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VDigestor.ini
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[Params]
# True --> SEQ_PATH contains FASTA
# False --> SEQ_PATH contains UniProt ID
fasta_mode = true
#
# FILE PATHS
#
# Path to file containing fasta or Uniprot ID
seq_path = C:\Users\rbarreror\home\Proteomics\GroupTools\VDigestor\test\test2\q1.fa
# Outfile path
outfile_path = C:\Users\rbarreror\home\Proteomics\GroupTools\VDigestor\test\test2
# Path to UniMod Table
unimod_path = C:\Users\rbarreror\home\Proteomics\GroupTools\VDigestor\unimod_filtered.tsv
#
# PEPTIDE OPTIONS
#
# Remove peptides with less or equal number of aminoacids
minsize = 5
# Maximum number of miscleavages
miscleavages = 1
# Maximum number of modifications (Write 0 to generate non modified peptides only)
modnumber = 2
# Add TMT to K
tmt = false
# Modified aminoacids (comma separated). If empty, all aa will be considered
aa = C,W,P,M,H,K,S,T,Y
# Modifications
mod =
# Title of modifications that avoid tryptic cut (comma-separated)
kx = Acetyl, GG
# Threads
nproc = 4
[Aminoacids]
A = 71.037114
R = 156.101111
N = 114.042927
D = 115.026943
C = 103.009185
E = 129.042593
Q = 128.058578
G = 57.021464
H = 137.058912
I = 113.084064
L = 113.084064
K = 128.094963
M = 131.040485
F = 147.068414
P = 97.052764
S = 87.032028
T = 101.047679
U = 150.953630
W = 186.079313
Y = 163.063329
V = 99.068414
O = 132.089878
Z = 129.042594
X = 178.9849
; Title mono_mass
; Met-loss -131.040485
; Lys-loss -128.094963
; Tyr->Dha -94.041865
; Met-loss+Acetyl -89.02992
; Gly-loss+Amide -58.005479
; Met->Hsl -48.003371
; Arg->GluSA -43.053433
; Cys->Dha -33.987721
; Cys->PyruvicAcid -33.003705
; Met->AspSA -32.008456
; Pro->Pyrrolidinone -30.010565
; Decarboxylation -30.010565
; Met->Hse -29.992806
; Pro->Pyrrolidone -27.994915
; azole -20.026215
; 15N-oxobutanoic -18.023584
; Dehydrated -18.010565
; Cys->Oxoalanine -17.992806
; Ammonia-loss -17.026549
; Deoxy -15.994915
; Ser->LacticAcid -15.010899
; Aspartylurea -10.031969
; Cys->methylaminoAla -2.945522
; Didehydro -2.01565
; Lys->Allysine -1.031634
; Amidated -0.984016
; Deamidated 0.984016
; Trp->Kynurenin 3.994915
; Formylasparagine 4.97893
; Cys->ethylaminoAla 11.070128
; Thiazolidine 12
; Phe->CamCys 12.962234
; Pro->pyro-Glu 13.979265
; Trp->Oxolactone 13.979265
; Carbonyl 13.979265
; Methyl 14.01565
; Lys->AminoadipicAcid 14.96328
; Methyl+Deamidated 14.999666
; Amino 15.010899
; Carboxy->Thiocarboxy 15.977156
; Oxidation 15.994915
; Fluoro 17.990578
; Pro->HAVA 18.010565
; Lys->MetOx 18.940436
; Trp->Hydroxykynurenin 19.989829
; glyoxalAGE 21.98435
; Cyano 24.995249
; ethylamino 27.047285
; Delta:H(-4)O(2) 27.958529
; Formyl 27.994915
; Dimethyl 28.0313
; Ethyl 28.0313
; Nitrosyl 28.990164
; Ethyl+Deamidated 29.015316
; Delta:H(5)C(2) 29.039125
; Quinone 29.974179
; Hydroxymethyl 30.010565
; methylol 30.010565
; Lys->CamCys 31.935685
; Sulfide 31.972071
; Dioxidation 31.989829
; Leu->MetOx 33.951335
; Propargylamine 37.031634
; AzidoF 41.001397
; Amidine 41.026549
; Acetyl 42.010565
; Guanidinyl 42.021798
; Amidino 42.021798
; Trimethyl 42.04695
; Propyl 42.04695
; Carbamyl 43.005814
; Ethanolamine 43.042199
; Delta:H(-4)O(3) 43.953444
; Carboxy 43.989829
; Delta:H(4)C(2)O(-1)S(1) 44.008456
; Ethanolyl 44.026215
; Nitro 44.985078
; Methylthio 45.987721
; Trioxidation 47.984744
; Delta:H(2)C(3)O(1) 54.010565
; Xlink:DSSO[54] 54.010565
; Xlink:DST[56] 55.989829
; Propionyl 56.026215
; Diethyl 56.0626
; Carbamidomethyl 57.021464
; Carboxymethyl 58.005479
; Carbofuran 58.029289
; Delta:H(6)C(3)O(1) 58.041865
; AEC-MAEC 59.019355
; Hydroxytrimethyl 59.04969
; MercaptoEthanol 60.003371
; Carboxymethyl:13C(2) 60.012189
; Delta:H(2)C(5) 62.01565
; SulfurDioxide 63.9619
; Furan 66.010565
; dichlorination 67.922055
; Crotonyl 68.026215
; Piperidine 68.0626
; PyruvicAcidIminyl 70.005479
; Butyryl 70.041865
; Propionamide 71.037114
; Deoxyhypusine 71.073499
; Dimethylaminoethyl 71.073499
; Carboxyethyl 72.021129
; Ethoxyformyl 72.021129
; Ethanedithiol 75.980527
; DeStreak 75.998285
; Bromo 77.910511
; Methylphosphonate 77.987066
; DimethylpyrroleAdduct 78.04695
; Delta:Se(1) 79.91652
; Sulfo 79.956815
; Phospho 79.966331
; Delta:H(4)C(5)O(1) 80.026215
; Arg->Npo 80.985078
; Xlink:BuUrBu[85] 85.052764
; Pentylamine 85.089149
; Xlink:DSSO[86] 85.982635
; Malonyl 86.000394
; HMVK 86.036779
; GEE 86.036779
; hydroxyisobutyryl 86.036779
; Xlink:DTBP[87] 87.01427
; glycidamide 87.032028
; DAET 87.050655
; Hypusine 87.068414
; Xlink:DTSSP[88] 87.998285
; Methamidophos-O 92.997965
; O-Methylphosphate 93.981981
; sulfo+amino 94.967714
; Xlink:BS2G[96] 96.021129
; Delta:H(8)C(6)O(1) 96.057515
; maleimide 97.016378
; Acetyldeoxyhypusine 97.089149
; MesitylOxide 98.073165
; NIPCAM 99.068414
; Succinyl 100.016044
; Methylmalonylation 100.016044
; Ub-Br2 100.063663
; HN2_mustard 101.084064
; DimethylArsino 103.960719
; Xlink:DSSO[104] 103.9932
; Pyridylethyl 105.057849
; methylsulfonylethyl 106.00885
; Saligenin 106.041865
; N-dimethylphosphate 107.013615
; AHA-Alkyne 107.077339
; MeMePhosphorothioate 107.979873
; O-Dimethylphosphate 107.997631
; Ethylphosphate 107.997631
; Methamidophos-S 108.975121
; Methylpyrroline 109.052764
; monomethylphosphothione 109.959137
; Nmethylmaleimide 111.032028
; Xlink:BuUrBu[111] 111.032028
; DMPO 111.068414
; Xlink:BS2G[113] 113.047679
; Acetylhypusine 113.084064
; Xlink:DST[114] 113.995309
; Gluratylation 114.031694
; Xlink:BS2G[114] 114.031694
; GG 114.042927
; Xlink:EGS[115] 115.026943
; 2-succinyl 116.010959
; HCysThiolactone 117.024835
; DHP 118.065674
; Label:2H(4)+GG 118.068034
; Pyridylacetyl 119.037114
; Phenylisocyanate 119.037114
; PS_Hapten 120.021129
; BEMAD_C 120.0245
; ethylsulfonylethyl 120.0245
; O-Isopropylmethylphosphonate 120.034017
; PET 121.035005
; Isopropylphospho 122.013281
; Xlink:DMP[122] 122.084398
; GPIanchor 123.00853
; Dimethylphosphothione 123.974787
; Phenylisocyanate:2H(5) 124.068498
; Nethylmaleimide 125.047679
; Iodo 125.896648
; Octanoyl 126.104465
; SMA 127.063329
; spermidine 128.131349
; Glu 129.042593
; Nmethylmaleimide+water 129.042593
; 2-monomethylsuccinyl 130.026609
; NEM:2H(5) 130.079062
; HN3_mustard 131.094629
; Xlink:DST[132] 132.005873
; HPG 132.021129
; Difuran 132.021129
; Pentose 132.042259
; Propiophenone 132.057515
; benzylguanidine 132.068748
; HCysteinyl 133.019749
; Iodoacetanilide 133.052764
; PyMIC 134.048013
; 2-nitrobenzyl 135.032028
; O-Et-N-diMePhospho 135.044916
; CAF 135.983029
; BEMAD_ST 136.001656
; Diethylphosphate 136.028931
; 4-ONE+Delta:H(-2)O(-1) 136.088815
; Xlink:DSS[138] 138.06808
; HNE-Delta:H(2)O 138.104465
; Iodoacetanilide:13C(6) 139.072893
; Xlink:DMP[139] 139.110947
; Xlink:DMP[140] 140.094963
; Oxidation+NEM 141.042593
; Diphthamide 142.110613
; Nethylmaleimide+water 143.058243
; 2-dimethylsuccinyl 144.042259
; CAMthiopropanoyl 145.019749
; Hydroxycinnamyl 146.036779
; dHex 146.057909
; Glycosyl 148.037173
; NEM:2H(5)+H2O 148.089627
; BITC 149.02992
; cGMP+RMP-loss 150.041585
; Diethylphosphothione 152.006087
; NBS 152.988449
; Glycerophospho 154.00311
; Delta:H(6)C(7)O(4) 154.026609
; UgiJoullieProGly 154.074228
; 4-ONE 154.09938
; Xlink:DMP[154] 154.110613
; Decanoyl 154.135765
; Xlink:DSS[155] 155.094629
; Dibromo 155.821022
; Xlink:DSS[156] 156.078644
; HNE 156.11503
; NEMsulfur 157.019749
; Xlink:DSSO[158] 158.003765
; HNE+Delta:H(2) 158.13068
; NBS:13C(6) 159.008578
; FormylMet 159.035399
; thioacylPA 159.035399
; serotonylation 159.068414
; pyrophospho 159.932662
; SulfanilicAcid:13C(6) 161.024228
; HexN 161.068808
; Hex 162.052824
; CarboxymethylDMAP 162.079313
; O-pinacolylmethylphosphonate 162.080967
; PEITC 163.04557
; Xlink:DFDNB 163.985807
; Diisopropylphosphate 164.060231
; DNCB_hapten 166.001457
; 3-phosphoglyceryl 167.982375
; phenylsulfonylethyl 168.0245
; His+O(2) 169.048741
; Cresylphosphate 170.013281
; Menadione 170.036779
; AccQTag 170.048013
; QAT 171.149738
; Xlink:DTBP[172] 172.01289
; Menadione-HQ 172.05243
; Ub-VME 173.092617
; Xlink:DTSSP[174] 173.980921
; Thiadiazole 174.025169
; NEMsulfurWater 175.030314
; Xlink:DSSO[175] 175.030314
; NDA 175.042199
; Xlink:DSSO[176] 176.01433
; Glucuronyl 176.032088
; Cys->SecNEM:2H(5) 178.023511
; Galactosyl 178.047738
; 3sulfo 183.983029
; MTSL 184.07961
; EQAT 184.157563
; spermine 185.189198
; Lipoyl 188.032956
; Bromobimane 190.074228
; Xlink:DTSSP[192] 191.991486
; Hep 192.063388
; Xlink:BuUrBu[196] 196.084792
; Ub-amide 196.108602
; Biotin:Thermo-88310 196.121178
; GlycerylPE 197.04531
; DNPS 198.981352
; Argbiotinhydrazide 199.066699
; Delta:Hg(1) 201.970617
; HexNAc 203.079373
; Haloxon 203.950987
; Farnesyl 204.187801
; Myristoyl+Delta:H(-4) 206.167065
; Myristoleyl 208.182715
; Myristoyl 210.198366
; TNBS 210.986535
; phosphoRibosyl 212.00859
; Xlink:BuUrBu[213] 213.111341
; Xlink:BuUrBu[214] 214.095357
; SPITC 214.971084
; Xlink:BS2G[217] 217.095023
; Xlink:SMCC[219] 219.089543
; Xlink:BMOE 220.048407
; Kdo 220.058303
; Hydroxyfarnesyl 220.182715
; SPITC:13C(6) 220.991213
; TMT 224.152478
; Dipyridyl 225.090212
; Iminobiotin 225.093583
; Xlink:EGS[226] 226.047738
; Biotin 226.077598
; C8-QAT 227.224915
; Bacillosamine 228.111007
; PyridoxalPhosphate 229.014009
; PyridoxalPhosphateH2 231.02966
; PropylNAGthiazoline 232.064354
; Dansyl 233.051049
; shTMT 235.176741
; Palmitoleyl 236.214016
; Xlink:SMCC[237] 237.100108
; Palmitoyl 238.229666
; Thrbiotinhydrazide 240.104482
; lapachenole 240.11503
; Lysbiotinhydrazide 241.088497
; PhosphoHex 242.019154
; pupylation 243.085521
; Xlink:EGS[244] 244.058303
; Diiodo 251.793296
; NO_SMX_SEMD 252.044287
; BDMAPP 253.010225
; Phosphogluconoylation 258.014069
; GluGlu 258.085186
; probiotinhydrazide 258.115047
; Xlink:DSS[259] 259.141973
; BMP-piperidinol 263.131014
; Pent(2) 264.084518
; Didehydroretinylidene 264.187801
; MM-diphenylpentanone 265.146664
; Arg2PG 266.057909
; EHD-diphenylpentanone 266.13068
; Retinylidene 266.203451
; NO_SMX_SIMD 267.031377
; DimethylamineGMBS 267.158292
; NO_SMX_SMCT 268.039202
; GeranylGeranyl 272.250401
; MurNAc 275.100502
; CresylSaligeninPhosphate 276.055146
; Xlink:DSSO[279] 279.077658
; 2HPG 282.052824
; s-GlcNAc 283.036187
; PhosphoHexNAc 283.045704
; EGCG2 287.055563
; LG-lactam-R 290.176961
; NeuAc 291.095417
; Hex(1)Pent(1) 294.095082
; CHDH 294.183109
; TMTpro_zero 295.189592
; biotinAcrolein298 298.146347
; LG-anhyropyrrole 298.19328
; cysTMT 299.166748
; PhosphoCytidine 305.041287
; Glutathione 305.068156
; PhosphoUridine 306.025302
; LG-Hlactam-R 306.171876
; NeuGc 307.090331
; dHex(1)Hex(1) 308.110732
; UgiJoullieProGlyProGly 308.148455
; AFB1_Dialdehyde 310.047738
; OxArgBiotin 310.135113
; Biotin:Thermo-21345 311.166748
; OxArgBiotinRed 312.150763
; LG-anhydrolactam 314.188195
; IBTP 316.138088
; LG-pyrrole 316.203845
; Xlink:BuUrBu[317] 317.158686
; ZQG 320.100836
; Xlink:SMCC[321] 321.205242
; IodoU-AMP 322.020217
; Hex(2) 324.105647
; iodoTMT 324.216141
; NA-LNO2 325.225309
; IED-Biotin 326.141261
; NA-OA-NO2 327.240959
; Phosphoadenosine 329.05252
; iodoTMT6plex 329.226595
; CIGG 330.136176
; LG-lactam-K 332.19876
; Andro-H2O 332.19876
; Pent(1)HexNAc(1) 335.121631
; Hex(1)HexA(1) 338.084912
; NHS-LC-Biotin 339.161662
; Phosphopantetheine 340.085794
; Glucosylgalactosyl 340.100562
; Diironsubcluster 342.786916
; cGMP 343.031785
; Phosphoguanosine 345.047435
; LG-Hlactam-K 348.193674
; HexNAc(1)dHex(1) 349.137281
; OxLysBiotin 352.156911
; OxLysBiotinRed 354.172562
; Biotin-PEO-Amine 356.188212
; Biotin-tyramide 361.146012
; Cytopiloyne 362.136553
; Dap-DSP 364.076278
; Hex(1)HexNAc(1) 365.132196
; Cholesterol 368.344302
; OxProBiotin 369.183461
; OxProBiotinRed 371.199111
; 4AcAllylGal 372.142033
; Triiodo 377.689944
; Cytopiloyne+water 380.147118
; MDCC 383.148121
; LRGG 383.228103
; MicrocinC7 386.110369
; Fluorescein 387.074287
; GluGluGlu 387.127779
; Biotin:Thermo-21328 389.090154
; LRGG+methyl 397.243753
; Hex(2)Sulf(1) 404.062462
; PhosphoHex(2) 404.071978
; HexNAc(2) 406.158745
; LRGG+dimethyl 411.259403
; Bodipy 414.167478
; PEO-Iodoacetyl-LC-Biotin 414.193691
; Dipyrrolylmethanemethyl 418.137616
; FTC 421.073241
; Hex(1)Pent(2) 426.137341
; FNEM 427.069202
; Biotin-HPDP 428.191582
; bisANS-sulfonates 437.201774
; FMN 438.094051
; Hex(1)Pent(2)Me(1) 440.152991
; Biotin:Thermo-88317 443.291294
; Hex(1)HexNAc(1)Sulf(1) 445.089011
; Hex(1)HexNAc(1)Phos(1) 445.098527
; Can-FP-biotin 447.195679
; Biotin:Sigma-B1267 449.17329
; IASD 452.034807
; Sulfo-NHS-LC-LC-Biotin 452.245726
; Hex(1)NeuAc(1) 453.14824
; Puromycin 453.212452
; FMNH 454.088965
; betaFNA 454.210387
; EGCG1 456.069261
; FMNC 456.104615
; Hex(1)NeuGc(1) 469.143155
; NQIGG 469.228496
; Triiodothyronine 469.716159
; dHex(1)Hex(2) 470.163556
; Withaferin 470.266839
; NHS-fluorescein 471.131802
; Biotin:Thermo-21330 473.219571
; Atto495Maleimide 474.250515
; HexNAc(2)Sulf(1) 486.11556
; Hex(3) 486.158471
; Biotin:Thermo-21360 487.246455
; EDT-iodoacetyl-PEO-biotin 490.174218
; Fluorescein-tyramine 493.116152
; HexNAc(1)NeuAc(1) 494.174789
; HexNAc(1)dHex(2) 495.19519