ASN.1 Type Definitions for Module OMSSA

Top-level module index.

Colors and Styles Used


Type NameValue

Is Used By

MSHitSet MSSearchSettings MSSpectrum NameValue ::=
SEQUENCE {
name VisibleString
value VisibleString
}  


Type MSSpectrum

Uses

NameValue

Is Used By

MSSpectrumset MSSpectrum ::=
SEQUENCE {
number INTEGER
charge SEQUENCE OF INTEGER
precursormz INTEGER
mz SEQUENCE OF INTEGER
abundance SEQUENCE OF INTEGER
iscale REAL
ids SEQUENCE OF VisibleString OPTIONAL
namevalue SEQUENCE OF NameValue OPTIONAL
}  


Type MSSpectrumset

Uses

MSSpectrum

Is Used By

MSRequest MSSpectrumset ::= SEQUENCE OF MSSpectrum

Type MSEnzymes

Is Used By

MSSearchSettings MSEnzymes ::=
INTEGER {
trypsin 0
argc 1
cnbr 2
chymotrypsin 3
formicacid 4
lysc 5
lysc-p 6
pepsin-a 7
tryp-cnbr 8
tryp-chymo 9
trypsin-p 10
whole-protein 11
aspn 12
gluc 13
aspngluc 14
top-down 15
semi-tryptic 16
no-enzyme 17
chymotrypsin-p 18
aspn-de 19
gluc-de 20
lysn 21
thermolysin-p 22
semi-chymotrypsin 23
semi-gluc 24
max 25
none 255
}  


Type MSMod

Is Used By

MSModHit MSModSpec MSSearchSettings MSMod ::=
INTEGER {
methylk 0
oxym 1
carboxymethylc 2
carbamidomethylc 3
deamidationkq 4
propionamidec 5
phosphorylations 6
phosphorylationt 7
phosphorylationy 8
ntermmcleave 9
ntermacetyl 10
ntermmethyl 11
ntermtrimethyl 12
methythiold 13
methylq 14
trimethylk 15
methyld 16
methyle 17
ctermpepmethyl 18
trideuteromethyld 19
trideuteromethyle 20
ctermpeptrideuteromethyl 21
nformylmet 22
twoamino3oxobutanoicacid 23
acetylk 24
ctermamide 25
bmethylthiold 26
carbamidomethylk 27
carbamidometylh 28
carbamidomethyld 29
carbamidomethyle 30
carbamylk 31
ntermcarbamyl 32
citrullinationr 33
cysteicacidc 34
diiodinationy 35
dimethylk 36
dimethylr 37
ntermpepdimethyl 38
dihydroxyf 39
thioacetylk 40
ntermpeptioacetyl 41
farnesylationc 42
formylk 43
ntermpepformyl 44
formylkynureninw 45
phef 46
gammacarboxyld 47
gammacarboxyle 48
geranylgeranylc 49
ntermpepglucuronylg 50
glutathionec 51
glyglyk 52
guanidinationk 53
his2asnh 54
his2asph 55
ctermpephsem 56
ctermpephselactm 57
hydroxykynureninw 58
hydroxylationd 59
hydroxylationk 60
hydroxylationn 61
hydroxylationp 62
hydroxylationf 63
hydroxylationy 64
iodinationy 65
kynureninw 66
lipoylk 67
ctermpepmeester 68
meesterd 69
meestere 70
meesters 71
meestery 72
methylc 73
methylh 74
methyln 75
ntermpepmethyl 76
methylr 77
ntermpepmyristoyeylationg 78
ntermpepmyristoyl4hg 79
ntermpepmyristoylationg 80
myristoylationk 81
ntermformyl 82
nemc 83
nipcam 84
nitrow 85
nitroy 86
ctermpepo18 87
ctermpepdio18 88
oxyh 89
oxyw 90
ppantetheines 91
palmitoylationc 92
palmitoylationk 93
palmitoylations 94
palmitoylationt 95
phospholosss 96
phospholosst 97
phospholossy 98
phosphoneutrallossc 99
phosphoneutrallossd 100
phosphoneutrallossh 101
propionylk 102
ntermpeppropionyl 103
propionylheavyk 104
ntermpeppropionylheavy 105
pyridylk 106
ntermpeppyridyl 107
ntermpeppyrocmc 108
ntermpeppyroe 109
ntermpeppyroq 110
pyroglutamicp 111
spyridylethylc 112
semetm 113
sulfationy 114
suphonem 115
triiodinationy 116
trimethylationr 117
ntermpeptripalmitatec 118
usermod1 119
usermod2 120
usermod3 121
usermod4 122
usermod5 123
usermod6 124
usermod7 125
usermod8 126
usermod9 127
usermod10 128
icatlight 129
icatheavy 130
camthiopropanoylk 131
phosphoneutrallosss 132
phosphoneutrallosst 133
phosphoetdlosss 134
phosphoetdlosst 135
arg-13c6 136
arg-13c6-15n4 137
lys-13c6 138
oxy18 139
beta-elim-s 140
beta-elim-t 141
usermod11 142
usermod12 143
usermod13 144
usermod14 145
usermod15 146
usermod16 147
usermod17 148
usermod18 149
usermod19 150
usermod20 151
usermod21 152
usermod22 153
usermod23 154
usermod24 155
usermod25 156
usermod26 157
usermod27 158
usermod28 159
usermod29 160
usermod30 161
sulfinicacid 162
arg2orn 163
dehydro 164
carboxykynurenin 165
sumoylation 166
iTRAQ114nterm 167
iTRAQ114K 168
iTRAQ114Y 169
iTRAQ115nterm 170
iTRAQ115K 171
iTRAQ115Y 172
iTRAQ116nterm 173
iTRAQ116K 174
iTRAQ116Y 175
iTRAQ117nterm 176
iTRAQ117K 177
iTRAQ117Y 178
mmts 179
lys-2H4 180
lys-13C615N2 181
hexNAcN 182
dHexHexNAcN 183
hexNAcS 184
hexNAcT 185
mod186 186
mod187 187
mod188 188
mod189 189
mod190 190
mod191 191
mod192 192
mod193 193
mod194 194
mod195 195
mod196 196
mod197 197
mod198 198
mod199 199
mod200 200
mod201 201
mod202 202
mod203 203
mod204 204
mod205 205
mod206 206
mod207 207
mod208 208
mod209 209
mod210 210
mod211 211
mod212 212
mod213 213
mod214 214
mod215 215
mod216 216
mod217 217
mod218 218
mod219 219
mod220 220
mod221 221
mod222 222
mod223 223
mod224 224
mod225 225
mod226 226
mod227 227
mod228 228
mod229 229
mod230 230
max 231
unknown 9999
none 10000
}  


Type MSModType

Is Used By

MSModSpec MSModType ::=
INTEGER {
modaa 0
modn 1
modnaa 2
modc 3
modcaa 4
modnp 5
modnpaa 6
modcp 7
modcpaa 8
modmax 9
}  


Type MSMassSet

Is Used By

MSModSpec MSMassSet ::=
SEQUENCE {
monomass REAL
averagemass REAL
n15mass REAL
}  


Type MSModSpec

Uses

MSMassSet MSMod MSModType

Is Used By

MSModSpecSet MSModSpec ::=
SEQUENCE {
mod MSMod
type MSModType
name VisibleString
monomass REAL
averagemass REAL
n15mass REAL
residues SEQUENCE OF VisibleString OPTIONAL
neutralloss MSMassSet OPTIONAL
unimod INTEGER OPTIONAL
psi-ms VisibleString OPTIONAL
}  


Type MSModSpecSet

Uses

MSModSpec

Is Used By

MSRequest MSSearchSettings MSModSpecSet ::= SEQUENCE OF MSModSpec

Type MSCalcPlusOne

Is Used By

MSChargeHandle MSCalcPlusOne ::=
INTEGER {
dontcalc 0
calc 1
}  


Type MSCalcCharge

Is Used By

MSChargeHandle MSCalcCharge ::=
INTEGER {
calculate 0
usefile 1
userange 2
}  


Type MSChargeHandle

Uses

MSCalcCharge MSCalcPlusOne

Is Used By

MSSearchSettings MSChargeHandle ::=
SEQUENCE {
calcplusone MSCalcPlusOne DEFAULT calc
calccharge MSCalcCharge DEFAULT userange
mincharge INTEGER DEFAULT 2
maxcharge INTEGER DEFAULT 3
considermult INTEGER DEFAULT 3
plusone REAL
maxproductcharge INTEGER OPTIONAL
prodlesspre BOOLEAN OPTIONAL
negative INTEGER DEFAULT 1
}  


Type MSSearchType

Is Used By

MSSearchSettings MSSearchType ::=
INTEGER {
monoisotopic 0
average 1
monon15 2
exact 3
multiisotope 4
max 5
}  


Type MSZdependence

Is Used By

MSSearchSettings MSZdependence ::=
INTEGER {
independent 0
linearwithz 1
max 2
}  


Type MSIterativeSettings

Is Used By

MSSearchSettings MSIterativeSettings ::=
SEQUENCE {
researchthresh REAL
subsetthresh REAL
replacethresh REAL
}  


Type MSLibrarySettings

Is Used By

MSSearchSettings MSLibrarySettings ::=
SEQUENCE {
libnames SEQUENCE OF VisibleString
presearch BOOLEAN
useomssascore BOOLEAN
usereplicatescore BOOLEAN
qtofscore BOOLEAN
}  


Type MSSearchSettings

Uses

MSChargeHandle MSEnzymes MSInFile MSIonType MSIterativeSettings MSLibrarySettings MSMod MSModSpecSet MSOutFile MSSearchType MSZdependence NameValue

Is Used By

MSRequest MSSearchSettingsSet MSSearchSettings ::=
SEQUENCE {
precursorsearchtype MSSearchType
productsearchtype MSSearchType
ionstosearch SEQUENCE OF MSIonType
peptol REAL
msmstol REAL
zdep MSZdependence
cutoff REAL
cutlo REAL
cuthi REAL
cutinc REAL
singlewin INTEGER
doublewin INTEGER
singlenum INTEGER
doublenum INTEGER
fixed SEQUENCE OF MSMod
variable SEQUENCE OF MSMod
enzyme MSEnzymes
missedcleave INTEGER
hitlistlen INTEGER DEFAULT 25
db VisibleString
tophitnum INTEGER
minhit INTEGER DEFAULT 2
minspectra INTEGER DEFAULT 4
scale INTEGER DEFAULT 100
maxmods INTEGER DEFAULT 64
taxids SEQUENCE OF INTEGER OPTIONAL
chargehandling MSChargeHandle OPTIONAL
usermods MSModSpecSet OPTIONAL
pseudocount INTEGER DEFAULT 1
searchb1 INTEGER DEFAULT 0
searchctermproduct INTEGER DEFAULT 0
maxproductions INTEGER DEFAULT 0
minnoenzyme INTEGER DEFAULT 4
maxnoenzyme INTEGER DEFAULT 0
exactmass REAL OPTIONAL
settingid INTEGER OPTIONAL
iterativesettings MSIterativeSettings OPTIONAL
precursorcull INTEGER OPTIONAL
infiles SEQUENCE OF MSInFile OPTIONAL
outfiles SEQUENCE OF MSOutFile OPTIONAL
nocorrelationscore INTEGER OPTIONAL
probfollowingion REAL OPTIONAL
nmethionine BOOLEAN OPTIONAL
automassadjust REAL OPTIONAL
lomasscutoff REAL OPTIONAL
libsearchsettings MSLibrarySettings OPTIONAL
noprolineions SEQUENCE OF MSIonType OPTIONAL
reversesearch BOOLEAN OPTIONAL
othersettings SEQUENCE OF NameValue OPTIONAL
numisotopes INTEGER OPTIONAL
pepppm BOOLEAN OPTIONAL
msmsppm BOOLEAN OPTIONAL
reportedhitcount INTEGER OPTIONAL
}  


Type MSSerialDataFormat

Is Used By

MSOutFile MSSerialDataFormat ::=
INTEGER {
none 0
asntext 1
asnbinary 2
xml 3
csv 4
pepxml 5
xmlbz2 6
}  


Type MSOutFile

Uses

MSSerialDataFormat

Is Used By

MSSearchSettings MSOutFile ::=
SEQUENCE {
outfile VisibleString
outfiletype MSSerialDataFormat
includerequest BOOLEAN
}  


Type MSSpectrumFileType

Is Used By

MSInFile MSSpectrumFileType ::=
INTEGER {
dta 0
dtablank 1
dtaxml 2
asc 3
pkl 4
pks 5
sciex 6
mgf 7
unknown 8
oms 9
omx 10
xml 11
omxbz2 12
}  


Type MSInFile

Uses

MSSpectrumFileType

Is Used By

MSSearchSettings MSInFile ::=
SEQUENCE {
infile VisibleString
infiletype MSSpectrumFileType
}  


Type MSSearchSettingsSet

Uses

MSSearchSettings

Is Used By

MSRequest MSSearchSettingsSet ::= SEQUENCE OF MSSearchSettings

Type MSRequest

Uses

MSModSpecSet MSSearchSettings MSSearchSettingsSet MSSpectrumset

Is Used By

MSSearch MSRequest ::=
SEQUENCE {
spectra MSSpectrumset
settings MSSearchSettings
rid VisibleString OPTIONAL
moresettings MSSearchSettingsSet OPTIONAL
modset MSModSpecSet OPTIONAL
}  


Type MSIonType

Is Used By

MSMZHit MSSearchSettings MSIonType ::=
INTEGER {
a 0
b 1
c 2
x 3
y 4
z 5
parent 6
internal 7
immonium 8
unknown 9
adot 10
x-CO2 11
adot-CO2 12
max 13
}  


Type MSIonNeutralLoss

Is Used By

MSIon MSIonNeutralLoss ::=
INTEGER {
water 0
ammonia 1
}  


Type MSIonIsotopicType

Is Used By

MSIon MSIonIsotopicType ::=
INTEGER {
monoisotopic 0
c13 1
c13two 2
c13three 3
c13four 4
}  


Type MSImmonium

Is Used By

MSIon MSImmonium ::=
SEQUENCE {
parent VisibleString
product VisibleString OPTIONAL
}  


Type MSIon

Uses

MSImmonium MSIonIsotopicType MSIonNeutralLoss

Is Used By

MSMZHit MSIon ::=
SEQUENCE {
neutralloss MSIonNeutralLoss OPTIONAL
isotope MSIonIsotopicType OPTIONAL
internal VisibleString OPTIONAL
immonium MSImmonium OPTIONAL
}  


Type MSIonAnnot

Is Used By

MSMZHit MSIonAnnot ::=
SEQUENCE {
suspect BOOLEAN OPTIONAL
massdiff REAL OPTIONAL
missingisotope BOOLEAN OPTIONAL
}  


Type MSMZHit

Uses

MSIon MSIonAnnot MSIonType

Is Used By

MSHits MSMZHit ::=
SEQUENCE {
ion MSIonType
charge INTEGER
number INTEGER
mz INTEGER
index INTEGER OPTIONAL
moreion MSIon OPTIONAL
annotation MSIonAnnot OPTIONAL
}  


Type MSPepHit

Is Used By

MSHits MSPepHit ::=
SEQUENCE {
start INTEGER
stop INTEGER
gi INTEGER OPTIONAL
accession VisibleString OPTIONAL
defline VisibleString OPTIONAL
protlength INTEGER OPTIONAL
oid INTEGER OPTIONAL
reversed BOOLEAN OPTIONAL
pepstart VisibleString OPTIONAL
pepstop VisibleString OPTIONAL
}  


Type MSModHit

Uses

MSMod

Is Used By

MSHits MSModHit ::=
SEQUENCE {
site INTEGER
modtype MSMod
}  


Type MSScoreSet

Is Used By

MSHits MSScoreSet ::=
SEQUENCE {
name VisibleString
value REAL
}  


Type MSHits

Uses

MSModHit MSMZHit MSPepHit MSScoreSet

Is Used By

MSHitSet MSHits ::=
SEQUENCE {
evalue REAL
pvalue REAL
charge INTEGER
pephits SEQUENCE OF MSPepHit
mzhits SEQUENCE OF MSMZHit OPTIONAL
pepstring VisibleString OPTIONAL
mass INTEGER OPTIONAL
mods SEQUENCE OF MSModHit OPTIONAL
pepstart VisibleString OPTIONAL
pepstop VisibleString OPTIONAL
protlength INTEGER OPTIONAL
theomass INTEGER OPTIONAL
oid INTEGER OPTIONAL
scores SEQUENCE OF MSScoreSet OPTIONAL
libaccession VisibleString OPTIONAL
}  


Type MSHitError

Is Used By

MSHitSet MSHitError ::=
INTEGER {
none 0
generalerr 1
unable2read 2
notenuffpeaks 3
}  


Type MSUserAnnot

Is Used By

MSHitSet MSUserAnnot ::=
INTEGER {
none 0
delete 1
flag 2
}  


Type MSHitSet

Uses

MSHitError MSHits MSUserAnnot NameValue

Is Used By

MSResponse MSHitSet ::=
SEQUENCE {
number INTEGER
error MSHitError OPTIONAL
hits SEQUENCE OF MSHits OPTIONAL
ids SEQUENCE OF VisibleString OPTIONAL
namevalue SEQUENCE OF NameValue OPTIONAL
settingid INTEGER OPTIONAL
userannotation MSUserAnnot OPTIONAL
}  


Type MSResponseError

Is Used By

MSResponse MSResponseError ::=
INTEGER {
none 0
generalerr 1
noblastdb 2
noinput 3
}  


Type MSBioseq

Uses

Bioseq

Is Used By

MSBioseqSet MSBioseq ::=
SEQUENCE {
oid INTEGER
seq Bioseq
}  


Type MSBioseqSet

Uses

MSBioseq

Is Used By

MSResponse MSBioseqSet ::= SEQUENCE OF MSBioseq

Type MSResponse

Uses

MSBioseqSet MSHitSet MSResponseError

Is Used By

MSSearch MSResponse ::=
SEQUENCE {
hitsets SEQUENCE OF MSHitSet
scale INTEGER DEFAULT 100
rid VisibleString OPTIONAL
error MSResponseError OPTIONAL
version VisibleString OPTIONAL
email VisibleString OPTIONAL
dbversion INTEGER OPTIONAL
bioseqs MSBioseqSet OPTIONAL
}  


Type MSSearch

Uses

MSRequest MSResponse MSSearch ::=
SEQUENCE {
request SEQUENCE OF MSRequest OPTIONAL
response SEQUENCE OF MSResponse OPTIONAL
}  


Top-level module index.