# this is a parameter file for SearchXLinks version 3.0.9.

# apart from the license section, ALL sections are included here. this is the
# reason why this file is rather long. usually, however, most of the databases
# will be read from separate files giving much shorter parameter files.

# you can use this file as a starting point for your own parameter file. to
# this end, select this frame and save it to your disk as a text file. (if you
# don't know how to do that from whithin your browser, use copy & paste.) 
# modify the parameter file with a text editor like notepad or emacs according
# to your needs, then upload it back again to the SearchXLinks website. 
# usually, modifying the parameter file "externally" and uploading it is much
# faster than using the input mask offered by the website. this way, one can
# also modify SearchXLinks' standard rules or add completely new ones,
# something which is impossible to do via the mask.

# this file is read in a case sensitive manner.
# the sequence of the sections is irrelevant.
# lines consisting exclusively of white space (blanks, tabs, etc.) are ignored.
# comment lines start with a `#' in column 1.
# tokens on a line are separated by white space.

@general_parameters
output_stream                 stdout
error_stream                  stdout
print_infos                   1
print_warnings                1
debug                         -
print_long_messages           0
wait_on_error                 0
fatal_handling                exit
program_home                  -
path_licenses                 licenses
input_type                    normal

@databases
path_link_rules               _included_
path_modification_rules       _included_
path_cleavage_rules           _included_
path_compounds                _included_
path_atom_types               _included_

@proteins
#
# protein  protein
#  label    path
#
     1     _included_
     2     _included_

@problem_to_solve
path_peak_list                _included_
cleavage_rule                 trypsin

@optional_links
link_rule                                                egs
linked_residues                                          *
min_nof_linked_residues_per_peptide                      0
max_nof_linked_residues_per_peptide                      2
use_linker_as_optional_modification                      1
min_nof_optional_linker_modifications_per_peptide        0
max_nof_optional_linker_modifications_per_peptide        2
linked_residues_preventing_nterm_cleavage                -
linked_residues_preventing_cterm_cleavage                -

@known_links
#                             linked residues
# link rule       linked        preventing
#   label        residues    nterm       cterm
#                                cleavage
#

@modifications
#                         modified residues              min      max
# mod rule     modified     preventing         known/    nof opt mods
#  label       residues   nterm      cterm    optional   per peptide
#                            cleavage                                   

@search_parameters
max_nof_missed_cleavages_per_peptide            2
max_mass_deviation                              500. ppm
mass_window                                     defined_by_peak_list 1 1
ion_type                                        m+h
mass_type                                       monoisotopic
max_nof_assigned_peptides                       -1
max_nof_isomers_per_peptide                     -1

@output_control
output_type                                     html
print_html_tooltips                             1
print_version                                   1
print_parameter_file                            0
print_list_of_amino_acid_chains                 1
print_digest                                    1
print_sorted_list_of_assignments                1
print_peptide_isomers                           1
print_protein_coverage                          1
print_peak_list                                 1
print_timing                                    0

@isd_rules_to_be_applied
#
# if no isd rules are selected, isd analysis is skipped.
#
#                    min         max
#  label          number of matching isd
#                multiplets per parent peak
#

@isd_parameters
isd_filter                                      0
isd_rule_combination                            and
isd_max_mass_deviation_for_multiplet_screening  50. ppm
isd_print_detailed_lists_of_assignments         1
isd_path_database                               _included_

@psd_rules_to_be_applied
#
# if no psd rules are selected, psd analysis is skipped.
#
a b b' b" b-NH3 b-H2O b(n-1)+H2O y y' y" y-NH3 y-H2O
legs5 legs6 legs7 legs8 legs9 legs11 legs12 legs14 legs15 legs16 legs17 regs5 regs6 regs7 regs8 regs9 regs11 regs12 regs14 regs15 regs16 regs17

@psd_peak_lists
#
# if no psd peak lists are specified, psd analysis is skipped.
#
#        selected
# list    parent
# label    mass    pathname
#

1 1251.934 _included_
 
2 1542.509 _included_
 
3 927.400 _included_
 
4 1418.573 _included_
 
5 1295.914 _included_
 
6 983.462 _included_
  
7 1273.996 _included_
 
8 1405.492 _included_ 

@psd_parameters
psd_filter                                      1
psd_max_nof_top_scores_per_peak_list            -1
psd_max_nof_isomers_per_peptide                 -1
psd_min_score                                   1.5
psd_max_parent_mass_deviation                   2.0 Da
psd_max_mass_deviation                          2.0 Da
psd_intensity_scoring_exponent                  -1.
psd_percentage_of_intense_peaks                 50
psd_print_concise_lists_of_assignments          1
psd_print_detailed_lists_of_assignments         1
psd_print_peak_lists                            1
psd_path_database                               _included_

##############################################################################
#
# _included_ sections
#
##############################################################################
      
@protein_1
#
# fasta format
#
>TP
AEISGILCSDKATIKRTWATVTDLPSFGRNVFLSVFAAKPEYKNLFVEFRNIPASELASSERLLYHGGRVLSSIDEAIAGIDTPDRAVKTLLALGERHISRGTVRRHFEAFSYAFIDELKQRGVESADLAAWRRGWDNIVNVLEAGLLRRQIDLEVTGLSCVDVANIQESWSKVSGDLKTTGSVVFQRMINGHPEYQQLFRQFRDVDLDKLGESNSFVAHVFRVVAAFDGIIHELDNNQFIVSTLKKLGEQHIARGTDISHFQNFRVTLLEYLKENGMNGAQKASWNKAFDAFEKYISMGLSSLKRVDPITGLSGLEKNAILSTWGKVRGNLQEVGKATFGKLFTAHPEYQQMFRFSQGMPLASLVESPKFAAHTQRVVSALDQTLLALNRPSDFVYMIKELGLDHINRGTDRSHFENYQVVFIEYLKETLGDSLDEFTVKSFNHVFEVIISFLNEGLRQADIVDPVTHLTGRQKEMIKASWSKARTDLRSLGQELFMRMFKAHPEYQTLFVNKGFADVPLVSLREDERFISHMANVLGGFDTLLQNLDESSYFIYSLRNLGDAHIQRKAGTQHFRSFEAILIPYLQESQGLDAASVEAWKKFFDVSIGVIAQGLKVATSEEADPVTGLYGKEIVALRQAFAAVTPRNVEIGKRVFAKLFAAHPEYKNLFKKFEQYSVEELPSTDAFHYHISLVMNRFSSIGKVIDDNVSFVYLLKKLGREHIKRGLSRKQFDQFVELYIAEISSELSDTGRNGLEKVLTFATGVIEQGLFQLGQVDSNTLTALEKQSIQDIWSNLRSTGLQDLAVKIFTRLFSAHPEYKLLFTGRFGNVDNINENAPFKAHLHRVLSAFDIVISTLDDSEHLIRQLKDLGLFHTRLGMTRSHFDNFATAFLSVAQDIAPNQLTVLGRESLNKGFKLMHGVIEEGLLQLERINPITGLSAREVAVVKQTWNLVKPDLMGVGMRIFKSLFEAFPAYQAVFPKFSDVPLDKLEDTPAVGKHAISVTTKLDELIQTLDEPANLALLARQLGEDHIVLRVNKPMFKSFGKVLVRLLENDLGQRFSSFASRSWHKAYDVIVEYIEEGLQQSYKQDPVTGITDAEKALVQESWDLLKPDLLGLGRKIFTKVFTKHPDYQILFTRTGFGDTPLTKLDDNPAFGTHIIKVMRAFDHVIQILGKPKTLMAYLRSVGADHIARNVERRHFQAFSNALIPVMQHELKAQLRPDAVAAWRKGLDRIIGIIDQGLIGLKEVNPQNAFSAYDIQAVQRTWALAKPDLMGKGAMVFKQLFTDHGYQPLFSNLAQYEITGLEGSPELNTHARNVMAQLDTLVGSLQNSIELGQSLAQLGKDHVPRKVNRVHFKDFAEHFIPLMKADLGDEFTPLAESAWKKAFDVMIATIEQGQRARRSVATFLTNPVA
      
@protein_2
#
# fasta format
#
>CP
AEVRGILCSDKATIKRTWSIVNDLPSFGRNVFLSVFAAKPEYKNLFVEFRNIPASELANSERLLYHGGRVLASIDEVISEIDSPDSAAKKLVALGERHITRGTVRRHFEAFSYAFIDELKQRGVASADLAAWRKGWDSIVDILEAGLLKRQIDLEVTGLSCVDVANVQESWATVSANLKNTGSILFQRLINDHPEYQQLFRQFRDVELAKLGESNGFVAHVFRVVAAFDGIIKELDNNPFIVSTLKRLGEQHIARGTDISHFQNFRTTLLVYLNENGMNQAQEASWNKAFDAIEKYISIGLKSLGRVDPITGLSGLEKNAILNTWGKVRGNLQEVGKATFGKLFAAHPEYQQMFRFFQGVQLAELVDSPKFAAHTQRVVSALDQTLLALNRPSDFVYMIKELGLDHINRGTDRSHFENYQVVFVEYLKETLGDSVDEFTVKSFNHVFEVIINFLNEGLRQANVVDPVTHLTGRQKEAIKASWSVARTDLRFLGQELFMRMFNLNPEYQSLFVNKGFADVPLVSLREDERFISHMANVLRGFDTLLQNLDDTSYFVYALRNLGDAHIQRKAGTEHFRSFEAILIPYLQESQGLDAAGVEAWKIFFDVSIGVIAQGLKVASSEEADPVTGLYGKEVVALRQAFAAISPRNVEIGKRVFAKLFTSHPEYKNLFKKFEQYSVEELPSTDAFDYHISLVMNRFSAVGKVIDDNVSFVYLLKKLGREHIKRGLSRKQFDQFVELYIAEISPELSETGRSGLEKVLTFATGVIEQGLFQLGQVDSKALTALEKQSIQDIWTSLRPTGLEELAVKMFTRLFADHPEYKLLFTGRLGNVDNINENAPFRAHLHRVLSAFDIVITSLDNNALLIRQLKDLGLFHTRLGMTRAHFDNFATAFFSVAEDIVPNLLTALGRESLGKGFKLMVAVIEEGLLQLERIDPITGLSVREVEVVKQTWNLVKPDLMGVGMRIFKSLFEKFPAYQAVFPKFSDVPLDKLEDIPAVGKHAISVTTKLDELIQTLDEPANLALLARQLGEDHIVLGVNKPMFKSFGEVLVRLLENDLGQRFSNFASKSWHRAYDVIVEYIEEGLQQSYKQDPVTGITDAEKVLVQRSWELLKPDLLGLGRKIFGVIFTKHPEYQILFTRVGFGDTPLTQLDNNPAFGEHIIKVMRAFDYVIRNLGKPKTLLAYLKNVGADHIARNVERRHFQAFSEALIPVMQRELKAQLKPEAVAAWRKGLDRIIGVIDQGLLGLKEVNPQIAFSAADIEAIQKTWALAKPDLMGKGASVFRQLFTDHGYQPLFSNLVEYEVTGLEGSPELNTHARNVMAQLDTLVGSLQNSIELGKSLNQLGKDHVPRKVNKVHFDDFAEHFVPLMKANLGDEFTPLAESAWKKAFNVMVATIEQGQRARRSIATFLTNPVA
   
@peak_list
#
#    m/z    further_tokens(ignored)
#
927.400
983.462
1251.934
1273.996
1295.914
1405.492
1418.573
1542.509
   
@psd_peak_list_1
#
#    m/z      intensity(optional)  further_tokens(ignored)
#

1229.788
1170.844
1080.000
992.283
902.500
815.586
628.177
595.179
551.000
516.277
508.000
436.000
376.103
243.000
214.840
   
@psd_peak_list_2
#
#    m/z      intensity(optional)  further_tokens(ignored)
#

1542.600
1525.467
1524.467
1513.467
1507.500
1499.667
1498.533
1496.467
1489.000
1481.000
1480.467
1469.500
1468.600
1451.533
1442.600
1427.600
1422.500
1411.400
1403.500
1397.467
1385.200
1357.267
1355.533
1334.667
1339.500
1341.000
1328.167
1323.500
1315.533
1298.667
1230.000
1204.000
1167.000
1113.867
1105.533
1044.500                                                                                                                              
1016.267
951.333
931.500
915.000
881.400
793.133
731.200
680.000
570.533
536.200

@psd_peak_list_3
351.500
550.500
578.000
723.333
870.000
814.467
813.333
795.333
755.600
698.333
680.267
652.400
625.467
581.333
568.333
553.267
538.333
468.067
455.267
437.067
322.000
926.467
908.333
891.467
707.000
854.000
896.000

@psd_peak_list_4
441.892
489.193
645.500
659.038
725.167
733.500
751.500
781.516
828.485
859.087
861.083
939.386
943.500
961.500
963.000
978.438
1056.000
1052.284
1074.438
1008.509
1100.000
1118.346
1119.667
1134.500
1186.338
1242.000
1247.500
1214.678
1230.000
1259.651
1286.661
1303.500
1330.503
1344.541
1347.500
1356.582
1357.380
1374.545
1401.621
1402.553
1418.320

@psd_peak_list_5
1277.200
1273.867
1137.000
1109.533
1049.000
1017.000
903.400
857.533
818.667
727.533
683.467
665.067
626.667
582.400
571.500
550.667
542.733
470.067
428.600
425.500
375.267
359.733
357.733

@psd_peak_list_6
449.400
482.733
527.133
548.333
582.267
621.000
669.467
720.133
738.267
764.667
773.467
782.667
797.000
797.400
808.133
821.533
851.133
869.000
907.400
924.067
964.400
965.333
982.467
982.733

@psd_peak_list_7
453.400
464.500
479.500
507.467
593.200
633.467
656.667
683.733
744.333
815.667
877.800
903.600
965.000
991.533
1009.867
1027.500
1079.933
1124.500
1135.500
1157.000
1168.000
1170.000
1179.667
1186.733
1214.000
1229.800
1274.000

@psd_peak_list_8
1406.000
1388.600
1290.533
1272.533
1260.467
1203.400
1175.467
1128.333
1088.533
979.400
931.400
893.267
865.533
816.467
750.400
703.333
634.200
559.400
461.000

@atom_types
#
# for each atom type, one must provide an "atom_type" keyword line and at
# least one isotope record of the following structure:
#
# "atom_type" atomic_symbol  atomic number  nof_isotopes
# nof_nucleons_isotope_1  mass_1  abundance_in_percent_1
# ...
#
# NOTE: an atomic symbol must always start with an upper case letter followed
#       by lower case letters and/or pairs of square brackets. the latter may
#       contain any sequence of non-white space characters, e.g., "C[13]".
#

atom_type  H  1  2 
1        1.007825        99.985  
2        2.0140          0.015   

atom_type  D  1  1
2        2.0140          100

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 7
168      167.933894      0.13
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     

@compounds
#
# label1  label2  compound_type  composition
#
# amino acids
#
A ALA amino_acid H2NCH(CH3)COOH
R ARG amino_acid H2NCH(CH2CH2CH2NHC(NH2)(NH))COOH
N ASN amino_acid H2NCH(CH2CONH2)COOH
D ASP amino_acid H2NCH(CH2COOH)COOH
C CYS amino_acid H2NCH(CH2SH)COOH
E GLU amino_acid H2NCH(CH2CH2COOH)COOH
Q GLN amino_acid H2NCH(CH2CH2CONH2)COOH
G GLY amino_acid H2NCH(H)COOH
H HIS amino_acid H2NCH(CH2(C3N2H3))COOH
I ILE amino_acid H2NCH(CH(CH3)(CH2CH3))COOH
L LEU amino_acid H2NCH(CH2CH(CH3)2)COOH
K LYS amino_acid H2NCH(CH2CH2CH2CH2NH2)COOH
M MET amino_acid H2NCH(CH2CH2SCH3)COOH
F PHE amino_acid H2NCH(CH2(C6H5))COOH
P PRO amino_acid (HNCHCH2CH2CH2)COOH
S SER amino_acid H2NCH(CH2OH)COOH
T THR amino_acid H2NCH(CH(CH3)(OH))COOH
U SEC amino_acid H2NCH(CH2SeH)COOH
W TRP amino_acid H2NCH(CH2(C8NH6))COOH
Y TYR amino_acid H2NCH(CH2(C6H4)OH)COOH
V VAL amino_acid H2NCH(CH(CH3)2)COOH
#
# linkers
#
# in general, the following molecules are NOT identical to the cross-linkers
# actually used in the experiments. for simplicity, however, we chose the same
# names. 
#
dma              -       linker      CH3OC(NH)(CH2)4C(NH)OCH3
dmp              -       linker      CH3OC(NH)(CH2)5C(NH)OCH3
dms              -       linker      CH3OC(NH)(CH2)6C(NH)OCH3
dss              -       linker      HOOC(CH2)6COOH
dsp              -       linker      HOOC(CH2)2SS(CH2)2COOH
dst              -       linker      HOOC(HCOH)2COOH
dtbp             -       linker      CH3OC(NH)(CH2)2SS(CH2)2C(NH)OCH3
egs              -       linker      HOOC(CH2)2COO(CH2)2OCO(CH2)2COOH
heme             -       linker      C34H32N4O4Fe
smcc             -       linker      HOOC(C6H10)CH2N(CO)2(CH)2
#
# general
#
acetic_acid                -       general     CH3COOH
acetic_acid_amide          -       general     CH3CONH2
cyclo_hexane_di_one        -       general     CO(CH2)4CO
ethyl_pyridine             -       general     CH3CH2C5H4N
propionic_acid_amide       -       general     CH3CH2CONH2
sulfonyl_acetic_acid       -       general     HOSO2CH2COOH 
sulfonyl_benzoic_acid      -       general     HOSO2C6H4COOH

@link_rules
#
#                     linked                         change of composition at 
# label              residues       compound           left           right   
#                                                        side upon binding
#
bs3                (K,[)-(K,[)        dss               -H2O           -H2O
cyclization          ([)-(])           -                -H             -OH
disulfide            (C)-(C)           -                -H             -H
dma                (K,[)-(K,[)        dma               -CH3OH         -CH3OH
dmp                (K,[)-(K,[)        dmp               -CH3OH         -CH3OH
dms                (K,[)-(K,[)        dms               -CH3OH         -CH3OH
dsp            (K,[,Y,S)-(K,[,Y,S)    dsp               -H2O           -H2O
dss                (K,[)-(K,[)        dss               -H2O           -H2O
dst                (K,[)-(K,[)        dst               -H2O           -H2O
dtbp               (K,[)-(K,[)        dtbp              -CH3OH         -CH3OH
dtssp          (K,[,Y,S)-(K,[,Y,S)    dsp               -H2O           -H2O
edc                (K,[)-(D,E,])       -                -OH            -H
egs                (K,[)-(K,[)        egs               -H2O           -H2O
heme                 (C)-(C)          heme              -              - 
smcc               (K,[)-(C)          smcc              -H2O           -

@modification_rules
#                  
#                     modified                               change of
# label               residues          compound            composition
#                                                           upon reaction
#                     
acetyl                [,K,S,T     acetic_acid                   -H2O
amide                    ]                 -                    -H2O+NH3
carbamidomethyl          C        acetic_acid_amide             -H2
carboxymethyl            C        acetic_acid                   -H2
cdap_cn                  C                 -                    -H+CN
deamidation              N                 -                    -NH3+H2O
deprotonated             C                 -                    -H
dhch                     R        cyclo_hexane_di_one            -
di_oxidation             W                 -                     O2
formyl                   [                 -                    -H2O+HCOOH
methylen                 M                 -                     CH2
oxidation               M,W                -                     O
phosphorylation        S,T,Y               -                    -H2O+H3PO4
propionamide             C        propionic_acid_amide          -H2
pyridylethyl             C        ethyl_pyridine                -H2
pyro_gln                 Q                 -                    -NH3
sulfatation            S,T,Y               -                    -H2O+H2SO4
sulfobenzoate           [,K       sulfonyl_benzoic_acid         -H2O
sulfonic_acid            C                 -                     O3
sulfonylacetyl           [        sulfonyl_acetic_acid          -H2O

@cleavage_rules
#
#                                   cleavage             change of composition
# label                              sites                before        after
#                                                           the bond cleaved  
#
arg_c                               (R)-(*\P)                 OH          H   
asn_c                               (N)-(*)                   OH          H 
asp_n                               (*)-(D)                   OH          H 
chymotrypsin                (W,Y,F,L,M)-(*\P)                 OH          H 
lys_c                               (K)-(*\P)                 OH          H 
post_pro                            (P)-(*)                   OH          H
prae_pro                            (*)-(P)                   OH          H
staph_au_1                          (E)-(*\E,P)               OH          H
staph_au_2                        (E,D)-(*\E,P)               OH          H
trypsin                           (K,R)-(*\P)                 OH          H
trypsin_chymotrypsin    (K,R,W,Y,F,L,M)-(*\P)                 OH          H 
trypsin_chymo_gluC_cdap (K,R,W,Y,F,L,M)-(*\P),(E)-(*\E,P),(*)-(C)  OH     H
trypsin_gluC                (K,R)-(*\P),(E,D)-(*\P)           OH          H
trypsin_no_excls                  (K,R)-(*)                   OH          H
trypsin_no_exo                  (K,R\[)-(*\P,])               OH          H
unspecific_hydrolysis               (*)-(*)                   OH          H

@isd_rules_for_linker_fragmentations
#
# NOTE: THE FOLLOWING RULES APPLY TO ION TYPE m+h !!!
#                                                              
#                                number of   change    change     allow
#                                fragments     of        of      swapping
#           link       linked      to be     compos.   compos.   of comp.
# label     rule      residues   detected    (left)    (right)   changes
#                                         
ds1       disulfide      *           1         +H        +H         0
ds2       disulfide      *           2         +H        +H         0

@psd_rules_for_simple_chain_fragmentations
#
# NOTE: THE FOLLOWING RULES APPLY TO ION TYPE m+h !!!
#
#            backbone     fragment  prereq.  prereq.  change    scoring
# label       bonds         to be    amino    mods      of       func.
#           to be cut     detected   acids            compos.   
#                                                   
a            (*)-(*)        nterm      -        -     -COOH       exp 
b          (*\P)-(*)        nterm      -        -     -OH         exp 
b'     (D,E)-(*),(*)-(P)    nterm      -        -     -OH         const
b"     (D,E)-(*),(*)-(P)    nterm      R        -     -OH         const 
b-NH3        (*)-(*)        nterm      R        -     -OH-NH3     exp   
b-H2O        (*)-(*)        nterm     S,T       -     -OH-H2O     exp   
b(n-1)+H2O    last          nterm      R        -     +H          const
c             (*)-(*\P)      nterm      -        -     -OH+NH3    const
x            (*)-(*)        cterm      -        -     -H+CO     const
y          (*\P)-(*)        cterm      -        -     +H          exp
y'     (D,E)-(*),(*)-(P)    cterm      -        -     +H          const
y"     (D,E)-(*),(*)-(P)    cterm      R        -     +H          const
y-NH3        (*)-(*)        cterm      R        -     +H-NH3      exp
y-H2O        (*)-(*)        cterm     S,T       -     +H-H2O      exp
z            (*)-(*\P)      cterm      -        -     -NH2         const

@psd_rules_for_linker_fragmentations
#
# NOTE: THE FOLLOWING RULES APPLY TO ION TYPE m+h !!!
#
#                     linked   fragment   prereq.   prereq.   change   scoring
# label  link rule   residues    to be     amino     mods       of      func.
#                              detected    acids              compos.
#                                                                    
ds1l     disulfide      *        left        -         -       -SH      const
ds2l     disulfide      *        left        -         -       -H       const
ds3l     disulfide      *        left        -         -       +H       const
ds4l     disulfide      *        left        -         -       +SH      const
ds1r     disulfide      *        right       -         -       -SH      const
ds2r     disulfide      *        right       -         -       -H       const
ds3r     disulfide      *        right       -         -       +H       const
ds4r     disulfide      *        right       -         -       +SH      const
legs5    egs            *        left        -         -    -H+H+H      const
legs6    egs            *        left        -         -     -H+CO      const
legs7    egs            *        left        -         - -H+COCH2+H     const
legs8    egs            *        left        -         - -H+CO(CH2)2+H  const
legs9    egs            *        left        -         - -H+CO(CH2)2CO  const
legs11   egs            *        left        -    - -H+CO(CH2)2COOCH2+H const
legs12   egs            *        left        - - -H+CO(CH2)2COO(CH2)2+H const
legs14   egs            *        left       - - -H+CO(CH2)2COO(CH2)2OOC const
legs15   egs            *        left  - - -H+CO(CH2)2COO(CH2)2OOCCH2+H const
legs16   egs            *      left - - -H+CO(CH2)2COO(CH2)2OOC(CH2)2+H const
legs17   egs            *      left - - -H+CO(CH2)2COO(CH2)2OOC(CH2)2CO const 
regs5    egs            *        right       -         -    -H+H+H      const
regs6    egs            *        right       -         -     -H+CO      const
regs7    egs            *        right       -         - -H+COCH2+H     const
regs8    egs            *        right       -         - -H+CO(CH2)2+H  const
regs9    egs            *        right       -         - -H+CO(CH2)2CO  const
regs11   egs            *        right       -    - -H+CO(CH2)2COOCH2+H const
regs12   egs            *        right       - - -H+CO(CH2)2COO(CH2)2+H const
regs14   egs            *        right      - - -H+CO(CH2)2COO(CH2)2OOC const
regs15   egs            *        right - - -H+CO(CH2)2COO(CH2)2OOCCH2+H const
regs16   egs            *     right - - -H+CO(CH2)2COO(CH2)2OOC(CH2)2+H const
regs17   egs            *     right - - -H+CO(CH2)2COO(CH2)2OOC(CH2)2CO const

@psd_prerequisite_assignments
#
# a dependant psd rule matches only, if all prequisite rules match. a given
# record is always evaluated with respect to a certain fragmentation site. 
# hence, for a given record dependant and prerequisite rules must always
# belong to the same "family" of psd rules. e.g., a linker fragmentation can
# never be a prerequisite for a simple chain fragmentation.
#
# dependants    | prerequisites
#
a b-NH3         | b
ds2l ds3l       | ds1l ds4l
ds2r ds3r       | ds1r ds4r

@psd_simultaneous_assignments
#
# via this section it is possible to reward the simultaneous matching of a set
# of psd rules. alternatively, one may penalize a situation, where not all
# members of a set match. a given record is always evaluated with respect to a
# certain fragmentation site. hence, all rules of a set must belong to the
# same "family" of psd rules, one can never mix, e.g., a linker fragmentation
# with a simple chain fragmentation. in case of a simultaneous match, the
# score of every single match is multiplied by the "match factor". if
# simultaneous matching fails, the scores for those rules that match are
# multiplied by the "mismatch factor". if the latter is negative or if it is
# set to "reject", the complete set of matches is rejected.
#
#                       |   scoring  factor
# psd rule set          |       for a
#                       |  match    mismatch
#
ds1l ds4l               |    1.      reject  
ds1r ds4r               |    1.      reject
ds1l ds4l ds1r ds4r     |    2.        1. 

@psd_scoring_functions
#
# used to calculate the contribution of a match to the total score. functions
# of type "linear" and "exponential" take into account the number of
# contiguous matches within an ion series: if there are n-1 contiguous
# matches, the contribution of the n-th match is a*n (a**n) for
# linear (exponential) functions. for functions of type "constant" the
# contribution is always a.
#  
#                      parameter
# label     type           a    
#
const       constant       1.5
lin         linear         1.5
exp         exponential    2.0