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new_cv_terms.txt
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[Term]
id: MS:XXXXX0
name: complex modification
def: "Declares a modification to be a complex structure or unordered molecular composition." [PSI:PI]
is_a: MS:1001471 ! peptide modification details
[Term]
id: MS:XXXXX1
name: glycosylation modification
def: "Declares a modification to be a glycan or glycan aggregate." [PSI:PI]
is_a: MS:XXXXX0 ! complex modification
[Term]
id: MS:XXXXX2
name: monosaccharide count
def: "A single type of known monosaccharide or substituent with an associated quantity present in a glycan composition." [PSI:PI]
is_a: MS:1001471 ! peptide modification details
has_regexp: MS:XXXX99 ! (Hex|HexNAc|dHex|Fuc|NeuAc|NeuGc|Pen|S|P):(\d+)
[Term]
id: MS:XXXXX3
name: unknown monosaccharide count
def: "A single type of unknown or user-defined monosaccharide or substituent with an associated unit mass and quantity present in a glycan composition." [PSI:PI]
is_a: MS:1001471 ! peptide modification details
has_regexp: MS:XXX100 ! ([^:]):(\d+(.\d+?)?):(\d+)
[Term]
id: MS:XXXXX4
name: glycan class
def: "The type of glycosylation event that the identification process assumed." [PSI:PI]
is_a: MS:1001471 ! peptide modification details
[Term]
id: MS:XXXXX5
name: N-glycan
def: "A glycan that is co-translationally attached to an asparagine amine, usually at a canonical motif N[^P][ST]." [PSI:PI]
is_a: MS:XXXXX4 ! glycan class
[Term]
id: MS:XXXXX6
name: O-glycan
def: "A glycan that is co-translationally attached to a hydroxyl group, usually on a serine or threonine." [PSI:PI]
is_a: MS:XXXXX4 ! glycan class
[Term]
id: MS:XXXX16
name: O-GalNAc O-glycan
def: "An O-linked glycan initiated by the addition of a GalNAc residue, usually the basis for mucin-type O-glycans." [PSI:PI]
is_a: MS:XXXXX6 ! O-glycan
[Term]
id: MS:XXXXX7
name: glycosaminoglycan
def: "A glycan that is co-translationally attached to a serine or occaisionally other amino acid hydroxyl group usually at a canonical motif S[AG]X[AG]." [PSI:PI]
is_a: MS:XXXXX4 ! glycan class
[Term]
id: MS:XXXX11
name: other glycan class
def: "A glycan class not covered by any other terms." [PSI:PI]
is_a: MS:XXXXX4 ! glycan class
[Term]
id: MS:XXXX12
name: glycan interpretation
def: "How the glycan molecule was interpreted by the identification software." [PSI:PI]
is_a: MS:1001471 ! peptide modification details
[Term]
id: MS:XXXX13
name: glycan topology
def: "The glycan was interpreted to have a defined topology with or without defined linkage." [PSI:PI]
is_a: MS:XXXX12 ! glycan interpretation
[Term]
id: MS:XXXX14
name: glycan composition
def: "The glycan was interpreted without taking into account monosaccharide connectivity." [PSI:PI]
is_a: MS:XXXX12 ! glycan interpretation
[Term]
id: MS:XXXX15
name: glycan aggregate
def: "In addition to being treated as a composition, this glycan is an aggregate across multiple glycosylation sites." [PSI:PI]
is_a: MS:XXXX12 ! glycan composition
[Term]
id: MS:XXXX16
name: glycosylated ion series
def: "Denotes a glycopeptide ion series including a combination of peptide and glycan reaction products" [PSI:PI]
is_a: MS:1002473 ! ion series considered in search
[Term]
id: MS:XXXX17
name: param: peptide + glycan Y ion
def: "Parameter information, type of product: intact peptide with reducing end glycan Y fragment attached" [PSI:PI]
is_a: MS:XXXX16 ! glycosylated ion series
[Term]
id: MS:XXXX18
name: param: peptide b + glycan Y ion
def: "Parameter information, type of product: peptide b fragment with reducing end glycan Y fragment attached" [PSI:PI]
is_a: MS:XXXX16 ! glycosylated ion series
[Term]
id: MS:XXXX19
name: param: peptide y + glycan Y ion
def: "Parameter information, type of product: peptide y fragment with reducing end glycan Y fragment attached" [PSI:PI]
is_a: MS:XXXX16 ! glycosylated ion series
[Term]
id: MS:XXXX20
name: param: peptide c + glycan Y ion
def: "Parameter information, type of product: peptide c fragment with reducing end glycan Y fragment attached" [PSI:PI]
is_a: MS:XXXX16 ! glycosylated ion series
[Term]
id: MS:XXXX21
name: param: peptide z + glycan Y ion
def: "Parameter information, type of product: peptide z fragment with reducing end glycan Y fragment attached" [PSI:PI]
is_a: MS:XXXX16 ! glycosylated ion series
[Term]
id: MS:XXXX22
name: param: oxonium ion
def: "Parameter information, type of product: glycan oxonium ion" [PSI:PI]
is_a: MS:XXXX16 ! glycosylated ion series
[Term]
id: MS:XXXX98
name: glycopeptide search
def: "glycopeptide search performed." [PSI:PI]
is_a: MS:1002489 ! special processing
[Term]
id: MS:XXXX99
name: (Hex|HexNAc|dHex|Fuc|NeuAc|NeuGc|Pen|S|P):(\d+)
def: "The pattern for a known monosaccharide with an associated count present in the glycan composition." [PSI:PI]
relationship: part_of MS:1001471 ! peptide modification details
is_a: MS:1002479 ! regular expression
[Term]
id: MS:XXX100
name: ([^:]):(\d+(.\d+?)?):(\d+)
def: "A single type of unknown monosaccharide or substituent with an associated quantity present in a glycan composition." [PSI:PI]
relationship: part_of MS:1001471 ! peptide modification details
is_a: MS:1002479 ! regular expression
[Term]
name: glycopeptide confidence measure
id: MS:XXX101
def: "Parent term glycopeptide scoring values." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001153 ! search engine specific score
[Term]
name: glycopeptide peptide score
id: MS:XXX102
def: "glycopeptide scoring value describing the evidence for the peptide sequence." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:XXX101 ! glycopeptide confidence measure
[Term]
name: glycopeptide glycan score
id: MS:XXX103
def: "glycopeptide scoring value describing the evidence for the attached glycan or glycans." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:XXX101 ! glycopeptide confidence measure
[Term]
name: glycopeptide score
id: MS:XXX104
def: "glycopeptide scoring value describing the evidence for the glycopeptide combining all sources of evidence." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:XXX101 ! glycopeptide confidence measure
[Term]
id: MS:XXX105
name: glycopeptide false discovery rate dimension control strategy
def: "Parent term for strategies used to control glycopeptide false discovery rates." [PSI:PI]
is_a: MS:1002489 ! special processing
[Term]
id: MS:XXX106
name: peptide glycopeptide false discovery rate control strategy
def: "The false discovery rate of the peptide sequence of a glycopeptide identification was controlled for." [PSI:PI]
is_a: MS:XXX105 ! glycopeptide false discovery rate dimension control strategy
[Term]
id: MS:XXX107
name: glycan glycopeptide false discovery rate control strategy
def: "The false discovery rate of the glycan structure or composition of a glycopeptide identification was controlled for." [PSI:PI]
is_a: MS:XXX105 ! glycopeptide false discovery rate dimension control strategy
[Term]
id: MS:XXX108
name: glycopeptide false discovery rate control strategy
def: "The false discovery rate of the glycopeptide identification was controlled for." [PSI:PI]
is_a: MS:XXX105 ! glycopeptide false discovery rate dimension control strategy
[Term]
id: MS:XXX11A
name: joint glycopeptide false discovery rate control strategy
def: "The false discovery rate of the glycopeptide identification was controlled for through a combination of separate false discovery rates from multiple statistics." [PSI:PI]
is_a: MS:XXX105 ! glycopeptide false discovery rate dimension control strategy
[Term]
id: MS:XXX109
name: glycopeptide attribute
def: "Glycopeptide attribute." [PSI:PI]
is_a: MS:1002694 ! single identification result attribute
[Term]
id: MS:XXX110
name: glycan dissociation mode
def: "Parent term for describing what kind of dissociation the search engine expected the glycan to undergo for a given spectrum." [PSI:PI]
is_a: MS:XXX109 ! glycopeptide attribute
[Term]
id: MS:XXX111
name: glycan dissociating, peptide preserving
def: "Indicates that the glycan dissociation products were considered, with the peptide mostly intact, as is case with lower energy collisional dissociation methods." [PSI:PI]
is_a: MS:XXX110 ! glycan dissociation mode
[Term]
id: MS:XXX112
name: glycan preserving, peptide dissociating
def: "Indicates that the glycan was assumed to be mostly intact in the generated product ions, as is the case with electron-driven dissociation methods." [PSI:PI]
is_a: MS:XXX110 ! glycan dissociation mode
[Term]
id: MS:XXX113
name: glycan dissociating, peptide dissociating
def: "Indicates that the glycopeptide dissociated along both the peptide and the glycan structures, producing a mixture of product ions, as is commonly the case for combinations of electron-based and collisional dissociation (e.g. EThcD)." [PSI:PI]
is_a: MS:XXX110 ! glycan dissociation mode
[Term]
id: MS:XXX114
name: glycan eliminated, peptide dissociating
def: "Indicates that the glycopeptide dissociated along both the peptide and the glycan structures, almost entirely eliminating the glycan while dissociating the peptide, as is common with higher energy collisional dissociation methods." [PSI:PI]
is_a: MS:XXX110 ! glycan dissociation mode
[Term]
id: MS:XXX115
name: glycan-specific statistic
def: "A statistic for a spectrum match or structure-level identification that describes evidence for the glycan or glycans attached to a glycopeptide."
is_a: MS:XXX109 ! glycopeptide attribute
[Term]
id: MS:XXX116
name: peptide-specific statistic
def: "A statistic for a spectrum match or structure-level identification that describes evidence for the peptide sequence of a glycopeptide."
is_a: MS:XXX109 ! glycopeptide attribute
[Term]
id: MS:XXX117
name: glycopeptide statistic
def: "A statistic for a spectrum match or structure-level identification that describes evidence for a glycopeptide in total, combining peptide and glycan evidence."
is_a: MS:XXX109 ! glycopeptide attribute
[Term]
id: MS:XXX118
name: joint glycopeptide statistic
def: "A statistic for a spectrum match or structure-level identification that describes evidence for a glycopeptide jointly, combining separate statistics from multiple sources of evidence."
is_a: MS:XXX109 ! glycopeptide attribute