# this file is read in a case sensitive manner. # the sequence of the sections is irrelevant. # the sequence of the lines within a section is irrelevant. # the amount of white space within a line doesn't matter. # blank and/or empty lines are possible. # comment lines start with a `#' in column 1. @general_parameters print_infos 0 print_warnings 1 debug 0 print_long_messages 0 wait_on_error 0 fatal_handling exit program_home / output_stream stdout error_stream stderr input_type normal path_licenses _included_ @licenses 94a8141e f776f40c 1 perpetual 5dd6ce45 cbbe7f51 bbada0da 2be44fd6 43c8a6be @databases path_atom_types _included_ path_compounds _included_ path_link_rules _included_ path_cleavage_rules _included_ path_modification_rules _included_ @problem_to_solve path_protein _included_ path_peaklist _included_ cleavage_rule trypsin_chymo_gluC_cdap @optional_links link_rule disulfide linked_residues * max_nof_optional_links_per_fragment 3 min_nof_optional_links_per_fragment 0 linked_residues_preventing_nterm_cleavage - linked_residues_preventing_cterm_cleavage - use_linker_as_optional_modification 0 max_nof_optional_linker_modifications_per_fragment -1 min_nof_optional_linker_modifications_per_fragment -1 @search_parameters max_nof_uncleaved_peptide_bonds_per_fragment -1 max_mass_deviation 150 ppm mass_window defined_by_peaklist 1 1 ion_type m+h max_nof_assigned_fragments -1 max_nof_configs_per_fragment -1 @output_control print_version 1 print_parameter_file 0 print_digest 0 print_peaklist 0 print_sorted_list_of_assignments 1 print_raw_list_of_assignments 0 print_fragment_configurations 1 fragment_configuration_output_mode outlines print_timing 0 @known_links # linked residues # linked preventing # link_rule residues nterm cterm # cleavage @modifications # modified residues min max # modified preventing known/ nof opt. mods. # mod_rule residues nterm cterm optional per fragment # cleavage cdap_cn C - - optional -1 3 cdap_el C C\C84,C40,C26 - optional -1 3 cdap_hy C C\C84,C40,C26 - optional -1 3 #carbamidomethyl C,M,H C\C84,C40,C26 - optional -1 3 #M_iam_elim M - - optional -1 3 pyro_Gln Q11,Q74 - - optional -1 1 cyclo_NQED N71,N94,E2,E9,E86 - - optional -1 1 oxidation_m M - - optional -1 3 oxidation_w W - - optional -1 3 NEM_C C - - optional -1 3 NEM_hydro_C C - - optional -1 3 oxidation_w2 W - - optional -1 3 @protein >RNP_BOVIN (P00656):RNAseA, bovine KETAAAKFERQHMDSSTSAASSSNYCNQMMKSRNLTKDRCKPVNTFVHESLADVQAVCSQ KNVACKNGQTNCYQSYSTMSITDCRETGSSKYPNCAYKTTQANKHIIVACEGNPYVPVHF DASV @peaklist # 1 1708.8 # 2 2028.9 # 3 2030.0 4 3301.3 @compounds # # amino acids A ALA amino_acid C3H7NO2 R ARG amino_acid C6H14N4O2 N ASN amino_acid C4H8N2O3 D ASP amino_acid C4H7NO4 C CYS amino_acid C3H7NO2S E GLU amino_acid C5H9N1O4 Q GLN amino_acid C5H10N2O3 G GLY amino_acid C2H5NO2 H HIS amino_acid C6H9N3O2 I ILE amino_acid C6H13NO2 L LEU amino_acid C6H13NO2 K LYS amino_acid C6H14N2O2 M MET amino_acid C5H11NO2S F PHE amino_acid C9H11NO2 P PRO amino_acid C5H9NO2 S SER amino_acid C3H7NO3 T THR amino_acid C4H9NO3 U SEC amino_acid C3H7NO2Se W TRP amino_acid C11H12N2O2 Y TYR amino_acid C9H11NO3 V VAL amino_acid C5H11NO2 # linkers dss - linker C8H14O4 heme - linker C34H32N4O4Fe # general acetic_acid - general CH3COOH acetic_acid_amide - general CH3CONH2 cyclo_hexane_di_one - general COCH2CH2CH2CH2CO ethyl_pyridine - general CH3CH2C5H4N propionic_acid_amide - general CH3CH2CONH2 sulfonyl_acetic_acid - general HOSO2CH2COOH sulfonyl_benzoic_acid - general HOSO2C6H4COOH @link_rules # # matching compound change of composition at # label pattern label left right # side upon binding # disulfide (C)-(C) - -H -H dss (K)-(K) dss -H2O -H2O heme (C)-(C) heme - - @cleavage_rules # # matching change of composition at # label pattern n-terminus c-terminus # of the bond cleaved # trypsin (K,R)-(*\P) OH H chymotrypsin (W,Y,F,L,M)-(*\P) OH H staph-au-1 (E)-(*\E,P) OH H staph-au-2 (E,D)-(*\E,P) OH H asp-n (*)-(D) OH H arg-c (R)-(*\P) OH H lys-c (K)-(*\P) OH H asn-c (N)-(*) OH H prae-pro (*)-(P) OH H post-pro (P)-(*) OH H trypsin_cdap (K,R)-(*\P),(*)-(C) OH H chymotrypsin_cdap (W,Y,F,L,M)-(*\P),(*)-(C) OH H trypsin_chymo_cdap (K,R,W,Y,F,L,M)-(*\P),(*)-(C) OH H trypsin_chymo (K,R,W,Y,F,L,M)-(*\P) OH H trypsin_gluC (K,R)-(*\P),(E)-(*\E,P) OH H trypsin_chymo_gluC (K,R,W,Y,F,L,M)-(*\P),(E)-(*\E,P) OH H trypsin_chymo_gluC_cdap (K,R,W,Y,F,L,M)-(*\P),(E)-(*\E,P),(*)-(C) OH H @modification_rules # # matching compound change of # label pattern label composition # upon binding # s_deprotonated C - -H sulfonic_acid C - O3 propionamide C propionic_acid_amide -H2 carbamidomethyl C,M,H,Y acetic_acid_amide -H2 carboxymethyl C acetic_acid -H2 s_pyridylethyl C ethyl_pyridine -H2 sulfatation S,T,Y - -H2O+H2SO4 phosphorylation S,T,Y - -H2O+H3PO4 acetyl K,S,T acetic_acid -H2O dhch R cyclo_hexane_di_one - sulfobenzoate_k K sulfonyl_benzoic_acid -H2O methylen M - CH2 oxidation_m M - O oxidation_w W - O oxidation_w2 W - O2 cdap_cn C - -H+CN cdap_el C - -H2S cdap_hy C - -H+CONH2 M_iam_elim M - -SCH4 pyro_Gln Q - -NH3 cyclo_NQED D,E,N,Q - -H2O NEM_C C - +C6H7NO2 NEM_hydro_C C - +C6H9NO3 # n-terminal modifications pyro_glu_n Q - -NH3 sulfonylacetyl_n * sulfonyl_acetic_acid -H2O sulfbenzoate_n * sulfonyl_benzoic_acid -H2O acetyl_n * acetic_acid -H2O formyl_n * - -H2O+HCOOH # c-cterminal modifications amide_c * - -H2O+NH3 @atom_types # # #<..._2> ... # # NOTE: a symbol can only consist of letters with the first letter being an # upper case letter! # atom_type H 1 2 1 1.007825 99.985 2 2.0140 0.015 atom_type He 2 2 3 3.01603 0.00013 4 4.00260 99.99987 atom_type Li 3 2 6 6.01512 7.5 7 7.01600 92.5 atom_type Be 4 1 9 9.0122 100 atom_type B 5 2 10 10.0129 20 11 11.00931 80 atom_type C 6 2 12 12.000 98.9 13 13.00335 1.1 atom_type N 7 2 14 14.00307 99.64 15 15.00011 0.36 atom_type O 8 3 16 15.99491 99.76 17 16.999131 0.04 18 17.999160 0.20 atom_type F 9 1 19 18.99840 100 atom_type Ne 10 3 20 19.99244 90.51 21 20.99395 0.27 22 21.99138 9.22 atom_type Na 11 1 23 22.9898 100 atom_type Mg 12 3 24 23.98504 78.99 25 24.98584 10.00 26 25.98259 11.01 atom_type Al 13 1 27 26.98153 100 atom_type Si 14 3 28 27.97693 92.23 29 28.97649 4.67 30 29.97376 3.10 atom_type P 15 1 31 30.97376 100 atom_type S 16 4 32 31.97207 95.0 33 32.97146 0.76 34 33.96786 4.22 36 35.96709 0.02 atom_type Cl 17 2 35 34.96885 75.77 37 36.99999 24.23 atom_type Ar 18 3 36 35.96755 0.34 38 37.96272 0.07 40 39.96999 99.59 atom_type K 19 3 39 38.96371 93.2581 40 39.963999 0.012 41 40.961825 6.7302 atom_type Ca 20 6 40 39.962591 96.941 42 41.958618 0.647 43 42.958766 0.135 44 43.955480 2.086 46 45.953689 0.004 48 47.952533 0.187 atom_type Sc 21 1 45 44.959404 100 atom_type Ti 22 5 46 45.952629 8.0 47 46.951764 7.3 48 47.947947 73.8 49 48.947871 5.5 50 49.944792 5.4 atom_type V 23 2 50 49.947161 0.25 51 50.943962 99.75 atom_type Cr 24 4 50 49.946046 4.35 52 51.940509 83.79 53 52.940651 9.50 54 53.938882 2.36 atom_type Mn 25 1 55 54.938047 100 atom_type Fe 26 4 54 53.939612 5.82 56 55.934939 91.8 57 56.935396 2.1 58 57.933277 0.28 atom_type Co 27 1 59 58.933198 100 atom_type Ni 28 5 58 57.935346 68.27 60 59.930788 26.10 61 60.931058 1.13 62 61.928346 3.59 64 63.927968 0.91 atom_type Cu 29 2 63 62.939598 69.17 65 64.927793 30.83 atom_type Zn 30 5 64 63.929145 48.6 66 65.926034 27.9 67 66.927129 4.1 68 67.924846 18.8 70 69.925325 0.6 atom_type Ga 31 2 69 68.925580 60.11 71 70.924700 39.89 atom_type Ge 32 5 70 69.924250 20.5 72 71.922079 27.4 73 72.923463 7.8 74 73.921177 36.5 76 75.921401 7.8 atom_type As 33 1 75 74.921594 100 atom_type Se 34 6 74 73.922475 0.9 76 75.919212 9.2 77 76.919912 7.6 78 77.919 23.7 80 79.916520 49.8 82 81.916698 8.8 atom_type Br 35 2 79 78.918336 50.69 81 80.916289 49.31 atom_type Kr 36 6 78 77.92 0.35 80 79.916380 2.25 82 81.913482 11.6 83 82.914135 11.5 84 83.911507 57.0 86 85.910616 17.3 atom_type Rb 37 2 85 84.911794 72.17 87 86.909187 27.83 atom_type Sr 38 4 84 83.913430 0.56 86 85.909267 9.86 87 86.908884 7.00 88 87.905619 82.58 atom_type Y 39 1 89 88.905849 100 atom_type Zr 40 5 90 89.904703 51.45 91 90.905644 11.22 92 91.905039 17.15 94 93.906314 17.38 96 95.908275 2.80 atom_type Nb 41 1 93 92.906377 100 atom_type Mo 42 7 92 91.906808 14.84 94 93.905085 9.25 95 94.905840 15.92 96 95.904678 16.68 97 96.906020 9.55 98 97.905406 24.13 100 99.907477 9.63 atom_type Tc 43 1 99 98.9062 100 atom_type Ru 44 7 96 95.907599 5.53 98 97.905287 1.87 99 98.905939 12.7 100 99.904219 12.6 101 100.905582 17.1 102 101.904348 31.6 104 103.905424 18.6 atom_type Rh 45 1 103 102.905500 100 atom_type Pd 46 6 102 101.905634 1.02 104 103.904029 11.14 105 104.905079 22.33 106 105.903478 27.33 108 107.903895 26.46 110 109.905167 11.72 atom_type Ag 47 2 107 106.905092 51.84 109 108.904757 48.16 atom_type Cd 48 8 106 105.906461 1.25 108 107.904176 0.89 110 109.903005 12.49 111 110.904182 12.80 112 111.902758 24.13 113 112.904400 12.22 114 113.903357 28.73 116 115.904754 7.49 atom_type In 49 2 113 112.904061 4.3 115 114.903880 95.7 atom_type Sn 50 10 112 111.904826 0.97 114 113.902784 0.65 115 114.903348 0.36 116 115.901747 14.53 117 116.902956 7.68 118 117.901609 24.22 119 118.903310 8.58 120 119.902200 32.59 122 121.903440 4.63 124 123.905274 5.79 atom_type Sb 51 2 121 120.903821 57.3 123 122.904216 42.7 atom_type Te 52 8 120 119.904048 0.009 122 121.903054 2.57 123 122.904271 0.89 124 123.902823 4.76 125 124.904433 7.10 126 125.903314 18.89 128 127.904463 31.73 130 129.906229 33.97 atom_type I 53 1 127 126.904473 100 atom_type Xe 54 9 124 123.905894 0.10 126 125.904281 0.09 128 127.903531 1.91 129 128.904780 26.4 130 129.903509 4.1 131 130.905072 21.2 132 131.904144 26.9 134 133.905395 10.4 136 135.907214 8.9 atom_type Cs 55 1 133 132.9051 100 atom_type Ba 56 7 130 129.906282 0.11 132 131.905042 0.10 134 133.904486 2.42 135 134.905665 6.59 136 135.904553 7.85 137 136.905812 11.23 138 137.905232 71.70 atom_type La 57 2 138 137.907105 0.09 139 138.906346 99.91 atom_type Ce 58 4 136 135.907140 0.19 138 137.905985 0.25 140 139.905433 88.48 142 141.909241 11.08 atom_type Pr 59 1 141 140.907647 100 atom_type Nd 60 7 142 141.907719 27.13 143 142.909810 12.18 144 143.910083 23.80 145 144.912570 8.30 146 145.913113 17.19 148 147.916889 5.76 150 149.920887 5.64 atom_type Pm 61 1 147 147 100 atom_type Sm 62 7 144 143.911998 3.1 147 146.914895 15.0 148 147.914820 11.3 149 148.917181 13.8 150 149.917273 7.4 152 151.919729 26.7 154 153.922206 22.7 atom_type Eu 63 2 151 150.919847 47.8 153 152.921225 52.2 atom_type Gd 64 7 152 151.919786 0.20 154 153.920861 2.18 155 154.922618 14.80 156 155.922118 20.47 157 156.923956 15.65 158 157.924099 24.84 160 159.927049 21.86 atom_type Tb 65 1 159 158.925342 100 atom_type Dy 66 7 156 155.925277 0.06 158 157.924403 0.10 160 159.925193 2.34 161 160.926930 18.9 162 161.926795 25.5 163 162.928728 24.9 164 163.929171 28.2 atom_type Ho 67 1 165 164.930319 100 atom_type Er 68 6 162 161.928775 0.14 164 163.929198 1.61 166 165.930290 33.6 167 166.932046 22.95 168 167.932368 26.8 170 169.935461 14.9 atom_type Tm 69 1 169 168.934212 100 atom_type Yb 70 6 170 169.934759 3.05 171 170.936323 14.3 172 171.936387 21.9 173 172.938208 16.12 174 173.938859 31.8 176 175.942564 12.7 atom_type Lu 71 2 175 174.940770 97.41 176 175.942679 2.59 atom_type Hf 72 6 174 173.94004 0.16 176 175.941406 5.21 177 176.943217 18.6 178 177.943696 27.30 179 178.945812 13.63 180 179.946545 35.10 atom_type Ta 73 2 180 179.947462 0.012 181 180.947992 99.998 atom_type W 74 5 180 179.946701 0.12 182 181.948202 26.3 183 182.950220 14.28 184 183.950928 30.7 186 185.954357 28.6 atom_type Re 75 2 185 184.952951 37.40 187 186.955744 62.6 atom_type Os 76 7 184 183.952488 0.02 186 185.953830 1.58 187 186.955741 1.6 188 187.955860 13.3 189 188.958137 16.1 190 189.958436 26.4 192 191.961467 41.0 atom_type Ir 77 2 191 190.960584 37.3 193 192.962917 62.7 atom_type Pt 78 6 190 189.959917 0.01 192 191.961019 0.79 194 193.962655 32.9 195 194.964766 33.8 196 195.964926 25.3 198 197.967869 7.2 atom_type Au 79 1 197 196.966543 100 atom_type Hg 80 7 196 195.965807 0.15 198 197.966743 10.1 199 198.968254 17 200 199.968300 23.1 201 200.970277 13.2 202 201.970617 29.65 204 203.973467 6.85 atom_type Tl 81 2 203 202.972320 29.52 205 204.974401 70.48 atom_type Pb 82 4 204 203.973020 1.4 206 205.974440 24.1 207 206.975872 22.1 208 207.976627 52.4 atom_type Bi 83 1 209 208.980374 100