Update gptmd mods

[trishorts]

Recently reanalyzed modification counts in the human uniprot xml. Table below. I aimed to update the gptmd mod collection to contain all mods such that ~99% of those below were covered. After some back and forth with the previous list, I arrived at the mods in this PR. Any mods removed from the previous common biological set were placed into the less common list.

Note, I moved allysine from the uniprot ptmlist to the common biological.

Note also the big increase in the modification list used for top-down. Will post below the effect observed from this change on the jenkins top-down dataset.

Modification Count in UniProt Running Fraction
Phosphoserine 33146 0.598865361
Phosphothreonine 6013 0.70750524
N6-acetyllysine 4321 0.785574908
Phosphotyrosine 2136 0.824167088
N6-succinyllysine 1265 0.847022476
Omega-N-methylarginine 1027 0.865577799
N-acetylalanine 949 0.882723856
N-acetylmethionine 847 0.898027029
Asymmetric dimethylarginine 548 0.907928019
4-hydroxyproline 450 0.916058394
N6-(2-hydroxyisobutyryl)lysine 420 0.923646744
N-acetylserine 410 0.931054419
N6-(beta-hydroxybutyryl)lysine 277 0.936059117
N6-lactoyllysine 272 0.940973477
N6-glutaryllysine 264 0.945743297
N6-methyllysine 256 0.950368577
N6-crotonyllysine 222 0.954379562
Sulfotyrosine 151 0.957107755
Cysteine methyl ester 129 0.959438462
N6,N6-dimethyllysine 122 0.961642697
N6,N6,N6-trimethyllysine 120 0.963810797
Citrulline 117 0.965924695
4-carboxyglutamate 104 0.967803715
Hydroxyproline 104 0.969682735
Pyrrolidone carboxylic acid 96 0.971417215
N-acetylthreonine 81 0.972880682
S-nitrosocysteine 80 0.974326082
5-hydroxylysine 78 0.975735347
Dimethylated arginine 71 0.97701814
N6-butyryllysine 62 0.978138325
3'-nitrotyrosine 61 0.979240442
ADP-ribosylserine 60 0.980324492
Symmetric dimethylarginine 54 0.981300137
N6-(pyridoxal phosphate)lysine 47 0.98214931
N6-malonyllysine 45 0.982962347
Allysine 41 0.983703115
PolyADP-ribosyl glutamic acid 36 0.984353545
Deamidated asparagine 33 0.984949772
N-acetylglycine 30 0.985491797
ADP-ribosyl glutamic acid 28 0.985997687
N6-methylated lysine 28 0.986503577
(3S)-3-hydroxyasparagine 27 0.9869914
N5-methylglutamine 27 0.987479222
3-hydroxyproline 24 0.987912842
S-(2-succinyl)cysteine 23 0.988328395
N-acetylproline 22 0.98872588
5-glutamyl polyglutamate 19 0.989069162
ADP-ribosylarginine 19 0.989412445
ADP-ribosylcysteine 19 0.989755727
Iodotyrosine 17 0.990062875
3-oxoalanine (Cys) 17 0.990370022
Methionine (R)-sulfoxide 16 0.990659102
N-acetylvaline 14 0.990912047
Deamidated glutamine 13 0.991146925
(Microbial infection) O-acetylthreonine 13 0.991381802
Phenylalanine amide 13 0.99161668
Cysteine sulfenic acid (-SOH) 12 0.99183349
Pros-methylhistidine 12 0.9920503
S-glutathionyl cysteine 11 0.992249042
N-acetylcysteine 11 0.992447785
Methionine sulfoxide 11 0.992646527
5-glutamyl serotonin 11 0.99284527
N6-propionyllysine 11 0.993044012
(3R)-3-hydroxyasparagine 10 0.993224687
(Microbial infection) O-acetylserine 10 0.993405362
N6-(ADP-ribosyl)lysine 10 0.993586037
Cysteine sulfonic acid (-SO3H) 9 0.993748645
Methionine amide 9 0.993911252
Diiodotyrosine 9 0.99407386
Proline amide 8 0.9942184
2',4',5'-topaquinone 8 0.99436294
Cysteine persulfide 8 0.99450748
Tele-methylhistidine 8 0.99465202
(3R)-3-hydroxyaspartate 8 0.99479656
N,N,N-trimethylalanine 8 0.9949411
5-glutamyl dopamine 8 0.99508564
ADP-ribosyl aspartic acid 7 0.995212112
N6-lipoyllysine 6 0.995320517
Leucine amide 6 0.995428922
Tyrosine amide 6 0.995537327
N6-(retinylidene)lysine"> 6 0.995645732
S-methylcysteine 6 0.995754137
N6-(pyridoxal phosphate)lysine"> 6 0.995862542
5-glutamyl glycerylphosphorylethanolamine 6 0.995970947
N6-biotinyllysine 5 0.996061285
O-(pantetheine 4'-phosphoryl)serine 5 0.996151622
Glycine amide 5 0.99624196
Thyroxine 5 0.996332297
N6-(retinylidene)lysine 5 0.996422635
N,N,N-trimethylglycine 5 0.996512972
5-glutamyl glycine 5 0.99660331
Omega-N-methylated arginine 5 0.996693647
S-(2,3-dicarboxypropyl)cysteine 5 0.996783985
(Microbial infection) ADP-riboxanated arginine 5 0.996874322
Phosphohistidine 4 0.996946592
(Microbial infection) Phosphothreonine 4 0.997018862
(Microbial infection) Deamidated asparagine 4 0.997091132
Valine amide 4 0.997163402
Triiodothyronine 4 0.997235672
Arginine amide 4 0.997307942
ADP-ribosylasparagine 4 0.997380212
(Microbial infection) ADP-ribosylthreonine 4 0.997452482
ADP-ribosylglycine 4 0.997524752
O-AMP-tyrosine 4 0.997597022
(3S)-3-hydroxyhistidine 4 0.997669292
(Microbial infection) O-AMP-tyrosine 4 0.997741562
ADP-ribosylhistidine 3 0.997795765
(Microbial infection) Phosphoserine 3 0.997849967
Asparagine amide 3 0.99790417
Isoleucine amide 3 0.997958372
PolyADP-ribosyl aspartic acid 3 0.998012575
O-AMP-threonine 3 0.998066777
N6-carboxylysine 3 0.99812098
Aspartate 1-(chondroitin 4-sulfate)-ester"> 3 0.998175182
S-8alpha-FAD cysteine 3 0.998229385
Tele-8alpha-FAD histidine 3 0.998283587
Leucine methyl ester 3 0.99833779
(Microbial infection) O-AMP-threonine 3 0.998391992
N-acetylglutamate 3 0.998446195
(Microbial infection) O-(2-cholinephosphoryl)serine 3 0.998500397
Hypusine 3 0.9985546
Diphosphoserine 3 0.998608802
(Microbial infection) Deamidated glutamine 3 0.998663005
(Microbial infection) S-methylcysteine 3 0.998717207
3-hydroxyasparagine 3 0.99877141
4-hydroxynonenal-conjugated cysteine 3 0.998825612
(3R)-3-hydroxyarginine 2 0.998861747
Alanine amide 2 0.998897882
1-thioglycine 2 0.998934017
5-glutamyl histamine 2 0.998970152
Pyruvic acid (Ser) 2 0.999006287
Cysteine sulfinic acid (-SO2H) 2 0.999042422
Lysine amide 2 0.999078557
(3S)-3-hydroxylysine 2 0.999114692
ADP-ribosyltyrosine 2 0.999150827
N6-acetyl-N6-methyllysine 2 0.999186962
Sulfoserine 2 0.999223097
S-cysteinyl cysteine 2 0.999259232
4-hydroxynonenal-conjugated histidine 2 0.999295367
Hydroxyarginine 1 0.999313435
Glycyl adenylate 1 0.999331502
S-cysteinyl cysteine"> 1 0.99934957
Beta-decarboxylated aspartate 1 0.999367637
Glutamic acid 1-amide 1 0.999385705
Sulfocysteine 1 0.999403772
Blocked amino end (Ser) 1 0.99942184
N,N-dimethylproline 1 0.999439907
Blocked amino end (Thr)"> 1 0.999457975
N,N-dimethylglycine 1 0.999476042
N-methylglycine 1 0.99949411
S-(dipyrrolylmethanemethyl)cysteine 1 0.999512177
3'-bromotyrosine 1 0.999530245
N4,N4-dimethylasparagine 1 0.999548312
(Microbial infection) ADP-ribosyldiphthamide 1 0.99956638
Diphthamide 1 0.999584447
N6-1-carboxyethyl lysine 1 0.999602515
(3S)-3-hydroxyaspartate 1 0.999620582
N,N,N-trimethylserine 1 0.99963865
N,N-dimethylserine 1 0.999656717
N-methylserine 1 0.999674785
Blocked amino end (Ser)"> 1 0.999692852
O-acetylserine 1 0.99971092
N-acetylaspartate 1 0.999728987
(Microbial infection) ADP-ribosylasparagine 1 0.999747055
4-hydroxylysine 1 0.999765122
N-pyruvate 2-iminyl-valine 1 0.99978319
S-cGMP-cysteine 1 0.999801257
O-(2-cholinephosphoryl)serine 1 0.999819325
5-glutamyl glutamate 1 0.999837392
Thiazolidine linkage to a ring-opened DNA abasic site 1 0.99985546
(4R)-5-hydroxyleucine 1 0.999873527
(4R)-5-oxoleucine 1 0.999891595
Glutamine amide 1 0.999909662
O-AMP-serine 1 0.99992773
Pyrrolidone carboxylic acid (Glu) 1 0.999945797
(Microbial infection) N6-acetyllysine 1 0.999963865
4-hydroxynonenal-conjugated lysine 1 0.999981932
2,3-didehydroalanine (Ser) 1 1

[trishorts]

original jenkins top down

[trishorts]

This PR

[nbollis]

Lgtm.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 93.81%. Comparing base (b82cfaf) to head (31d75bd).

Additional details and impacted files

@@           Coverage Diff           @@
##           master    #2446   +/-   ##
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  Coverage   93.81%   93.81%           
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  Files         141      141           
  Lines       21993    21993           
  Branches     3014     3014           
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  Hits        20633    20633           
  Misses        910      910           
  Partials      450      450