736 lines
24 KiB
Groff
736 lines
24 KiB
Groff
-- $Id: omssa.asn 192083 2010-05-19 22:28:08Z lewisg $
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--**********************************************************************
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--
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-- OMSSA (Open Mass Spectrometry Search Algorithm) data definitions
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-- Lewis Geer, 2003
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--
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-- make using something like
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-- "datatool -m omssa.asn -oc ObjOmssa -oA -od omssa.def"
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--
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-- note that this file requires omssa.def
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--
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--**********************************************************************
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OMSSA DEFINITIONS ::=
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BEGIN
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IMPORTS Bioseq FROM NCBI-Sequence;
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-- Generic holder for experimental info
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NameValue ::= SEQUENCE {
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name VisibleString,
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value VisibleString
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}
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-- Holds a single spectrum
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MSSpectrum ::= SEQUENCE {
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number INTEGER, -- unique number of spectrum
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charge SEQUENCE OF INTEGER, -- may be more than one if unknown
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precursormz INTEGER, -- scaled precursor m/z, scale is in MSSearchSettings
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mz SEQUENCE OF INTEGER, -- scaled product m/z
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abundance SEQUENCE OF INTEGER, -- scaled product abundance
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iscale REAL, -- abundance scale, float to integer
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ids SEQUENCE OF VisibleString OPTIONAL, -- ids/filenames
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namevalue SEQUENCE OF NameValue OPTIONAL -- extra info: retention times, etc.
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}
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-- Holds a set of spectra
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MSSpectrumset ::= SEQUENCE OF MSSpectrum
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-- enumerate enzymes
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MSEnzymes ::= INTEGER {
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trypsin (0),
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argc (1),
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cnbr (2),
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chymotrypsin (3),
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formicacid (4),
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lysc (5),
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lysc-p (6),
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pepsin-a (7),
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tryp-cnbr (8),
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tryp-chymo (9),
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trypsin-p (10),
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whole-protein (11),
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aspn (12),
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gluc (13),
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aspngluc (14),
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top-down (15),
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semi-tryptic (16),
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no-enzyme (17),
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chymotrypsin-p (18),
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aspn-de (19),
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gluc-de (20),
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lysn (21),
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thermolysin-p (22),
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semi-chymotrypsin (23),
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semi-gluc (24),
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max(25),
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none (255)
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}
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-- enumerate modifications
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MSMod ::= INTEGER {
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methylk (0), -- methylation of K
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oxym (1), -- oxidation of methionine
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carboxymethylc (2), -- carboxymethyl cysteine
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carbamidomethylc(3), -- carbamidomethyl cysteine
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deamidationkq (4), -- deamidation of K and Q
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propionamidec (5), -- propionamide cysteine
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phosphorylations (6), -- phosphorylation of S
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phosphorylationt (7), -- phosphorylation of T
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phosphorylationy (8), -- phosphorylation of Y
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ntermmcleave (9), -- N terminal methionine cleavage
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ntermacetyl (10), -- N terminal protein acetyl
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ntermmethyl (11), -- N terminal protein methyl
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ntermtrimethyl (12), -- N terminal protein trimethyl
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methythiold (13), -- beta methythiolation of D
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methylq (14), -- methylation of Q
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trimethylk (15), -- trimethylation of K
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methyld (16), -- methylation of D
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methyle (17), -- methylation of E
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ctermpepmethyl (18), -- C terminal methylation
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trideuteromethyld (19), -- trideuteromethylation of D
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trideuteromethyle (20), -- trideuteromethylation of E
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ctermpeptrideuteromethyl (21), -- C terminal trideuteromethylation
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nformylmet (22),
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twoamino3oxobutanoicacid (23),
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acetylk (24),
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ctermamide (25),
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bmethylthiold (26),
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carbamidomethylk (27),
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carbamidometylh (28),
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carbamidomethyld (29),
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carbamidomethyle (30),
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carbamylk (31),
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ntermcarbamyl (32),
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citrullinationr (33),
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cysteicacidc (34),
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diiodinationy (35),
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dimethylk (36),
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dimethylr (37),
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ntermpepdimethyl (38),
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dihydroxyf (39),
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thioacetylk (40),
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ntermpeptioacetyl (41),
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farnesylationc (42),
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formylk (43),
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ntermpepformyl (44),
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formylkynureninw (45),
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phef (46),
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gammacarboxyld (47),
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gammacarboxyle (48),
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geranylgeranylc (49),
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ntermpepglucuronylg (50),
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glutathionec (51),
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glyglyk (52),
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guanidinationk (53),
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his2asnh (54),
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his2asph (55),
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ctermpephsem (56),
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ctermpephselactm (57),
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hydroxykynureninw (58),
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hydroxylationd (59),
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hydroxylationk (60),
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hydroxylationn (61),
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hydroxylationp (62),
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hydroxylationf (63),
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hydroxylationy (64),
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iodinationy (65),
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kynureninw (66),
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lipoylk (67),
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ctermpepmeester (68),
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meesterd (69),
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meestere (70),
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meesters (71),
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meestery (72),
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methylc (73),
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methylh (74),
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methyln (75),
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ntermpepmethyl (76),
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methylr (77),
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ntermpepmyristoyeylationg (78),
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ntermpepmyristoyl4hg (79),
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ntermpepmyristoylationg (80),
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myristoylationk (81),
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ntermformyl (82),
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nemc (83),
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nipcam (84),
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nitrow (85),
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nitroy (86),
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ctermpepo18 (87),
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ctermpepdio18 (88),
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oxyh (89),
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oxyw (90),
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ppantetheines (91),
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palmitoylationc (92),
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palmitoylationk (93),
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palmitoylations (94),
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palmitoylationt (95),
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phospholosss (96),
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phospholosst (97),
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phospholossy (98),
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phosphoneutrallossc (99),
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phosphoneutrallossd (100),
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phosphoneutrallossh (101),
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propionylk (102),
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ntermpeppropionyl (103),
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propionylheavyk (104),
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ntermpeppropionylheavy (105),
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pyridylk (106),
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ntermpeppyridyl (107),
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ntermpeppyrocmc (108),
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ntermpeppyroe (109),
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ntermpeppyroq (110),
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pyroglutamicp (111),
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spyridylethylc (112),
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semetm (113),
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sulfationy (114),
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suphonem (115),
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triiodinationy (116),
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trimethylationr (117),
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ntermpeptripalmitatec (118),
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usermod1 (119), -- start of user defined mods
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usermod2 (120),
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usermod3 (121),
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usermod4 (122),
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usermod5 (123),
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usermod6 (124),
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usermod7 (125),
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usermod8 (126),
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usermod9 (127),
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usermod10 (128), -- end of user defined mods
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icatlight (129),
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icatheavy (130),
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camthiopropanoylk (131),
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phosphoneutrallosss (132),
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phosphoneutrallosst (133),
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phosphoetdlosss (134),
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phosphoetdlosst (135),
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arg-13c6 (136),
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arg-13c6-15n4 (137),
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lys-13c6 (138),
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oxy18 (139),
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beta-elim-s (140),
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beta-elim-t (141),
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usermod11 (142),
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usermod12 (143),
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usermod13 (144),
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usermod14 (145),
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usermod15 (146),
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usermod16 (147),
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usermod17 (148),
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usermod18 (149),
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usermod19 (150),
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usermod20 (151),
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usermod21 (152),
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usermod22 (153),
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usermod23 (154),
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usermod24 (155),
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usermod25 (156),
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usermod26 (157),
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usermod27 (158),
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usermod28 (159),
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usermod29 (160),
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usermod30 (161),
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sulfinicacid (162),
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arg2orn (163),
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dehydro (164),
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carboxykynurenin (165),
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sumoylation (166),
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iTRAQ114nterm (167),
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iTRAQ114K (168),
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iTRAQ114Y (169),
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iTRAQ115nterm (170),
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iTRAQ115K (171),
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iTRAQ115Y (172),
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iTRAQ116nterm (173),
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iTRAQ116K (174),
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iTRAQ116Y (175),
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iTRAQ117nterm (176),
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iTRAQ117K (177),
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iTRAQ117Y (178),
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mmts (179),
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lys-2H4 (180),
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lys-13C615N2 (181),
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hexNAcN (182),
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dHexHexNAcN (183),
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hexNAcS (184),
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hexNAcT (185),
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mod186 (186),
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mod187 (187),
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mod188 (188),
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mod189 (189),
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mod190 (190),
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mod191 (191),
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mod192 (192),
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mod193 (193),
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mod194 (194),
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mod195 (195),
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mod196 (196),
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mod197 (197),
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mod198 (198),
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mod199 (199),
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mod200 (200),
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mod201 (201),
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mod202 (202),
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mod203 (203),
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mod204 (204),
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mod205 (205),
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mod206 (206),
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mod207 (207),
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mod208 (208),
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mod209 (209),
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mod210 (210),
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mod211 (211),
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mod212 (212),
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mod213 (213),
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mod214 (214),
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mod215 (215),
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mod216 (216),
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mod217 (217),
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mod218 (218),
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mod219 (219),
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mod220 (220),
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mod221 (221),
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mod222 (222),
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mod223 (223),
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mod224 (224),
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mod225 (225),
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mod226 (226),
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mod227 (227),
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mod228 (228),
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mod229 (229),
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mod230 (230),
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max (231), -- maximum number of mods
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unknown(9999), -- modification of unknown type
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none(10000)
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}
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-- enumerate modification types
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MSModType ::= INTEGER {
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modaa (0), -- at particular amino acids
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modn (1), -- at the N terminus of a protein
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modnaa (2), -- at the N terminus of a protein at particular amino acids
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modc (3), -- at the C terminus of a protein
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modcaa (4), -- at the C terminus of a protein at particular amino acids
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modnp (5), -- at the N terminus of a peptide
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modnpaa (6), -- at the N terminus of a peptide at particular amino acids
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modcp (7), -- at the C terminus of a peptide
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modcpaa (8), -- at the C terminus of a peptide at particular amino acids
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modmax (9) -- the max number of modification types
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}
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-- mass container
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MSMassSet ::= SEQUENCE {
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monomass REAL,
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averagemass REAL,
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n15mass REAL
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}
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-- Modification Definition
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MSModSpec ::= SEQUENCE {
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mod MSMod, -- what is the mod
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type MSModType, -- modification type
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name VisibleString, -- friendly name of mod
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monomass REAL, -- monoisotopic mass
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averagemass REAL, -- average mass
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n15mass REAL, -- monoisotopic n15 mass
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residues SEQUENCE OF VisibleString OPTIONAL, -- residues to apply mod to
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neutralloss MSMassSet OPTIONAL, -- loss after precursor mass determination
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unimod INTEGER OPTIONAL, -- the equivalent Unimod Accession number
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psi-ms VisibleString OPTIONAL -- the PSI-MS equivalent name
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}
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-- Holds a set of modifications
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MSModSpecSet ::= SEQUENCE OF MSModSpec
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-- How is charge to be handled? Some input files are not clear
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-- on this. For example, a dta file only specifies one charge,
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-- even though the charge is not really known.
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MSCalcPlusOne ::= INTEGER {
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dontcalc (0), -- don't guess charge one
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calc (1) -- guess charge one
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}
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-- user instructions on whether to believe charges in input file
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MSCalcCharge ::= INTEGER {
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calculate (0), -- guess the charge(s) from the data
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usefile (1), -- use what the input file says
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userange (2) -- use the charge range specified
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}
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-- How to handle precursor charge
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MSChargeHandle ::= SEQUENCE {
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calcplusone MSCalcPlusOne DEFAULT 1, -- do we guess charge one?
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calccharge MSCalcCharge DEFAULT 2, -- how do we handle charges?
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mincharge INTEGER DEFAULT 2, -- if userange, what is the min?
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maxcharge INTEGER DEFAULT 3, -- if userange, what is the max?
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considermult INTEGER DEFAULT 3, -- at which precursor charge to consider +2 ions?
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plusone REAL, -- what % of peaks below precursor needed to call as +1
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maxproductcharge INTEGER OPTIONAL, -- maximum product ion charge
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prodlesspre BOOLEAN OPTIONAL, -- product charge always less thanor equal to precursor?
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negative INTEGER DEFAULT 1 -- negative ion search if -1, positive ion if 1
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}
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-- what type of atomic mass to use
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MSSearchType ::= INTEGER {
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monoisotopic(0),
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average(1),
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monon15(2),
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exact(3),
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multiisotope(4),
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max(5)
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}
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-- what is the charge dependence of the mass tolerance?
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MSZdependence ::= INTEGER {
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independent(0), -- mass tol. invariant with charge
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linearwithz(1), -- mass tol. scales with charge
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max(2)
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}
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-- Iterative search settings
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MSIterativeSettings ::= SEQUENCE {
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researchthresh REAL, -- e-val threshold for re-searching spectra, 0 = always re-search
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subsetthresh REAL, -- e-val threshold for picking sequence subset, 0 = all sequences
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replacethresh REAL -- e-val threshold for replacing hitset, 0 = only if better
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}
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-- Library search settings
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MSLibrarySettings ::= SEQUENCE {
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libnames SEQUENCE OF VisibleString, -- names of search libraries
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presearch BOOLEAN, -- should there be a restriction on precursor mass?
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useomssascore BOOLEAN, -- use the omssa score?
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usereplicatescore BOOLEAN, -- use the number of replicates score?
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qtofscore BOOLEAN -- use the qtof score?
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}
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-- Generic search settings
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MSSearchSettings ::= SEQUENCE {
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precursorsearchtype MSSearchType, -- average or monoisotopic?
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productsearchtype MSSearchType, -- average or monoisotopic?
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ionstosearch SEQUENCE OF MSIonType, -- which ions to search?
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peptol REAL, -- peptide mass tolerance
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msmstol REAL, -- msms mass tolerance
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zdep MSZdependence, -- what is the charge dependence of the mass tolerance?
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cutoff REAL, -- evalue cutoff
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-- next 3 fields define intensity fraction below
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-- which peaks will be discard
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cutlo REAL, -- the start of the cutoff, fraction of most intense peak
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cuthi REAL, -- the end of the cutoff
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cutinc REAL, -- the increment of the cutoff
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singlewin INTEGER, -- the size of the single charge filtering window
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doublewin INTEGER, -- the size of the double charge filtering window
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singlenum INTEGER, -- the number of peaks allowed in the single window
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doublenum INTEGER, -- the number of peaks allowed in the double window
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fixed SEQUENCE OF MSMod, -- fixed PTM's
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variable SEQUENCE OF MSMod, -- variable PTM's
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enzyme MSEnzymes, -- digestion enzyme
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missedcleave INTEGER, -- number of missed cleaves allowed
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hitlistlen INTEGER DEFAULT 25, -- the number of hits kept in memory
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-- for a spectrum
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db VisibleString, -- sequence set to search, e.g. "nr"
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tophitnum INTEGER, -- number of m/z to consider in first pass
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minhit INTEGER DEFAULT 2, -- minimum number of m/z values for a valid hit
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minspectra INTEGER DEFAULT 4, -- minimum number of m/z for a valid spectra
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scale INTEGER DEFAULT 100, -- scale for m/z float to integer
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maxmods INTEGER DEFAULT 64, -- maximum number of mass ladders per
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-- database peptide
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taxids SEQUENCE OF INTEGER OPTIONAL, -- taxa to limit search
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chargehandling MSChargeHandle OPTIONAL, -- how to deal with charges
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usermods MSModSpecSet OPTIONAL, -- user defined modifications
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pseudocount INTEGER DEFAULT 1, -- min number of counts per precursor bin
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searchb1 INTEGER DEFAULT 0, -- should b1 product be in search (1=no, 0=yes)
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searchctermproduct INTEGER DEFAULT 0, -- should c terminus ion be searched (1=no, 0=yes)
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maxproductions INTEGER DEFAULT 0, -- max number of ions in each series (0=all)
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minnoenzyme INTEGER DEFAULT 4, -- min number of AA in peptide for noenzyme search
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maxnoenzyme INTEGER DEFAULT 0, -- max number of AA in peptide for noenzyme search (0=none)
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exactmass REAL OPTIONAL, -- the threshold in Da for adding neutron
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settingid INTEGER OPTIONAL, -- id of the search settings
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iterativesettings MSIterativeSettings OPTIONAL, -- iterative search settings
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precursorcull INTEGER OPTIONAL, -- turn on aggressive precursor culling for ETD (0=none)
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infiles SEQUENCE OF MSInFile OPTIONAL, -- input files
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outfiles SEQUENCE OF MSOutFile OPTIONAL, -- output files
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nocorrelationscore INTEGER OPTIONAL, -- turn on correlation score (1=nocorr)
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probfollowingion REAL OPTIONAL, -- probability of a consecutive ion (used in correlation)
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nmethionine BOOLEAN OPTIONAL, -- should nmethionine be cleaved?
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automassadjust REAL OPTIONAL, -- fraction allowable adjustment of product mass tolerance
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lomasscutoff REAL OPTIONAL, -- low mass filter in Daltons, unscaled
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libsearchsettings MSLibrarySettings OPTIONAL, -- library search settings
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noprolineions SEQUENCE OF MSIonType OPTIONAL, -- which ions to use no proline rule
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reversesearch BOOLEAN OPTIONAL, -- do reverse search
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othersettings SEQUENCE OF NameValue OPTIONAL, -- extra search settings
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numisotopes INTEGER OPTIONAL, -- number of isotopic peaks to search when using MSSearchType multiisotope
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pepppm BOOLEAN OPTIONAL, -- search precursor as ppm
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msmsppm BOOLEAN OPTIONAL, -- search product as ppm
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reportedhitcount INTEGER OPTIONAL -- the maximum number of hits to report per spectrum, 0=all
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}
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MSSerialDataFormat ::= INTEGER {
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none (0) ,
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asntext (1), -- open ASN.1 text format
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asnbinary (2), -- open ASN.1 binary format
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xml (3), -- open XML format
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csv (4), -- csv (excel)
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pepxml (5), -- pepXML format
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xmlbz2 (6) -- bzip2 XML format
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}
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MSOutFile ::= SEQUENCE {
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outfile VisibleString, -- output file name
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outfiletype MSSerialDataFormat, -- output file type
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includerequest BOOLEAN -- should the output include the request?
|
|
}
|
|
|
|
MSSpectrumFileType ::= INTEGER {
|
|
dta(0),
|
|
dtablank(1),
|
|
dtaxml(2),
|
|
asc(3),
|
|
pkl(4),
|
|
pks(5),
|
|
sciex(6),
|
|
mgf(7),
|
|
unknown(8),
|
|
oms(9), -- asn.1 binary for iterative search
|
|
omx(10), -- xml for iterative search
|
|
xml(11), -- xml MSRequest
|
|
omxbz2 (12) -- bzip2 omx file
|
|
}
|
|
|
|
MSInFile ::= SEQUENCE {
|
|
infile VisibleString, -- input file name
|
|
infiletype MSSpectrumFileType -- input file type
|
|
}
|
|
|
|
MSSearchSettingsSet ::= SEQUENCE OF MSSearchSettings
|
|
|
|
-- The search request that is given to the OMSSA algorithm
|
|
|
|
MSRequest ::= SEQUENCE {
|
|
spectra MSSpectrumset, -- the set of spectra
|
|
settings MSSearchSettings, -- the search settings
|
|
rid VisibleString OPTIONAL, -- request id
|
|
moresettings MSSearchSettingsSet OPTIONAL, -- additional search runs
|
|
modset MSModSpecSet OPTIONAL -- list of mods that can be used in search
|
|
}
|
|
|
|
|
|
-- enumeration of ion types
|
|
|
|
MSIonType ::= INTEGER {
|
|
a (0),
|
|
b (1),
|
|
c (2),
|
|
x (3),
|
|
y (4),
|
|
z (5), -- actually zdot
|
|
parent(6),
|
|
internal(7),
|
|
immonium(8),
|
|
unknown(9),
|
|
adot (10),
|
|
x-CO2 (11),
|
|
adot-CO2 (12),
|
|
max (13)
|
|
}
|
|
|
|
-- types of neutral loss
|
|
|
|
MSIonNeutralLoss ::= INTEGER {
|
|
water (0), -- minus 18 Da
|
|
ammonia (1) -- minus 17 Da
|
|
}
|
|
|
|
-- iosotopic type of ion
|
|
|
|
MSIonIsotopicType ::= INTEGER {
|
|
monoisotopic (0), -- no c13s in molecule
|
|
c13 (1), -- one c13 in molecule
|
|
c13two (2), -- two c13s in molecule, and so on...
|
|
c13three (3),
|
|
c13four (4)
|
|
}
|
|
|
|
-- type of immonium ion
|
|
|
|
MSImmonium ::= SEQUENCE {
|
|
parent VisibleString, -- parent amino acid
|
|
product VisibleString OPTIONAL -- product ion code
|
|
}
|
|
|
|
-- ion type at a finer level than ion series
|
|
|
|
MSIon ::= SEQUENCE {
|
|
neutralloss MSIonNeutralLoss OPTIONAL, -- is this peak a neutral loss?
|
|
isotope MSIonIsotopicType OPTIONAL, -- isotopic composition of peak
|
|
internal VisibleString OPTIONAL, -- if iontype is internal, this is the internal sequence
|
|
immonium MSImmonium OPTIONAL -- if iontype is immonium, show characteristics
|
|
}
|
|
|
|
-- annotated comments about the ion
|
|
|
|
MSIonAnnot ::= SEQUENCE {
|
|
suspect BOOLEAN OPTIONAL, -- is this peak suspect?
|
|
massdiff REAL OPTIONAL, -- what is the difference in mass from library spectrum?
|
|
missingisotope BOOLEAN OPTIONAL -- are the lower mass peaks missing?
|
|
}
|
|
|
|
-- defines a particular ion
|
|
|
|
MSMZHit ::= SEQUENCE {
|
|
ion MSIonType, -- ion type, e.g. b
|
|
charge INTEGER, -- ion charge
|
|
number INTEGER, -- the sequential number of the ion
|
|
mz INTEGER, -- scaled m/z value in Da
|
|
index INTEGER OPTIONAL, -- the index of the peak in the original spectrum
|
|
moreion MSIon OPTIONAL, -- more information about the ion type
|
|
annotation MSIonAnnot OPTIONAL -- annotations on the ion
|
|
}
|
|
|
|
|
|
-- contains information about sequences with identical peptide
|
|
-- sequences
|
|
|
|
MSPepHit ::= SEQUENCE {
|
|
start INTEGER, -- start position (inclusive) in sequence
|
|
stop INTEGER, -- stop position (inclusive) in sequence
|
|
gi INTEGER OPTIONAL, -- genbank identifier
|
|
accession VisibleString OPTIONAL, -- sequence accession
|
|
defline VisibleString OPTIONAL, -- sequence description
|
|
protlength INTEGER OPTIONAL, -- length of protein
|
|
oid INTEGER OPTIONAL, -- blast library oid
|
|
reversed BOOLEAN OPTIONAL, -- reversed sequence
|
|
pepstart VisibleString OPTIONAL, -- AA before the peptide
|
|
pepstop VisibleString OPTIONAL -- AA after the peptide
|
|
}
|
|
|
|
-- modifications to a hit peptide
|
|
|
|
MSModHit ::= SEQUENCE {
|
|
site INTEGER, -- the position in the peptide
|
|
modtype MSMod -- the type of modification
|
|
}
|
|
|
|
|
|
-- sets of scores
|
|
|
|
MSScoreSet ::= SEQUENCE {
|
|
name VisibleString,
|
|
value REAL
|
|
}
|
|
|
|
-- hits to a given spectrum
|
|
|
|
MSHits ::= SEQUENCE {
|
|
evalue REAL, -- E-value (expect value)
|
|
pvalue REAL, -- P-value (probability value)
|
|
charge INTEGER, -- the charge state used in search. -1 == not +1
|
|
pephits SEQUENCE OF MSPepHit, -- peptides that match this hit
|
|
mzhits SEQUENCE OF MSMZHit OPTIONAL, -- ions hit
|
|
pepstring VisibleString OPTIONAL, -- the peptide sequence
|
|
mass INTEGER OPTIONAL, -- scaled experimental mass of peptide in Da
|
|
mods SEQUENCE OF MSModHit OPTIONAL, -- modifications to sequence
|
|
pepstart VisibleString OPTIONAL, -- AA before the peptide (depricated)
|
|
pepstop VisibleString OPTIONAL, -- AA after the peptide (depricated)
|
|
protlength INTEGER OPTIONAL, -- length of protein hit (depricated)
|
|
theomass INTEGER OPTIONAL, -- scaled theoretical mass of peptide hit
|
|
oid INTEGER OPTIONAL, -- blast library oid (depricated)
|
|
scores SEQUENCE OF MSScoreSet OPTIONAL, -- optional scores (for library search)
|
|
libaccession VisibleString OPTIONAL -- library search accesssion
|
|
}
|
|
|
|
|
|
-- error return for a particular spectrum's hitset
|
|
|
|
MSHitError ::= INTEGER {
|
|
none (0),
|
|
generalerr (1),
|
|
unable2read (2), -- can't read the spectrum
|
|
notenuffpeaks (3) -- not enough peaks to search
|
|
}
|
|
|
|
-- MSHitSet annotation by end user
|
|
|
|
MSUserAnnot ::= INTEGER {
|
|
none (0),
|
|
delete (1),
|
|
flag (2)
|
|
}
|
|
|
|
-- contains a set of hits to a single spectrum
|
|
|
|
MSHitSet ::= SEQUENCE {
|
|
number INTEGER, -- unique number of spectrum
|
|
error MSHitError OPTIONAL, -- error, if any
|
|
hits SEQUENCE OF MSHits OPTIONAL, -- set of hit to spectrum
|
|
ids SEQUENCE OF VisibleString OPTIONAL, -- filenames or other ids of spectra searched
|
|
namevalue SEQUENCE OF NameValue OPTIONAL,-- extra info: retention times, etc.
|
|
settingid INTEGER OPTIONAL, -- id of the search setting used
|
|
userannotation MSUserAnnot OPTIONAL -- allows users to flag certain
|
|
}
|
|
|
|
|
|
-- error return for the entire response
|
|
|
|
MSResponseError ::= INTEGER {
|
|
none (0),
|
|
generalerr (1),
|
|
noblastdb (2), -- unable to open blast library
|
|
noinput (3) -- input missing
|
|
}
|
|
|
|
|
|
-- bioseq container
|
|
|
|
MSBioseq ::= SEQUENCE {
|
|
oid INTEGER, -- blast library oid
|
|
seq Bioseq
|
|
}
|
|
|
|
MSBioseqSet ::= SEQUENCE OF MSBioseq
|
|
|
|
-- search results
|
|
|
|
MSResponse ::= SEQUENCE {
|
|
hitsets SEQUENCE OF MSHitSet, -- hits grouped by spectrum
|
|
scale INTEGER DEFAULT 100, -- scale to change m/z float to integer
|
|
rid VisibleString OPTIONAL, -- request id
|
|
error MSResponseError OPTIONAL, -- error response
|
|
version VisibleString OPTIONAL, -- version of OMSSA
|
|
email VisibleString OPTIONAL, -- email address for notification
|
|
dbversion INTEGER OPTIONAL, -- version of db searched (usually size)
|
|
bioseqs MSBioseqSet OPTIONAL -- sequences found in search
|
|
}
|
|
|
|
-- holds both search requests and responses
|
|
|
|
MSSearch ::= SEQUENCE {
|
|
request SEQUENCE OF MSRequest OPTIONAL,
|
|
response SEQUENCE OF MSResponse OPTIONAL
|
|
}
|
|
|
|
END
|