diff --git a/PSI-MOD.obo b/PSI-MOD.obo
index 741eb6d..1e7ac7a 100644
--- a/PSI-MOD.obo
+++ b/PSI-MOD.obo
@@ -1,6 +1,6 @@
format-version: 1.2
ontology: mod
-date: 10:02:2021 14:33
+date: 10:03:2021 14:36
saved-by: Paul M. Thomas
subsetdef: PSI-MOD-slim "subset of protein modifications"
synonymtypedef: DeltaMass-label "Label from MS DeltaMass" EXACT
@@ -17,9 +17,9 @@ synonymtypedef: Unimod-description "Description (full_name) from Unimod" RELATED
synonymtypedef: Unimod-interim "Interim label from Unimod" RELATED
synonymtypedef: UniProt-feature "Protein feature description from UniProtKB" EXACT
default-namespace: PSI-MOD
-remark: PSI-MOD version: 1.030.0
+remark: PSI-MOD version: 1.031.2
remark: RESID release: 75.00
-remark: ISO-8601 date: 2021-02-10 14:33Z
+remark: ISO-8601 date: 2021-03-10 14:36Z
remark: Annotation note 01 - "[PSI-MOD:ref]" has been replaced by PubMed:18688235.
remark: Annotation note 02 - When an entry in the RESID Database is annotated with different sources because the same modification can arise from different encoded amino acids, then the PSI-MOD definition for each different source instance carries the RESID cross-reference followed by a hash symbol "#" and a 3 or 4 character label. When an entry in the RESID Database is annotated as a general modification with the same enzymatic activity producing different chemical structures depending on natural variation in the nonproteinaceous substrate, on secondary modifications that do not change the nature of the primary modification, or on a combination of a primary and one or more secondary modifications on the same residue, then the PSI-MOD definition for each different instance carries the RESID cross-reference followed by the special tag "#var".
remark: Annotation note 03 - When an entry in the Unimod database is annotated as a general modification, and one or more instance sites are listed, then the PSI-MOD definition for each different site instance carries the Unimod cross-reference followed by a hash symbol and an amino acid code, "N-term" or "C-term".
@@ -5299,6 +5299,7 @@ xref: MassAvg: "114.10"
xref: MassMono: "114.042927"
xref: Origin: "N"
xref: Source: "natural"
+xref: Source: "natural"
xref: TermSpec: "none"
xref: UniProt: "PTM-0115"
is_a: MOD:00664 ! stereoisomerized residue
@@ -6231,7 +6232,7 @@ xref: Origin: "N"
xref: Source: "artifact"
xref: TermSpec: "none"
xref: Unimod: "Unimod:414"
-is_a: MOD:00160 ! N4-glycosyl-L-asparagine
+is_a: MOD:00903 ! modified L-asparagine residue
[Term]
id: MOD:00242
@@ -21740,7 +21741,7 @@ xref: Formula: "C 6 H 10 N 2 O 2 S 1"
xref: MassAvg: "174.22"
xref: MassMono: "174.046299"
xref: Origin: "C"
-xref: Source: "artifact
+xref: Source: "artifact"
xref: Remap: "MOD:00417"
is_obsolete: true
@@ -33352,7 +33353,7 @@ relationship: contains MOD:01673 ! N-acetylaminohexosylated residue
[Term]
id: MOD:01678
name: N6-carbamoyl-L-lysine
-def: "A protein modification that effectively coverts L-lysine to N6-carbamoyl-L-lysine." [DeltaMass:56, OMSSA:31, PubMed:10978403, PubMed:12203680, Unimod:5#K]
+def: "A protein modification that effectively coverts L-lysine to N6-carbamoyl-L-lysine." [DeltaMass:56, OMSSA:31, PubMed:10978403, PubMed:12203680, Unimod:5#K, ChEBI:144369]
comment: This modification can be produced by hydrogen cyanate, either as a reagent or as released by urea degradation in solution [JSG].
subset: PSI-MOD-slim
synonym: "2-amino-6-ureido-hexanoic acid" EXACT PSI-MOD-alternate []
@@ -33362,6 +33363,7 @@ synonym: "carbamylk" EXACT OMSSA-label []
synonym: "homocitrulline" EXACT PSI-MOD-alternate []
synonym: "N6-(aminocarbonyl)-L-lysine" EXACT PSI-MOD-alternate []
synonym: "N6CbmLys" EXACT PSI-MOD-label []
+synonym: "MOD_RES N6-carbamoyllysine" EXACT UniProt-feature []
xref: DiffAvg: "43.02"
xref: DiffFormula: "C 1 H 1 N 1 O 1"
xref: DiffMono: "43.005814"
@@ -33372,6 +33374,8 @@ xref: Origin: "K"
xref: Source: "artifact"
xref: TermSpec: "none"
xref: Unimod: "Unimod:5"
+xref: UniProt: "PTM-0675"
+is_a: MOD:00912 ! modified L-lysine residue
is_a: MOD:00398 ! carbamoylated residue
[Term]
@@ -38018,26 +38022,25 @@ is_a: MOD:01911 ! monochlorinated residue
[Term]
id: MOD:01914
name: O5-galactosyl-L-hydroxylysine
-def: "A protein modification that effectively converts an L-lysine residue to O5-galactosyl-L-hydroxylysine." [PMID:743239, PubMed:17516569, Unimod:907]
+def: "A protein modification that effectively converts a 5-hydroxy-L-lysine residue to O5-galactosyl-L-hydroxylysine." [PMID:743239, PubMed:17516569, Unimod:907]
comment: Secondary to RESID:AA0028. This intermediate is rarely observed [JSG].
subset: PSI-MOD-slim
synonym: "Galactosyl hydroxylysine" RELATED Unimod-description []
synonym: "OGal5HyLys" EXACT PSI-MOD-label []
synonym: "CARBOHYD O-linked (Gal) hydroxylysine" EXACT UniProt-feature []
-xref: DiffAvg: "178.14"
-xref: DiffFormula: "C 6 H 10 N 0 O 6"
-xref: DiffMono: "178.047738"
+xref: DiffAvg: "162.14"
+xref: DiffFormula: "C 6 H 10 O 5"
+xref: DiffMono: "162.052823"
xref: Formula: "C 16 H 22 N 2 O 7"
xref: MassAvg: "354.36"
xref: MassMono: "354.142701"
-xref: Origin: "K"
+xref: Origin: "MOD:00037"
xref: Source: "natural"
xref: TermSpec: "none"
xref: Unimod: "Unimod:907"
xref: UniProt: "PTM-0556"
-relationship: derives_from MOD:00037 ! 5-hydroxy-L-lysine
-is_a: MOD:00396 ! O-glycosylated residue
is_a: MOD:00476 ! monogalactosylated residue
+is_a: MOD:00396 ! O-glycosylated residue
[Term]
id: MOD:01915
@@ -40673,8 +40676,8 @@ name: crosslinked D-asparagine residue
def: "A protein modification that contains an D-asparagine residue crosslinked to one or more amino acid residues." [PubMed:18688235]
subset: PSI-MOD-slim
synonym: "XlnkDAsn" EXACT PSI-MOD-label []
-xref: Origin: "N"
-is_a: MOD:00203 ! D-asparagine
+xref: Origin: "MOD:00203"
+is_a: MOD:02097 ! modified D-asparagine residue
[Term]
id: MOD:02061
@@ -40993,6 +40996,173 @@ xref: TermSpec: "none"
is_a: MOD:00009 ! natural residue
is_a: MOD:01156 ! protein modification categorized by chemical process
+[Term]
+id: MOD:02089
+name: O-(phospho-5'-uridine)-L-serine
+def: "A protein modification that effectively crosslinks an L-serine residue and 5'-phosphouridine through a phosphodiester bond to form O-(phospho-5'-uridine)-L-serine." [DeltaMass:0, PubMed:22504181, Unimod:417#S, ChEBI:156051]
+subset: PSI-MOD-slim
+synonym: "MOD_RES O-UMP-serine" EXACT UniProt-feature []
+synonym: "OUMPSer" EXACT PSI-MOD-label []
+synonym: "PhosphoUridine" RELATED PSI-MS-label []
+xref: DiffAvg: "306.17"
+xref: DiffFormula: "C 9 H 11 N 2 O 8 P 1"
+xref: DiffMono: "306.025302"
+xref: Formula: "C 12 H 16 N 3 O 9 P 1"
+xref: MassAvg: "377.24"
+xref: MassMono: "377.062416"
+xref: Origin: "S"
+xref: Source: "natural"
+xref: TermSpec: "none"
+xref: Unimod: "Unimod:417"
+xref: UniProt: "PTM-0501"
+is_a: MOD:00916 ! modified L-serine residue
+is_a: MOD:01166 ! uridylated residue
+
+[Term]
+id: MOD:02090
+name: O-(phospho-5'-uridine)-L-threonine
+def: "A protein modification that effectively modifies an L-threonine residue with 5'-phosphouridine through a phosphodiester bond to form O-(phospho-5'-uridine)-L-threonine." [DeltaMass:0, PubMed:22504181, Unimod:417#T, ChEBI:156052]
+subset: PSI-MOD-slim
+synonym: "MOD_RES O-UMP-threonine" EXACT UniProt-feature []
+synonym: "OUMPThr" EXACT PSI-MOD-label []
+synonym: "PhosphoUridine" RELATED PSI-MS-label []
+xref: DiffAvg: "306.17"
+xref: DiffFormula: "C 9 H 11 N 2 O 8 P 1"
+xref: DiffMono: "306.025302"
+xref: Formula: "C 13 H 18 N 3 O 9 P 1"
+xref: MassAvg: "391.27"
+xref: MassMono: "391.078066"
+xref: Origin: "T"
+xref: Source: "natural"
+xref: TermSpec: "none"
+xref: Unimod: "Unimod:417"
+xref: UniProt: "PTM-0502"
+is_a: MOD:00917 ! modified L-threonine residue
+is_a: MOD:01166 ! uridylated residue
+
+[Term]
+id: MOD:02091
+name: O-(phospho-5'-adenosine)-L-serine
+def: "A protein modification that effectively modifies an L-serine residue with 5'-phosphoadenosine through a phosphodiester bond to form O-(phospho-5'-adenosine)-L-serine." [PubMed:21472612, Unimod:405#S]
+subset: PSI-MOD-slim
+synonym: "MOD_RES O-AMP-serine" EXACT UniProt-feature []
+synonym: "Phosphoadenosine" RELATED PSI-MS-label []
+xref: DiffAvg: "329.21"
+xref: DiffFormula: "C 10 H 12 N 5 O 6 P 1"
+xref: DiffMono: "329.052520"
+xref: Formula: "C 13 H 17 N 6 O 8 P 1"
+xref: MassAvg: "416.28"
+xref: MassMono: "416.084549"
+xref: Origin: "S"
+xref: Source: "natural"
+xref: TermSpec: "none"
+xref: Unimod: "Unimod:405"
+xref: UniProt: "PTM-0651"
+is_a: MOD:00916 ! modified L-serine residue
+is_a: MOD:01165 ! adenylated residue
+
+[Term]
+id: MOD:02092
+name: S-methylbutanedioic acid-L-cysteine
+def: "A protein modification that effectively converts an L-cysteine residue to form S-methylbutanedioic acid-L-cysteine by alkylation with itaconate through a thioether bond." [PubMed:29590092]
+subset: PSI-MOD-slim
+synonym: "MOD_RES S-(2,3-dicarboxypropyl)cysteine" EXACT UniProt-feature []
+xref: DiffAvg: "130.10"
+xref: DiffFormula: "C 5 H 6 N 0 O 4 P 0 S 0"
+xref: DiffMono: "130.026609"
+xref: Formula: "C 8 H 11 N 1 O 5 P 0 S 1"
+xref: MassAvg: "233.24"
+xref: MassMono: "233.035793"
+xref: Origin: "C"
+xref: Source: "natural"
+xref: TermSpec: "none"
+xref: UniProt: "PTM-0676"
+is_a: MOD:00905 ! modified L-cysteine residue
+is_a: MOD:00001 ! alkylated residue
+
+[Term]
+id: MOD:02093
+name: N6-(2-hydroxyisobutanoyl)-L-lysine
+def: "A protein modification that effectively converts an L-lysine residue to N6-(2-hydroxyisobutanoyl)-L-lysine." [PubMed:29775581, PubMed:24681537, ChEBI:144968, Unimod:1849]
+synonym: "MOD_RES N6-(2-hydroxyisobutyryl)lysine" EXACT UniProt-feature []
+xref: DiffAvg: "86.09"
+xref: DiffFormula: "C 4 H 6 N 0 O 2"
+xref: DiffMono: "86.036779"
+xref: Formula: "C 10 H 18 N 2 O 3"
+xref: MassAvg: "214.27"
+xref: MassMono: "214.131742"
+xref: Origin: "K"
+xref: Source: "natural"
+xref: TermSpec: "none"
+xref: Unimod: "Unimod:1849"
+xref: UniProt: "PTM-0638"
+is_a: MOD:01875 ! N6-acylated L-lysine
+
+[Term]
+id: MOD:02094
+name: N6-((3R)-3-hydroxybutanoyl)-L-lysine
+def: "A protein modification that effectively converts an L-lysine residue to N6-((3R)-3-hydroxybutanoyl)-L-lysine." [PubMed:27105115, ChEBI:149490]
+synonym: "MOD_RES N6-(beta-hydroxybutyryl)lysine" EXACT UniProt-feature []
+xref: DiffAvg: "86.09"
+xref: DiffFormula: "C 4 H 6 N 0 O 2"
+xref: DiffMono: "86.036779"
+xref: Formula: "C 10 H 18 N 2 O 3"
+xref: MassAvg: "214.27"
+xref: MassMono: "214.131742"
+xref: Origin: "K"
+xref: Source: "natural"
+xref: TermSpec: "none"
+xref: UniProt: "PTM-0499"
+is_a: MOD:01875 ! N6-acylated L-lysine
+
+[Term]
+id: MOD:02095
+name: N6-glutaryl-L-lysine
+def: "A protein modification that effectively converts an L-lysine residue to N6-glutaryl-L-lysine." [PubMed:24703693, ChEBI:87828]
+synonym: "MOD_RES N6-glutaryllysine" EXACT UniProt-feature []
+xref: DiffAvg: "114.10"
+xref: DiffFormula: "C 5 H 6 N 0 O 3"
+xref: DiffMono: "114.031694"
+xref: Formula: "C 11 H 18 N 2 O 4"
+xref: MassAvg: "242.28"
+xref: MassMono: "242.126657"
+xref: Origin: "K"
+xref: Source: "natural"
+xref: TermSpec: "none"
+xref: UniProt: "PTM-0487"
+is_a: MOD:01875 ! N6-acylated L-lysine
+
+[Term]
+id: MOD:02096
+name: N4-methyl-D-asparagine
+def: "A protein modification that effectively converts a D-asparagine residue to N4-methyl-D-asparagine." [PubMed:22983711, ChEBI:149514]
+subset: PSI-MOD-slim
+synonym: "MOD_RES N4-methyl-D-asparagine" EXACT UniProt-feature []
+synonym: "N4-methylated D-asparagine" EXACT PSI-MOD-alternate []
+xref: DiffAvg: "14.03"
+xref: DiffFormula: "C 1 H 2 N 0 O 0"
+xref: DiffMono: "14.015650"
+xref: Formula: "C 5 H 8 N 2 O 2"
+xref: MassAvg: "128.13"
+xref: MassMono: "128.058578"
+xref: Origin: "N"
+xref: Source: "natural"
+xref: TermSpec: "none"
+xref: UniProt: "PTM-0691"
+is_a: MOD:00599 ! monomethylated residue
+is_a: MOD:00602 ! N-methylated residue
+is_a: MOD:00673 ! methylated asparagine
+is_a: MOD:02097 ! modified D-asparagine residue
+is_a: MOD:00894 ! residues isobaric at 128.058578 Da
+
+[Term]
+id: MOD:02097
+name: modified D-asparagine residue
+def: "A protein modification that modifies a D-asparagine residue." [PubMed:18688235]
+subset: PSI-MOD-slim
+synonym: "ModDAsn" EXACT PSI-MOD-label []
+is_a: MOD:00203 ! D-asparagine
+
[Typedef]
id: contains
name: contains
diff --git a/PSI-MOD.owl b/PSI-MOD.owl
index 041ac68..69441e3 100644
--- a/PSI-MOD.owl
+++ b/PSI-MOD.owl
@@ -10,7 +10,7 @@
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
- 10:02:2021 14:33
+ 10:03:2021 14:36
PSI-MOD
1.2
Paul M. Thomas
@@ -24,8 +24,8 @@
Annotation note 08 - The DeltaMass listings for free amino acids have been removed. Most Unimod entries that have not been "approved" have by general agreement not been incorporated unless there has been a request for a specific term by a PRIDE submitter.
Annotation note 09 - The Open Mass Spectrometry Search Algorithm, OMSSA, enumerated list of modifications are being incorporated. The string values are synonyms with the synonymtypedef "OMSSA-label", and their integer values (which are supposed to be stable) are definition cross-references.
Annotation note 10 - GNOme is the Glycan Naming and Subsumption Ontology (https://gnome.glyomics.org/), an ontology for the support of glycomics. PSI-MOD does not have all possible glycans in its entries, just the ones that are noted to be on proteins and have been requested for addition. GNOme uses GlyTouCan (http://glytoucan.org/) to provide stable accessions for glycans described at varyious degrees of characterization, including compositions (no linkage) and topologies (no carbon bond positions or anomeric configurations).
- ISO-8601 date: 2021-02-10 14:33Z
- PSI-MOD version: 1.030.0
+ ISO-8601 date: 2021-03-10 14:36Z
+ PSI-MOD version: 1.031.2
RESID release: 75.00
@@ -35909,7 +35909,7 @@
-
+
A protein modification that effectively converts an L-asparagine residue to N4-hydroxymethyl-L-asparagine.
DiffAvg:
DiffFormula:
@@ -180542,6 +180542,7 @@
+
A protein modification that effectively coverts L-lysine to N6-carbamoyl-L-lysine.
DiffAvg:
DiffFormula:
@@ -180552,8 +180553,10 @@
Origin:
Source:
TermSpec:
+ UniProt:
Unimod:
2-amino-6-ureido-hexanoic acid
+ MOD_RES N6-carbamoyllysine
N6-(aminocarbonyl)-L-lysine
N6CbmLys
carbamylk
@@ -180570,6 +180573,7 @@
A protein modification that effectively coverts L-lysine to N6-carbamoyl-L-lysine.
+ ChEBI:144369
DeltaMass:56
OMSSA:31
PubMed:10978403
@@ -180630,6 +180634,12 @@
TermSpec:
none
+
+
+
+ UniProt:
+ PTM-0675
+
@@ -180642,6 +180652,12 @@
2-amino-6-ureido-hexanoic acid
+
+
+
+ MOD_RES N6-carbamoyllysine
+
+
@@ -205165,13 +205181,7 @@
-
-
-
-
-
-
- A protein modification that effectively converts an L-lysine residue to O5-galactosyl-L-hydroxylysine.
+ A protein modification that effectively converts a 5-hydroxy-L-lysine residue to O5-galactosyl-L-hydroxylysine.
DiffAvg:
DiffFormula:
DiffMono:
@@ -205195,7 +205205,7 @@
- A protein modification that effectively converts an L-lysine residue to O5-galactosyl-L-hydroxylysine.
+ A protein modification that effectively converts a 5-hydroxy-L-lysine residue to O5-galactosyl-L-hydroxylysine.
PMID:743239
PubMed:17516569
Unimod:907
@@ -205204,19 +205214,19 @@
DiffAvg:
- 178.14
+ 162.14
DiffFormula:
- C 6 H 10 N 0 O 6
+ C 6 H 10 O 5
DiffMono:
- 178.047738
+ 162.052823
@@ -205240,7 +205250,7 @@
Origin:
- K
+ MOD:00037
@@ -218868,7 +218878,7 @@
-
+
A protein modification that contains an D-asparagine residue crosslinked to one or more amino acid residues.
Origin:
XlnkDAsn
@@ -218887,7 +218897,7 @@
Origin:
- N
+ MOD:00203
@@ -220260,6 +220270,888 @@
TermSpec:
none
+
+
+
+
+
+
+
+
+ A protein modification that effectively crosslinks an L-serine residue and 5'-phosphouridine through a phosphodiester bond to form O-(phospho-5'-uridine)-L-serine.
+ DiffAvg:
+ DiffFormula:
+ DiffMono:
+ Formula:
+ MassAvg:
+ MassMono:
+ Origin:
+ Source:
+ TermSpec:
+ UniProt:
+ Unimod:
+ MOD_RES O-UMP-serine
+ OUMPSer
+ PSI-MOD
+ PhosphoUridine
+ MOD:02089
+
+ O-(phospho-5'-uridine)-L-serine
+
+
+
+
+ A protein modification that effectively crosslinks an L-serine residue and 5'-phosphouridine through a phosphodiester bond to form O-(phospho-5'-uridine)-L-serine.
+ ChEBI:156051
+ DeltaMass:0
+ PubMed:22504181
+ Unimod:417#S
+
+
+
+
+ DiffAvg:
+ 306.17
+
+
+
+
+ DiffFormula:
+ C 9 H 11 N 2 O 8 P 1
+
+
+
+
+ DiffMono:
+ 306.025302
+
+
+
+
+ Formula:
+ C 12 H 16 N 3 O 9 P 1
+
+
+
+
+ MassAvg:
+ 377.24
+
+
+
+
+ MassMono:
+ 377.062416
+
+
+
+
+ Origin:
+ S
+
+
+
+
+ Source:
+ natural
+
+
+
+
+ TermSpec:
+ none
+
+
+
+
+ UniProt:
+ PTM-0501
+
+
+
+
+ Unimod:
+ Unimod:417
+
+
+
+
+ MOD_RES O-UMP-serine
+
+
+
+
+
+ OUMPSer
+
+
+
+
+
+ PhosphoUridine
+
+
+
+
+
+
+
+
+
+
+ A protein modification that effectively modifies an L-threonine residue with 5'-phosphouridine through a phosphodiester bond to form O-(phospho-5'-uridine)-L-threonine.
+ DiffAvg:
+ DiffFormula:
+ DiffMono:
+ Formula:
+ MassAvg:
+ MassMono:
+ Origin:
+ Source:
+ TermSpec:
+ UniProt:
+ Unimod:
+ MOD_RES O-UMP-threonine
+ OUMPThr
+ PSI-MOD
+ PhosphoUridine
+ MOD:02090
+
+ O-(phospho-5'-uridine)-L-threonine
+
+
+
+
+ A protein modification that effectively modifies an L-threonine residue with 5'-phosphouridine through a phosphodiester bond to form O-(phospho-5'-uridine)-L-threonine.
+ ChEBI:156052
+ DeltaMass:0
+ PubMed:22504181
+ Unimod:417#T
+
+
+
+
+ DiffAvg:
+ 306.17
+
+
+
+
+ DiffFormula:
+ C 9 H 11 N 2 O 8 P 1
+
+
+
+
+ DiffMono:
+ 306.025302
+
+
+
+
+ Formula:
+ C 13 H 18 N 3 O 9 P 1
+
+
+
+
+ MassAvg:
+ 391.27
+
+
+
+
+ MassMono:
+ 391.078066
+
+
+
+
+ Origin:
+ T
+
+
+
+
+ Source:
+ natural
+
+
+
+
+ TermSpec:
+ none
+
+
+
+
+ UniProt:
+ PTM-0502
+
+
+
+
+ Unimod:
+ Unimod:417
+
+
+
+
+ MOD_RES O-UMP-threonine
+
+
+
+
+
+ OUMPThr
+
+
+
+
+
+ PhosphoUridine
+
+
+
+
+
+
+
+
+
+
+ A protein modification that effectively modifies an L-serine residue with 5'-phosphoadenosine through a phosphodiester bond to form O-(phospho-5'-adenosine)-L-serine.
+ DiffAvg:
+ DiffFormula:
+ DiffMono:
+ Formula:
+ MassAvg:
+ MassMono:
+ Origin:
+ Source:
+ TermSpec:
+ UniProt:
+ Unimod:
+ MOD_RES O-AMP-serine
+ PSI-MOD
+ Phosphoadenosine
+ MOD:02091
+
+ O-(phospho-5'-adenosine)-L-serine
+
+
+
+
+ A protein modification that effectively modifies an L-serine residue with 5'-phosphoadenosine through a phosphodiester bond to form O-(phospho-5'-adenosine)-L-serine.
+ PubMed:21472612
+ Unimod:405#S
+
+
+
+
+ DiffAvg:
+ 329.21
+
+
+
+
+ DiffFormula:
+ C 10 H 12 N 5 O 6 P 1
+
+
+
+
+ DiffMono:
+ 329.052520
+
+
+
+
+ Formula:
+ C 13 H 17 N 6 O 8 P 1
+
+
+
+
+ MassAvg:
+ 416.28
+
+
+
+
+ MassMono:
+ 416.084549
+
+
+
+
+ Origin:
+ S
+
+
+
+
+ Source:
+ natural
+
+
+
+
+ TermSpec:
+ none
+
+
+
+
+ UniProt:
+ PTM-0651
+
+
+
+
+ Unimod:
+ Unimod:405
+
+
+
+
+ MOD_RES O-AMP-serine
+
+
+
+
+
+ Phosphoadenosine
+
+
+
+
+
+
+
+
+
+
+ A protein modification that effectively converts an L-cysteine residue to form S-methylbutanedioic acid-L-cysteine by alkylation with itaconate through a thioether bond.
+ DiffAvg:
+ DiffFormula:
+ DiffMono:
+ Formula:
+ MassAvg:
+ MassMono:
+ Origin:
+ Source:
+ TermSpec:
+ UniProt:
+ MOD_RES S-(2,3-dicarboxypropyl)cysteine
+ PSI-MOD
+ MOD:02092
+
+ S-methylbutanedioic acid-L-cysteine
+
+
+
+
+ A protein modification that effectively converts an L-cysteine residue to form S-methylbutanedioic acid-L-cysteine by alkylation with itaconate through a thioether bond.
+ PubMed:29590092
+
+
+
+
+ DiffAvg:
+ 130.10
+
+
+
+
+ DiffFormula:
+ C 5 H 6 N 0 O 4 P 0 S 0
+
+
+
+
+ DiffMono:
+ 130.026609
+
+
+
+
+ Formula:
+ C 8 H 11 N 1 O 5 P 0 S 1
+
+
+
+
+ MassAvg:
+ 233.24
+
+
+
+
+ MassMono:
+ 233.035793
+
+
+
+
+ Origin:
+ C
+
+
+
+
+ Source:
+ natural
+
+
+
+
+ TermSpec:
+ none
+
+
+
+
+ UniProt:
+ PTM-0676
+
+
+
+
+ MOD_RES S-(2,3-dicarboxypropyl)cysteine
+
+
+
+
+
+
+
+
+
+ A protein modification that effectively converts an L-lysine residue to N6-(2-hydroxyisobutanoyl)-L-lysine.
+ DiffAvg:
+ DiffFormula:
+ DiffMono:
+ Formula:
+ MassAvg:
+ MassMono:
+ Origin:
+ Source:
+ TermSpec:
+ UniProt:
+ Unimod:
+ MOD_RES N6-(2-hydroxyisobutyryl)lysine
+ PSI-MOD
+ MOD:02093
+ N6-(2-hydroxyisobutanoyl)-L-lysine
+
+
+
+
+ A protein modification that effectively converts an L-lysine residue to N6-(2-hydroxyisobutanoyl)-L-lysine.
+ ChEBI:144968
+ PubMed:24681537
+ PubMed:29775581
+ Unimod:1849
+
+
+
+
+ DiffAvg:
+ 86.09
+
+
+
+
+ DiffFormula:
+ C 4 H 6 N 0 O 2
+
+
+
+
+ DiffMono:
+ 86.036779
+
+
+
+
+ Formula:
+ C 10 H 18 N 2 O 3
+
+
+
+
+ MassAvg:
+ 214.27
+
+
+
+
+ MassMono:
+ 214.131742
+
+
+
+
+ Origin:
+ K
+
+
+
+
+ Source:
+ natural
+
+
+
+
+ TermSpec:
+ none
+
+
+
+
+ UniProt:
+ PTM-0638
+
+
+
+
+ Unimod:
+ Unimod:1849
+
+
+
+
+ MOD_RES N6-(2-hydroxyisobutyryl)lysine
+
+
+
+
+
+
+
+
+
+ A protein modification that effectively converts an L-lysine residue to N6-((3R)-3-hydroxybutanoyl)-L-lysine.
+ DiffAvg:
+ DiffFormula:
+ DiffMono:
+ Formula:
+ MassAvg:
+ MassMono:
+ Origin:
+ Source:
+ TermSpec:
+ UniProt:
+ MOD_RES N6-(beta-hydroxybutyryl)lysine
+ PSI-MOD
+ MOD:02094
+ N6-((3R)-3-hydroxybutanoyl)-L-lysine
+
+
+
+
+ A protein modification that effectively converts an L-lysine residue to N6-((3R)-3-hydroxybutanoyl)-L-lysine.
+ ChEBI:149490
+ PubMed:27105115
+
+
+
+
+ DiffAvg:
+ 86.09
+
+
+
+
+ DiffFormula:
+ C 4 H 6 N 0 O 2
+
+
+
+
+ DiffMono:
+ 86.036779
+
+
+
+
+ Formula:
+ C 10 H 18 N 2 O 3
+
+
+
+
+ MassAvg:
+ 214.27
+
+
+
+
+ MassMono:
+ 214.131742
+
+
+
+
+ Origin:
+ K
+
+
+
+
+ Source:
+ natural
+
+
+
+
+ TermSpec:
+ none
+
+
+
+
+ UniProt:
+ PTM-0499
+
+
+
+
+ MOD_RES N6-(beta-hydroxybutyryl)lysine
+
+
+
+
+
+
+
+
+
+ A protein modification that effectively converts an L-lysine residue to N6-glutaryl-L-lysine.
+ DiffAvg:
+ DiffFormula:
+ DiffMono:
+ Formula:
+ MassAvg:
+ MassMono:
+ Origin:
+ Source:
+ TermSpec:
+ UniProt:
+ MOD_RES N6-glutaryllysine
+ PSI-MOD
+ MOD:02095
+ N6-glutaryl-L-lysine
+
+
+
+
+ A protein modification that effectively converts an L-lysine residue to N6-glutaryl-L-lysine.
+ ChEBI:87828
+ PubMed:24703693
+
+
+
+
+ DiffAvg:
+ 114.10
+
+
+
+
+ DiffFormula:
+ C 5 H 6 N 0 O 3
+
+
+
+
+ DiffMono:
+ 114.031694
+
+
+
+
+ Formula:
+ C 11 H 18 N 2 O 4
+
+
+
+
+ MassAvg:
+ 242.28
+
+
+
+
+ MassMono:
+ 242.126657
+
+
+
+
+ Origin:
+ K
+
+
+
+
+ Source:
+ natural
+
+
+
+
+ TermSpec:
+ none
+
+
+
+
+ UniProt:
+ PTM-0487
+
+
+
+
+ MOD_RES N6-glutaryllysine
+
+
+
+
+
+
+
+
+
+
+
+
+
+ A protein modification that effectively converts a D-asparagine residue to N4-methyl-D-asparagine.
+ DiffAvg:
+ DiffFormula:
+ DiffMono:
+ Formula:
+ MassAvg:
+ MassMono:
+ Origin:
+ Source:
+ TermSpec:
+ UniProt:
+ MOD_RES N4-methyl-D-asparagine
+ N4-methylated D-asparagine
+ PSI-MOD
+ MOD:02096
+
+ N4-methyl-D-asparagine
+
+
+
+
+ A protein modification that effectively converts a D-asparagine residue to N4-methyl-D-asparagine.
+ ChEBI:149514
+ PubMed:22983711
+
+
+
+
+ DiffAvg:
+ 14.03
+
+
+
+
+ DiffFormula:
+ C 1 H 2 N 0 O 0
+
+
+
+
+ DiffMono:
+ 14.015650
+
+
+
+
+ Formula:
+ C 5 H 8 N 2 O 2
+
+
+
+
+ MassAvg:
+ 128.13
+
+
+
+
+ MassMono:
+ 128.058578
+
+
+
+
+ Origin:
+ N
+
+
+
+
+ Source:
+ natural
+
+
+
+
+ TermSpec:
+ none
+
+
+
+
+ UniProt:
+ PTM-0691
+
+
+
+
+ MOD_RES N4-methyl-D-asparagine
+
+
+
+
+
+ N4-methylated D-asparagine
+
+
+
+
+
+
+
+
+
+ A protein modification that modifies a D-asparagine residue.
+ ModDAsn
+ PSI-MOD
+ MOD:02097
+
+ modified D-asparagine residue
+
+
+
+
+ A protein modification that modifies a D-asparagine residue.
+ PubMed:18688235
+
+
+
+
+ ModDAsn
+
+
diff --git a/README.md b/README.md
index afb189c..c1809a7 100644
--- a/README.md
+++ b/README.md
@@ -3,8 +3,15 @@
This repository contains the Human Proteome Organization (HUPO) Proteomics Standards Initiative (PSI) Mass Modifications Ontology (PSI-MOD). The content here was moved from the old SourceForge CVS site (https://sourceforge.net/projects/psidev/). It is the source repository of the PSI-MOD obo file, main deliverable PSI-MOD, which is reactivated in this repository.
## The PSI working group PSI-MOD
-The joint activies PSI-MOD working group is reactivated after a long stand-by period. Description on the project can be found [here](http://www.psidev.info/groups/protein-modifications).
+The joint activities PSI-MOD working group has been reactivated after a long stand-by period. Description of the project can be found [here](http://www.psidev.info/groups/protein-modifications).
-If you would like to comment on the PSI-MOD document, please submit a new issue through github.
+If you would like to comment on the PSI-MOD document, please submit a new issue through [GitHub](https://github.com/HUPO-PSI/psi-mod-CV/issues).
-The link (http://psidev.cvs.sourceforge.net/viewvc/*checkout*/psidev/psi/mod/data/psi-mod.obo) found in various files is supposed to be safely substituted with the link for the corresponding file (https://raw.githubusercontent.com/HUPO-PSI/psi-mod-CV/master/PSI-MOD.obo)
+This link (http://psidev.cvs.sourceforge.net/viewvc/*checkout*/psidev/psi/mod/data/psi-mod.obo) found in various files can be safely substituted with the PSI-MOD PURL: (http://purl.obolibrary.org/obo/mod.obo).
+
+## OBO-XML and OWL Files
+The OBO-XML [file format](http://www-legacy.geneontology.org/GO.format.shtml#OBO-XML) has been deprecated in favor of the more highly supported OWL [file format](https://www.w3.org/OWL/). Pull Requests MUST include updated OBO and OWL files. The [ROBOT Tool](http://robot.obolibrary.org/) is used to create compliant OWL files from the OBO using this syntax:
+
+ robot.bat convert --input "path-to-obo-file\psi-mod.obo" --output "path-to-obo-file\psi-mod.owl"
+
+Note that the master source file for this ontology is the obo file and the OWL file is a derivative of it.