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Update gptmd mods #2446

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Update gptmd mods #2446

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72ab679
parallel
trishorts Nov 26, 2024
99a08c4
threadsafeHashset
trishorts Nov 26, 2024
f31a6e6
new top down mods
trishorts Nov 26, 2024
f5f6ee9
unused code
trishorts Nov 26, 2024
8edf0bc
ninetyNine percent of human ptms in uniprot as common biological mods
trishorts Dec 3, 2024
7325742
hmmm
trishorts Dec 3, 2024
9027034
merge upstream
trishorts Dec 3, 2024
978542b
asfd
trishorts Dec 3, 2024
fc9a022
modlist update
trishorts Dec 3, 2024
a539322
update top-down mods
trishorts Dec 3, 2024
6a12c89
jf
trishorts Dec 4, 2024
fe72c6a
d
trishorts Dec 4, 2024
5bab206
gptmd mods updated
trishorts Dec 5, 2024
d7f735f
Merge branch 'master' into updateGptmdMods
trishorts Dec 6, 2024
58d280f
Merge remote-tracking branch 'upstream/master' into updateGptmdMods
trishorts Dec 9, 2024
dfb5474
Merge branch 'updateGptmdMods' of https://github.com/trishorts/MetaMo…
trishorts Dec 9, 2024
31d75bd
Merge remote-tracking branch 'upstream/master' into updateGptmdMods
trishorts Dec 11, 2024
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14 changes: 0 additions & 14 deletions MetaMorpheus/EngineLayer/Data/ptmlist.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -1738,20 +1738,6 @@ TR Eukaryota; taxId:9258 (Ornithorhynchus anatinus).
DR RESID; AA0515.
DR PSI-MOD; MOD:01618.
//
ID Allysine
AC PTM-0059
FT MOD_RES
TG Lysine.
PA Amino acid side chain.
PP Anywhere.
CF H-3 N-1 O1
MM -1.031634
MA -1.03
LC Extracellular and lumenal localisation.
TR Eukaryota; taxId:6052 (Ephydatia muelleri), taxId:7742 (Vertebrata).
DR RESID; AA0121.
DR PSI-MOD; MOD:00130.
//
ID Aminomalonic acid (Ser)
AC PTM-0321
FT MOD_RES
Expand Down
246 changes: 116 additions & 130 deletions MetaMorpheus/EngineLayer/Mods/Mods.txt
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Original file line number Diff line number Diff line change
@@ -1,19 +1,5 @@
Custom List
################################## COMMON BIOLOGICAL MODS
ID Hydroxylation
TG K or N
PP Anywhere.
CF O1
MT Common Biological
DR Unimod; 35.
//
ID Carboxylation
TG K or D or E
PP Anywhere.
MT Common Biological
CF C1 O2
DR Unimod; 299.
//
ID Phosphorylation
TG S or T
PP Anywhere.
Expand All @@ -32,37 +18,23 @@ DI HCD:C8 H10 N1 O4 P1
DR Unimod; 21.
//
ID Acetylation
TG X
PP N-terminal.
MT Common Biological
CF H2 C2 O1
DR Unimod; 1.
//
ID Acetylation
TG K
TG K or A or M or S or T or G or P
PP Anywhere.
MT Common Biological
NL ETD:45.0204
DI HCD:C7 H11 N1 O1
CF H2 C2 O1
DR Unimod; 1.
//
ID Lactylation
TG K
PP Anywhere.
MT Less Common
CF H3 C3 O2
//
ID Formylation
TG K
PP Anywhere.
ID Acetylation
TG X
PP N-terminal.
MT Common Biological
DI HCD:111.068423533
CF C1 O1
DR Unimod; 122.
CF H2 C2 O1
DR Unimod; 1.
//
ID Methylation
TG K or R
TG K or R or Q
PP Anywhere.
MT Common Biological
CF H2 C
Expand All @@ -84,13 +56,13 @@ MT Common Biological
CF H4 C2
DR Unimod; 36.
//
ID Trimethylation
TG K
ID Hydroxylation
TG P or K or N
PP Anywhere.
MT Common Biological
CF H6 C3
NL ETD:45.0204
DR Unimod; 37.
CF O1
DI HCD:170.069143
DR Unimod; 35.
//
ID Sulfonation
TG Y
Expand All @@ -100,6 +72,14 @@ MT Common Biological
CF O3 S1
DR Unimod; 40.
//
ID Trimethylation
TG K
PP Anywhere.
MT Common Biological
CF H6 C3
NL ETD:45.0204
DR Unimod; 37.
//
ID Citrullination
TG R
PP Anywhere.
Expand All @@ -109,80 +89,13 @@ NL HCD:43.0058
CF H-1 N-1 O1
DR Unimod; 7.
//
ID Hydroxylation
TG P
PP Anywhere.
MT Common Biological
CF O1
DI HCD:170.069143
DR Unimod; 35.
//
ID Nitrosylation
TG Y
PP Anywhere.
MT Common Biological
CF H-1 N1 O2
DI HCD:180.053523533
DR Unimod; 354.
//
ID Butyrylation
TG K
PP Anywhere.
MT Common Biological
DI HCD:153.115323533
CF C4 H6 O1
DR Unimod; 1289.
//
ID Crotonylation
TG K
PP Anywhere.
MT Common Biological
DI HCD:151.099723533
CF C4 H4 O1
DR Unimod; 1363.
//
ID Glutarylation
TG K
PP Anywhere.
MT Common Biological
DI HCD:181.110323533
NL ETD:115.0395
CF C5 H6 O3
DR Unimod; 1848.
//
ID Hydroxybutyrylation
TG K
PP Anywhere.
MT Common Biological
DI HCD:169.110323533
CF C4 H6 O2
//
ID Malonylation
ID Allysine
TG K
PA Amino acid side chain.
PP Anywhere.
MT Common Biological
DI HCD:C7 H11 N1 O1
DI HCD:169.073923533
NL HCD:43.9898
NL ETD:87.0082
CF C3 H2 O3
DR Unimod; 747.
//
ID Succinylation
TG K
PP Anywhere.
MT Common Biological
DI HCD:183.089523533
NL ETD:101.0239
CF C4 H4 O3
DR Unimod; 64.
//
ID Glu to PyroGlu
TG Q
PP N-terminal.
MT Common Biological
CF H-3 N-1
DR Unimod; 28.
CF H-3 N-1 O1
DR Unimod; 352.
//
ID HexNAc
TG Nxs or Nxt
Expand All @@ -200,26 +113,27 @@ CF C8H13NO5
MT Common Biological
DR Unimod; 43.
//
ID ADP-ribosylation
TG S
ID Carboxylation
TG E or D or K
PP Anywhere.
MT Common Biological
CF C15 H21 N5 O13 P2
DR Unimod; 213.
CF C1 O2
DR Unimod; 299.
//
ID Pyridoxal phosphate
ID Formylation
TG K
PP Anywhere.
MT Common Biological
CF C8 H8 N1 O5 P1
DR Unimod; 46.
CF C1 O1
DR Unimod; 122.
//
ID Nitrosylation
TG C
ID Crotonylation
TG K
PP Anywhere.
MT Common Biological
CF H-1 N1 O1
DR Unimod; 275.
DI HCD:151.099723533
CF C4 H4 O1
DR Unimod; 1363.
//
################################## COMMON ARTIFACT MODS
ID Deamidation
Expand Down Expand Up @@ -264,7 +178,86 @@ MT Common Artifact
CF H1 C1 N1 O1
DR Unimod; 5.
//

################################## LESS COMMON MODS
ID Succinylation
TG K or C
PP Anywhere.
MT Less Common
DI HCD:183.089523533
NL ETD:101.0239
CF C4 H4 O3
DR Unimod; 64.
//
ID Hydroxybutyrylation
TG K
PP Anywhere.
MT Less Common
DI HCD:169.110323533
CF C4 H6 O2
//
ID Lactylation
TG K
PP Anywhere.
MT Less Common
CF H3 C3 O2
//
ID Glutarylation
TG K
PP Anywhere.
MT Less Common
DI HCD:181.110323533
NL ETD:115.0395
CF C5 H6 O3
DR Unimod; 1848.
//
ID Glu to PyroGlu
TG Q
PP N-terminal.
MT Less Common
CF H-3 N-1
DR Unimod; 28.
//
ID Nitrosylation
TG C or Y
PP Anywhere.
MT Less Common
CF H-1 N1 O1
DR Unimod; 275.
//
ID Butyrylation
TG K
PP Anywhere.
MT Less Common
DI HCD:153.115323533
CF C4 H6 O1
DR Unimod; 1289.
//
ID ADP-ribosylation
TG S or E or R or C
PP Anywhere.
MT Less Common
CF C15 H21 N5 O13 P2
DR Unimod; 213.
//
ID Pyridoxal phosphate
TG K
PP Anywhere.
MT Less Common
CF C8 H8 N1 O5 P1
DR Unimod; 46.
//
ID Malonylation
TG K
PP Anywhere.
MT Less Common
DI HCD:C7 H11 N1 O1
DI HCD:169.073923533
NL HCD:43.9898
NL ETD:87.0082
CF C3 H2 O3
DR Unimod; 747.
//
ID Proline pyrrole to pyrrolidine six member ring
TG P
PP Anywhere.
Expand Down Expand Up @@ -334,13 +327,6 @@ MT Less Common
CF H3 C2 N1 O1
DR Unimod; 4.
//
ID Acetylation
TG S or T
PP Anywhere.
MT Less Common
CF H2 C2 O1
DR Unimod; 1.
//
ID Biotinylation
TG K
PP Anywhere.
Expand Down Expand Up @@ -413,7 +399,7 @@ CF C1 O1
DR Unimod; 122.
//
ID Methylation
TG C or H or N or Q or I or L or D or E or S or T
TG C or H or N or I or L or D or E or S or T
PP Anywhere.
MT Less Common
CF H2 C
Expand Down
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