-
-
Notifications
You must be signed in to change notification settings - Fork 318
/
CHANGELOG_PARAMS
232 lines (231 loc) · 36.1 KB
/
CHANGELOG_PARAMS
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
Tool name Added/removed Parameter name Type Default value Restrictions Supported formats
AssayGeneratorMetabo - consensus_spectrum_precursor_rt_tolerance double 5.0
AssayGeneratorMetabo - decoy_generation bool false
AssayGeneratorMetabo - decoy_generation_method string original original,resolve_overlap,add_shift,both
AssayGeneratorMetabo + deisotoping_annotate_charge bool false
AssayGeneratorMetabo - deisotoping:annotate_charge bool false
AssayGeneratorMetabo + deisotoping_fragment_tolerance double 1.0
AssayGeneratorMetabo - deisotoping:fragment_tolerance double 1.0
AssayGeneratorMetabo + deisotoping_fragment_unit string ppm ppm,Da
AssayGeneratorMetabo - deisotoping:fragment_unit string ppm ppm,Da
AssayGeneratorMetabo + deisotoping_keep_only_deisotoped bool false
AssayGeneratorMetabo - deisotoping:keep_only_deisotoped bool false
AssayGeneratorMetabo + deisotoping_max_charge int 1 1:
AssayGeneratorMetabo - deisotoping:max_charge int 1 1:
AssayGeneratorMetabo + deisotoping_max_isopeaks int 3 3:
AssayGeneratorMetabo - deisotoping:max_isopeaks int 3 3:
AssayGeneratorMetabo + deisotoping_min_charge int 1 1:
AssayGeneratorMetabo - deisotoping:min_charge int 1 1:
AssayGeneratorMetabo + deisotoping_min_isopeaks int 2 2:
AssayGeneratorMetabo - deisotoping:min_isopeaks int 2 2:
AssayGeneratorMetabo + deisotoping_use_deisotoper bool false
AssayGeneratorMetabo - deisotoping:use_deisotoper bool false
AssayGeneratorMetabo + feature_only string false false,true
AssayGeneratorMetabo + filter_by_num_masstraces int 1 1:
AssayGeneratorMetabo - fingerid:db string
AssayGeneratorMetabo - fragment_annotation_score_threshold double 0.8 0.0:1.0
AssayGeneratorMetabo - fragment_annotation string sirius none,sirius
AssayGeneratorMetabo + in_featureinfo input-file *.featureXML
AssayGeneratorMetabo - in_id input-file *.featureXML
AssayGeneratorMetabo - out_workspace_directory string
AssayGeneratorMetabo + precursor_consensus_spectrum_rt_tolerance double 5.0
AssayGeneratorMetabo + precursor_mz_tolerance double 10.0
AssayGeneratorMetabo + precursor_mz_tolerance_unit string ppm ppm,Da
AssayGeneratorMetabo + precursor_rt_tolerance double 5.0
AssayGeneratorMetabo - preprocessing:feature_only bool false
AssayGeneratorMetabo - preprocessing:filter_by_num_masstraces int 1 1:
AssayGeneratorMetabo - preprocessing:isotope_pattern_iterations int 3
AssayGeneratorMetabo - preprocessing:no_masstrace_info_isotope_pattern bool false
AssayGeneratorMetabo - preprocessing:precursor_mz_tolerance double 10.0
AssayGeneratorMetabo - preprocessing:precursor_mz_tolerance_unit string ppm Da,ppm
AssayGeneratorMetabo - preprocessing:precursor_rt_tolerance double 5.0
AssayGeneratorMetabo - project:ignore_formula bool false
AssayGeneratorMetabo - project:loglevel string
AssayGeneratorMetabo - project:maxmz int -1
AssayGeneratorMetabo - project:processors int 1
AssayGeneratorMetabo - project:q bool false
AssayGeneratorMetabo - read_sirius_stdout bool false
AssayGeneratorMetabo - sirius:candidates int 10 0:
AssayGeneratorMetabo - sirius:candidates_per_ion int 1
AssayGeneratorMetabo - sirius:compound_timeout int 100 0:
AssayGeneratorMetabo - sirius:db string none
AssayGeneratorMetabo - sirius:elements_considered string SBrClBSe
AssayGeneratorMetabo - sirius:elements_enforced string CHNOP
AssayGeneratorMetabo - sirius_executable input-file
AssayGeneratorMetabo - sirius:formulas string
AssayGeneratorMetabo - sirius:ions_considered string [M+H]+,[M+K]+,[M+Na]+,[M+H-H2O]+,[M+H-H4O2]+,[M+NH4]+,[M-H]-,[M+Cl]-,[M-H2O-H]-,[M+Br]-
AssayGeneratorMetabo - sirius:ions_enforced string
AssayGeneratorMetabo - sirius:no_isotope_filter bool false
AssayGeneratorMetabo - sirius:no_isotope_score bool false
AssayGeneratorMetabo - sirius:no_recalibration bool false
AssayGeneratorMetabo - sirius:ppm_max double 10.0
AssayGeneratorMetabo - sirius:ppm_max_ms2 double 10.0
AssayGeneratorMetabo - sirius:profile string default default,qtof,orbitrap,fticr
AssayGeneratorMetabo - sirius:solver string CLP
AssayGeneratorMetabo - sirius:tree_timeout int 100 0:
AssayGeneratorMetabo - use_exact_mass bool false
CometAdapter - enzyme string Trypsin Asp-N,Trypsin,Arg-C,Chymotrypsin,CNBr,no cleavage,unspecific cleavage,Lys-C,Lys-N,PepsinA,Trypsin/P,glutamyl endopeptidase
CometAdapter + enzyme string Trypsin glutamyl endopeptidase,Arg-C/P,Asp-N,Trypsin,Arg-C,no cleavage,unspecific cleavage,Chymotrypsin,CNBr,Lys-C,Lys-N,PepsinA,Trypsin/P
CometAdapter - PeptideIndexing:enzyme:name string auto auto,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,Trypsin,Arg-C,Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage
CometAdapter + PeptideIndexing:enzyme:name string auto auto,Trypsin/P,V8-DE,V8-E,leukocyte elastase,Trypsin,Arg-C,PepsinA,TrypChymo,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,Lys-N,Lys-C/P,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage
CometAdapter - second_enzyme string Asp-N,Trypsin,Arg-C,Chymotrypsin,CNBr,no cleavage,unspecific cleavage,Lys-C,Lys-N,PepsinA,Trypsin/P,glutamyl endopeptidase
CometAdapter + second_enzyme string glutamyl endopeptidase,Arg-C/P,Asp-N,Trypsin,Arg-C,no cleavage,unspecific cleavage,Chymotrypsin,CNBr,Lys-C,Lys-N,PepsinA,Trypsin/P
DecoyDatabase + enzyme string Trypsin Arg-C/P,Asp-N,Asp-N/B,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,Trypsin,Arg-C,glutamyl endopeptidase,Alpha-lytic protease,no cleavage,unspecific cleavage,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR
DecoyDatabase - enzyme string Trypsin glutamyl endopeptidase,Alpha-lytic protease,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Trypsin,Arg-C,Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR
Digestor + enzyme string Trypsin Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Trypsin,Arg-C,Arg-C/P,Asp-N,Asp-N/B,leukocyte elastase,proline endopeptidase,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate
Digestor - enzyme string Trypsin Trypsin,Arg-C,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,V8-E,leukocyte elastase,Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR
DigestorMotif + enzyme string Trypsin Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Trypsin,Arg-C,Arg-C/P,Asp-N,Asp-N/B,leukocyte elastase,proline endopeptidase,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate
DigestorMotif - enzyme string Trypsin Trypsin,Arg-C,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,V8-DE,V8-E,Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D
FeatureFinderCentroided + algorithm:advanced:pseudo_rt_shift double 500.0 1.0:
FeatureFinderCentroided - algorithm:debug:pseudo_rt_shift double 500.0 1.0:
FeatureFinderCentroided - out_mzq output-file *.mzq
FileConverter - change_im_format string none none,concatenated,multiple_spectra,mixed
FileConverter - include_noise bool false
FileConverter - NET_executable input-file
FileConverter - no_peak_picking bool false
FileConverter - no_zlib_compression bool false
FileConverter + RawToMzML:include_noise bool false
FileConverter + RawToMzML:NET_executable input-file
FileConverter + RawToMzML:no_peak_picking bool false
FileConverter + RawToMzML:no_zlib_compression bool false
FileConverter + RawToMzML:ThermoRaw_executable input-file ThermoRawFileParser.exe *.exe
FileConverter - ThermoRaw_executable input-file ThermoRawFileParser.exe *.exe
FileFilter + spectra:remove_activation string Collision-induced dissociation,Post-source decay,Plasma desorption,Surface-induced dissociation,Blackbody infrared radiative dissociation,Electron capture dissociation,Infrared multiphoton dissociation,Sustained off-resonance irradiation,High-energy collision-induced dissociation,Low-energy collision-induced dissociation,Photodissociation,Electron transfer dissociation,Electron transfer and collision-induced dissociation,Electron transfer and higher-energy collision dissociation,Pulsed q dissociation,trap-type collision-induced dissociation,beam-type collision-induced dissociation,in-source collision-induced dissociation,Bruker proprietary method
FileFilter - spectra:remove_activation string Collision-induced dissociation,Post-source decay,Plasma desorption,Surface-induced dissociation,Blackbody infrared radiative dissociation,Electron capture dissociation,Infrared multiphoton dissociation,Sustained off-resonance irradiation,High-energy collision-induced dissociation,Low-energy collision-induced dissociation,Photodissociation,Electron transfer dissociation,Pulsed q dissociation,trap-type collision-induced dissociation,beam-type collision-induced dissociation,in-source collision-induced dissociation,Bruker proprietary method
FileFilter + spectra:select_activation string Collision-induced dissociation,Post-source decay,Plasma desorption,Surface-induced dissociation,Blackbody infrared radiative dissociation,Electron capture dissociation,Infrared multiphoton dissociation,Sustained off-resonance irradiation,High-energy collision-induced dissociation,Low-energy collision-induced dissociation,Photodissociation,Electron transfer dissociation,Electron transfer and collision-induced dissociation,Electron transfer and higher-energy collision dissociation,Pulsed q dissociation,trap-type collision-induced dissociation,beam-type collision-induced dissociation,in-source collision-induced dissociation,Bruker proprietary method
FileFilter - spectra:select_activation string Collision-induced dissociation,Post-source decay,Plasma desorption,Surface-induced dissociation,Blackbody infrared radiative dissociation,Electron capture dissociation,Infrared multiphoton dissociation,Sustained off-resonance irradiation,High-energy collision-induced dissociation,Low-energy collision-induced dissociation,Photodissociation,Electron transfer dissociation,Pulsed q dissociation,trap-type collision-induced dissociation,beam-type collision-induced dissociation,in-source collision-induced dissociation,Bruker proprietary method
FileInfo - out_tsv output-file *.csv
FileInfo + out_tsv output-file *.tsv
IDFileConverter + fasta_to_mzml:add_zp1_ions bool false
IDFileConverter + fasta_to_mzml:add_zp2_ions bool false
IDFileConverter + fasta_to_mzml:enzyme string Trypsin Arg-C/P,Asp-N,Asp-N/B,Trypsin,Arg-C,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,leukocyte elastase,proline endopeptidase,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate
IDFileConverter - fasta_to_mzml:enzyme string Trypsin staphylococcal protease/D,proline-endopeptidase/HKR,Trypsin,Arg-C,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage
IDFilter - in_silico_digestion:enzyme string Trypsin Trypsin,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Arg-C,Arg-C/P,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Lys-C/P,PepsinA,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,TrypChymo,Trypsin/P,V8-DE,V8-E,Asp-N,Asp-N/B,Asp-N_ambic,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase
IDFilter + in_silico_digestion:enzyme string Trypsin Trypsin,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Asp-N,Asp-N/B,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,Arg-C,Arg-C/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase
IDFilter - missed_cleavages:enzyme string Trypsin Trypsin,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Arg-C,Arg-C/P,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Lys-C/P,PepsinA,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,TrypChymo,Trypsin/P,V8-DE,V8-E,Asp-N,Asp-N/B,Asp-N_ambic,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase
IDFilter + missed_cleavages:enzyme string Trypsin Trypsin,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Asp-N,Asp-N/B,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,Arg-C,Arg-C/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase
IDMapper + in input-file *.featureXML,*.consensusXML
IDMapper - in input-file *.featureXML,*.consensusXML,*.mzq
IDMapper + out output-file *.featureXML,*.consensusXML
IDMapper - out output-file *.featureXML,*.consensusXML,*.mzq
IsobaricAnalyzer + extraction:select_activation string auto auto,Collision-induced dissociation,Post-source decay,Plasma desorption,Surface-induced dissociation,Blackbody infrared radiative dissociation,Electron capture dissociation,Infrared multiphoton dissociation,Sustained off-resonance irradiation,High-energy collision-induced dissociation,Low-energy collision-induced dissociation,Photodissociation,Electron transfer dissociation,Electron transfer and collision-induced dissociation,Electron transfer and higher-energy collision dissociation,Pulsed q dissociation,trap-type collision-induced dissociation,beam-type collision-induced dissociation,in-source collision-induced dissociation,any
IsobaricAnalyzer - extraction:select_activation string auto auto,Collision-induced dissociation,Post-source decay,Plasma desorption,Surface-induced dissociation,Blackbody infrared radiative dissociation,Electron capture dissociation,Infrared multiphoton dissociation,Sustained off-resonance irradiation,High-energy collision-induced dissociation,Low-energy collision-induced dissociation,Photodissociation,Electron transfer dissociation,Pulsed q dissociation,trap-type collision-induced dissociation,beam-type collision-induced dissociation,in-source collision-induced dissociation,any
MRMTransitionGroupPicker + algorithm:PeakPickerChromatogram:gauss_width double 50.0
MRMTransitionGroupPicker + algorithm:PeakPickerChromatogram:method string corrected legacy,corrected,crawdad
MRMTransitionGroupPicker + algorithm:PeakPickerChromatogram:peak_width double -1.0
MRMTransitionGroupPicker + algorithm:PeakPickerChromatogram:remove_overlapping_peaks string false false,true
MRMTransitionGroupPicker + algorithm:PeakPickerChromatogram:sgolay_frame_length int 15
MRMTransitionGroupPicker + algorithm:PeakPickerChromatogram:sgolay_polynomial_order int 3
MRMTransitionGroupPicker + algorithm:PeakPickerChromatogram:signal_to_noise double 1.0 0.0:
MRMTransitionGroupPicker + algorithm:PeakPickerChromatogram:sn_bin_count int 30
MRMTransitionGroupPicker + algorithm:PeakPickerChromatogram:sn_win_len double 1000.0
MRMTransitionGroupPicker + algorithm:PeakPickerChromatogram:use_gauss string true false,true
MRMTransitionGroupPicker + algorithm:PeakPickerChromatogram:write_sn_log_messages bool false
MRMTransitionGroupPicker - algorithm:PeakPickerMRM:gauss_width double 50.0
MRMTransitionGroupPicker - algorithm:PeakPickerMRM:method string corrected legacy,corrected,crawdad
MRMTransitionGroupPicker - algorithm:PeakPickerMRM:peak_width double -1.0
MRMTransitionGroupPicker - algorithm:PeakPickerMRM:remove_overlapping_peaks string false false,true
MRMTransitionGroupPicker - algorithm:PeakPickerMRM:sgolay_frame_length int 15
MRMTransitionGroupPicker - algorithm:PeakPickerMRM:sgolay_polynomial_order int 3
MRMTransitionGroupPicker - algorithm:PeakPickerMRM:signal_to_noise double 1.0 0.0:
MRMTransitionGroupPicker - algorithm:PeakPickerMRM:sn_bin_count int 30
MRMTransitionGroupPicker - algorithm:PeakPickerMRM:sn_win_len double 1000.0
MRMTransitionGroupPicker - algorithm:PeakPickerMRM:use_gauss string true false,true
MRMTransitionGroupPicker - algorithm:PeakPickerMRM:write_sn_log_messages bool false
MSFraggerAdapter + digest:search_enzyme_name string Trypsin Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,2-iodobenzoate,iodosobenzoate,Trypsin,Arg-C,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P
MSFraggerAdapter - digest:search_enzyme_name string Trypsin Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,glutamyl endopeptidase,Alpha-lytic protease,Trypsin,Arg-C,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR
MSFraggerAdapter + PeptideIndexing:enzyme:name string auto auto,Lys-C,Lys-N,Trypsin,Arg-C,Lys-C/P,PepsinA,V8-E,leukocyte elastase,proline endopeptidase,Chymotrypsin/P,CNBr,Formic_acid,TrypChymo,Trypsin/P,V8-DE,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate
MSFraggerAdapter - PeptideIndexing:enzyme:name string auto auto,TrypChymo,Trypsin/P,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,Trypsin,Arg-C,V8-DE,V8-E,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,glutamyl endopeptidase,Alpha-lytic protease,Arg-C/P,Asp-N,Asp-N/B,leukocyte elastase,proline endopeptidase,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR
MSGFPlusAdapter + min_peaks int 10 10:
MSGFPlusAdapter + PeptideIndexing:enzyme:name string auto auto,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Trypsin,TrypChymo,Trypsin/P,V8-DE,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,Arg-C,Arg-C/P,Lys-C/P,PepsinA,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,V8-E,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase
MSGFPlusAdapter - PeptideIndexing:enzyme:name string auto auto,no cleavage,unspecific cleavage,Trypsin,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,Arg-C,Arg-C/P,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,Asp-N,Asp-N/B,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,Formic_acid,Lys-C,Lys-N,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,V8-DE,V8-E,leukocyte elastase,proline endopeptidase
NucleicAcidSearchEngine - oligo:enzyme string no cleavage mazF,colicin_E5,no cleavage,cusativin,RNase_A,RNase_MC1,RNase_H,unspecific cleavage,RNase_U2,RNase_T1
NucleicAcidSearchEngine + oligo:enzyme string no cleavage RNase_T1,RNase_T1_Phosphatase,cusativin,RNase_4,RNase_4p,mazF,colicin_E5,no cleavage,unspecific cleavage,RNase_U2,RNase_A,RNase_MC1,RNase_H
OpenPepXLLF + peptide:enzyme string Trypsin Arg-C,Arg-C/P,Asp-N,Trypsin,TrypChymo,Trypsin/P,V8-DE,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Lys-C/P,PepsinA,Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,V8-E,leukocyte elastase,proline endopeptidase,Formic_acid,Lys-C,Lys-N
OpenPepXLLF - peptide:enzyme string Trypsin Trypsin,Arg-C,Arg-C/P,Asp-N,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,Lys-C/P,PepsinA,Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,TrypChymo,Trypsin/P,V8-DE,V8-E,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage
OpenPepXL + peptide:enzyme string Trypsin leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,TrypChymo,Trypsin/P,V8-DE,V8-E,Trypsin,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,Lys-C/P,PepsinA,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Arg-C,Arg-C/P,no cleavage,unspecific cleavage
OpenPepXL - peptide:enzyme string Trypsin Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Arg-C,Arg-C/P,Asp-N
OpenSwathAnalyzer + algorithm:Scores:use_peak_shape_metrics string false
OpenSwathAnalyzer + algorithm:TransitionGroupPicker:PeakPickerChromatogram:gauss_width double 50.0
OpenSwathAnalyzer + algorithm:TransitionGroupPicker:PeakPickerChromatogram:method string corrected legacy,corrected,crawdad
OpenSwathAnalyzer + algorithm:TransitionGroupPicker:PeakPickerChromatogram:peak_width double -1.0
OpenSwathAnalyzer + algorithm:TransitionGroupPicker:PeakPickerChromatogram:remove_overlapping_peaks string false false,true
OpenSwathAnalyzer + algorithm:TransitionGroupPicker:PeakPickerChromatogram:sgolay_frame_length int 15
OpenSwathAnalyzer + algorithm:TransitionGroupPicker:PeakPickerChromatogram:sgolay_polynomial_order int 3
OpenSwathAnalyzer + algorithm:TransitionGroupPicker:PeakPickerChromatogram:signal_to_noise double 1.0 0.0:
OpenSwathAnalyzer + algorithm:TransitionGroupPicker:PeakPickerChromatogram:sn_bin_count int 30
OpenSwathAnalyzer + algorithm:TransitionGroupPicker:PeakPickerChromatogram:sn_win_len double 1000.0
OpenSwathAnalyzer + algorithm:TransitionGroupPicker:PeakPickerChromatogram:use_gauss string true false,true
OpenSwathAnalyzer + algorithm:TransitionGroupPicker:PeakPickerChromatogram:write_sn_log_messages bool false
OpenSwathAnalyzer - algorithm:TransitionGroupPicker:PeakPickerMRM:gauss_width double 50.0
OpenSwathAnalyzer - algorithm:TransitionGroupPicker:PeakPickerMRM:method string corrected legacy,corrected,crawdad
OpenSwathAnalyzer - algorithm:TransitionGroupPicker:PeakPickerMRM:peak_width double -1.0
OpenSwathAnalyzer - algorithm:TransitionGroupPicker:PeakPickerMRM:remove_overlapping_peaks string false false,true
OpenSwathAnalyzer - algorithm:TransitionGroupPicker:PeakPickerMRM:sgolay_frame_length int 15
OpenSwathAnalyzer - algorithm:TransitionGroupPicker:PeakPickerMRM:sgolay_polynomial_order int 3
OpenSwathAnalyzer - algorithm:TransitionGroupPicker:PeakPickerMRM:signal_to_noise double 1.0 0.0:
OpenSwathAnalyzer - algorithm:TransitionGroupPicker:PeakPickerMRM:sn_bin_count int 30
OpenSwathAnalyzer - algorithm:TransitionGroupPicker:PeakPickerMRM:sn_win_len double 1000.0
OpenSwathAnalyzer - algorithm:TransitionGroupPicker:PeakPickerMRM:use_gauss string true false,true
OpenSwathAnalyzer - algorithm:TransitionGroupPicker:PeakPickerMRM:write_sn_log_messages bool false
OpenSwathAnalyzer + algorithm:use_ms1_ion_mobility string true
OpenSwathRTNormalizer + algorithm:Scores:use_peak_shape_metrics string false
OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:PeakPickerChromatogram:gauss_width double 50.0
OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:PeakPickerChromatogram:method string corrected legacy,corrected,crawdad
OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:PeakPickerChromatogram:peak_width double -1.0
OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:PeakPickerChromatogram:remove_overlapping_peaks string false false,true
OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:PeakPickerChromatogram:sgolay_frame_length int 15
OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:PeakPickerChromatogram:sgolay_polynomial_order int 3
OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:PeakPickerChromatogram:signal_to_noise double 1.0 0.0:
OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:PeakPickerChromatogram:sn_bin_count int 30
OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:PeakPickerChromatogram:sn_win_len double 1000.0
OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:PeakPickerChromatogram:use_gauss string true false,true
OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:PeakPickerChromatogram:write_sn_log_messages bool false
OpenSwathRTNormalizer - algorithm:TransitionGroupPicker:PeakPickerMRM:gauss_width double 50.0
OpenSwathRTNormalizer - algorithm:TransitionGroupPicker:PeakPickerMRM:method string corrected legacy,corrected,crawdad
OpenSwathRTNormalizer - algorithm:TransitionGroupPicker:PeakPickerMRM:peak_width double -1.0
OpenSwathRTNormalizer - algorithm:TransitionGroupPicker:PeakPickerMRM:remove_overlapping_peaks string false false,true
OpenSwathRTNormalizer - algorithm:TransitionGroupPicker:PeakPickerMRM:sgolay_frame_length int 15
OpenSwathRTNormalizer - algorithm:TransitionGroupPicker:PeakPickerMRM:sgolay_polynomial_order int 3
OpenSwathRTNormalizer - algorithm:TransitionGroupPicker:PeakPickerMRM:signal_to_noise double 1.0 0.0:
OpenSwathRTNormalizer - algorithm:TransitionGroupPicker:PeakPickerMRM:sn_bin_count int 30
OpenSwathRTNormalizer - algorithm:TransitionGroupPicker:PeakPickerMRM:sn_win_len double 1000.0
OpenSwathRTNormalizer - algorithm:TransitionGroupPicker:PeakPickerMRM:use_gauss string true false,true
OpenSwathRTNormalizer - algorithm:TransitionGroupPicker:PeakPickerMRM:write_sn_log_messages bool false
OpenSwathRTNormalizer + algorithm:use_ms1_ion_mobility string true
OpenSwathWorkflow + Scoring:Scores:use_peak_shape_metrics string false
OpenSwathWorkflow + Scoring:TransitionGroupPicker:PeakPickerChromatogram:gauss_width double 30.0
OpenSwathWorkflow + Scoring:TransitionGroupPicker:PeakPickerChromatogram:method string corrected legacy,corrected,crawdad
OpenSwathWorkflow + Scoring:TransitionGroupPicker:PeakPickerChromatogram:peak_width double -1.0
OpenSwathWorkflow + Scoring:TransitionGroupPicker:PeakPickerChromatogram:remove_overlapping_peaks string true false,true
OpenSwathWorkflow + Scoring:TransitionGroupPicker:PeakPickerChromatogram:sgolay_frame_length int 11
OpenSwathWorkflow + Scoring:TransitionGroupPicker:PeakPickerChromatogram:sgolay_polynomial_order int 3
OpenSwathWorkflow + Scoring:TransitionGroupPicker:PeakPickerChromatogram:signal_to_noise double 0.1 0.0:
OpenSwathWorkflow + Scoring:TransitionGroupPicker:PeakPickerChromatogram:use_gauss string false false,true
OpenSwathWorkflow + Scoring:TransitionGroupPicker:PeakPickerChromatogram:write_sn_log_messages bool false
OpenSwathWorkflow - Scoring:TransitionGroupPicker:PeakPickerMRM:gauss_width double 30.0
OpenSwathWorkflow - Scoring:TransitionGroupPicker:PeakPickerMRM:method string corrected legacy,corrected,crawdad
OpenSwathWorkflow - Scoring:TransitionGroupPicker:PeakPickerMRM:peak_width double -1.0
OpenSwathWorkflow - Scoring:TransitionGroupPicker:PeakPickerMRM:remove_overlapping_peaks string true false,true
OpenSwathWorkflow - Scoring:TransitionGroupPicker:PeakPickerMRM:sgolay_frame_length int 11
OpenSwathWorkflow - Scoring:TransitionGroupPicker:PeakPickerMRM:sgolay_polynomial_order int 3
OpenSwathWorkflow - Scoring:TransitionGroupPicker:PeakPickerMRM:signal_to_noise double 0.1 0.0:
OpenSwathWorkflow - Scoring:TransitionGroupPicker:PeakPickerMRM:use_gauss string false false,true
OpenSwathWorkflow - Scoring:TransitionGroupPicker:PeakPickerMRM:write_sn_log_messages bool false
OpenSwathWorkflow + Scoring:use_ms1_ion_mobility string true
PeptideIndexer - enzyme:name string auto auto,Arg-C/P,Asp-N,Asp-N/B,TrypChymo,Trypsin/P,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,V8-DE,V8-E,leukocyte elastase,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Trypsin,Arg-C,Lys-C,Lys-N,Lys-C/P,PepsinA,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate
PeptideIndexer + enzyme:name string auto auto,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,elastase-trypsin-chymotrypsin,no cleavage,Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,TrypChymo,Trypsin/P,Trypsin,Arg-C,Lys-N,Lys-C/P,PepsinA,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,unspecific cleavage
RNADigestor - enzyme string RNase_T1 RNase_A,RNase_MC1,RNase_H,RNase_T1,RNase_U2,cusativin,mazF,colicin_E5,no cleavage,unspecific cleavage
RNADigestor + enzyme string RNase_T1 RNase_MC1,RNase_H,RNase_4,RNase_4p,cusativin,RNase_U2,RNase_A,RNase_T1,RNase_T1_Phosphatase,mazF,colicin_E5,no cleavage,unspecific cleavage
SageAdapter - enzyme string Trypsin Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,Lys-C,Lys-N,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,proline-endopeptidase/HKR,Glu-C+P,Trypsin,Arg-C,unspecific cleavage,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage
SageAdapter + enzyme string Trypsin glutamyl endopeptidase,Alpha-lytic protease,Arg-C/P,Asp-N,Asp-N/B,Trypsin,Arg-C,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR
SageAdapter - PeptideIndexing:enzyme:name string auto auto,Trypsin,Asp-N,Asp-N/B,Asp-N_ambic,TrypChymo,Trypsin/P,V8-DE,V8-E,no cleavage,unspecific cleavage,Lys-C/P,PepsinA,Arg-C,Arg-C/P,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease
SageAdapter + PeptideIndexing:enzyme:name string auto auto,Trypsin,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,Arg-C,Arg-C/P,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,TrypChymo,Trypsin/P,Asp-N,Asp-N/B,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Lys-C/P,PepsinA
SimpleSearchEngine + Search:enzyme string Trypsin glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,Trypsin,Asp-N,Asp-N/B,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Arg-C,Arg-C/P,Chymotrypsin/P,CNBr,Formic_acid,Asp-N_ambic,Chymotrypsin,TrypChymo,Trypsin/P,Lys-C/P,PepsinA,Lys-C,Lys-N
SimpleSearchEngine - Search:enzyme string Trypsin Lys-C,Lys-N,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,Arg-C,Arg-C/P,Trypsin,CNBr,Formic_acid,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Asp-N,Asp-N/B,Lys-C/P,PepsinA,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P
SpecLibSearcher - compare_function string ZhangSimilarityScore PeakAlignment,SpectrumAlignmentScore,SpectrumCheapDPCorr,SpectrumPrecursorComparator,SteinScottImproveScore,ZhangSimilarityScore
SpecLibSearcher + compare_function string ZhangSimilarityScore ZhangSimilarityScore,SpectraSTSimilarityScore
XTandemAdapter - enzyme string Trypsin Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Arg-C,Arg-C/P,Asp-N,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,no cleavage,unspecific cleavage,Trypsin,V8-DE,V8-E,leukocyte elastase,Formic_acid,Lys-C,Lys-N
XTandemAdapter + enzyme string Trypsin Lys-N,Lys-C/P,PepsinA,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Trypsin,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,glutamyl endopeptidase,Alpha-lytic protease,Asp-N/B,Asp-N_ambic,Chymotrypsin,2-iodobenzoate,Arg-C,Arg-C/P,Asp-N,no cleavage,unspecific cleavage
XTandemAdapter - PeptideIndexing:enzyme:name string auto auto,Asp-N,Asp-N/B,Asp-N_ambic,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,Chymotrypsin,Chymotrypsin/P,CNBr,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,Arg-C,Arg-C/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Trypsin,Formic_acid,Lys-C,Lys-N
XTandemAdapter + PeptideIndexing:enzyme:name string auto auto,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,TrypChymo,Trypsin/P,V8-DE,V8-E,Arg-C,Arg-C/P,Lys-C/P,PepsinA,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,Lys-C,Lys-N,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,Trypsin,unspecific cleavage,Asp-N,Asp-N/B,Asp-N_ambic