phosphorylation with prompt loss on Y, 
+99,phosphorylation with neutral loss on C, 
+100,phosphorylation with neutral loss on D, 
+101,phosphorylation with neutral loss on H, 
+102,propionyl light K, 
+103,propionyl light on peptide n-term, 
+104,propionyl heavy K, 
+105,propionyl heavy peptide n-term, 
+106,pyridyl K, 
+107,pyridyl peptide n-term, 
+108,pyro-cmC, 
+109,pyro-glu from n-term E, 
+110,pyro-glu from n-term Q, 
+111,oxidation of P to pyroglutamic acid, 
+112,s-pyridylethylation of C, 
+113,SeMet, 
+114,sulfation of Y, 
+115,sulphone of M,Dioxidation (M)
+116,tri-iodination of Y, 
+117,tri-methylation of R, 
+118,n-acyl diglyceride cysteine, 
+129,ICAT light, 
+130,ICAT heavy, 
+131,CAMthiopropanoyl K, 
+132,phosphorylation with neutral loss on S, 
+133,phosphorylation with neutral loss on T, 
+134,phosphorylation of S with ETD loss, 
+135,phosphorylation of T with ETD loss, 
+136,heavy arginine-13C6, 
+137,heavy arginine-13C6-15N4, 
+138,heavy lysine-13C6, 
+139,PNGasF in O18 water, 
+140,beta elimination of S, 
+141,beta elimination of T, 
+162,oxidation of C to sulfinic acid, 
+163,arginine to ornithine, 
+164,dehydro of S and T, 
+165,carboxykynurenin of W, 
+166,sumoylation of K, 
+167,iTRAQ114 on nterm, 
+168,iTRAQ114 on K, 
+169,iTRAQ114 on Y, 
+170,iTRAQ115 on nterm, 
+171,iTRAQ115 on K, 
+172,iTRAQ115 on Y, 
+173,iTRAQ116 on nterm, 
+174,iTRAQ116 on K, 
+175,iTRAQ116 on Y, 
+176,iTRAQ117 on nterm, 
+177,iTRAQ117 on K, 
+178,iTRAQ117 on Y, 
+179,MMTS on C, 
+180,heavy lysine - 2H4, 
+181,heavy lysine - 13C6 15N2, 
+182,Asparagine HexNAc, 
+183,Asparagine dHexHexNAc, 
+184,Serine HexNAc, 
+185,Threonine HexNAc, 
+