Should we update common biological modifications

[trishorts]

while reading katies TD paper it occured to me that maybe we want to update common biological mods. She did in her work, after looking at uniprot xml and taking enough to get 99% of the total. I repeated the analysis myself. We can argue about where to draw the cutoff. Maybe 99% total is good. But maybe you don't want to take any mod that is not present at 1% of the total. Anyway, here is the ranked list with numbers:

Running fraction	Running Sum	PTM count	PTM absolute fraction	PTM		TotalPTMs
0.600855779	32859	32859	0.600855779	Phosphoserine		54687
0.708541335	38748	5889	0.107685556	Phosphothreonine
0.786786622	43027	4279	0.078245287	N6-acetyllysine
0.824876113	45110	2083	0.038089491	Phosphotyrosine
0.848062611	46378	1268	0.023186498	N6-succinyllysine
0.866842211	47405	1027	0.0187796	Omega-N-methylarginine
0.884177227	48353	948	0.017335016	N-acetylalanine
0.899665368	49200	847	0.015488142	N-acetylmethionine
0.909484887	49737	537	0.009819518	Asymmetric dimethylarginine
0.917713533	50187	450	0.008228647	4-hydroxyproline
0.925393604	50607	420	0.00768007	N6-(2-hydroxyisobutyryl)lysine
0.932872529	51016	409	0.007478926	N-acetylserine
0.937937718	51293	277	0.005065189	N6-(beta-hydroxybutyryl)lysine
0.942783477	51558	265	0.004845759	N6-lactoyllysine
0.94761095	51822	264	0.004827473	N6-glutaryllysine
0.952200706	52073	251	0.004589756	N6-methyllysine
0.956260172	52295	222	0.004059466	N6-crotonyllysine
0.95902134	52446	151	0.002761168	Sulfotyrosine
0.961398504	52576	130	0.002377165	Cysteine methyl ester
0.963574524	52695	119	0.00217602	N6,N6,N6-trimethyllysine
0.965713972	52812	117	0.002139448	Citrulline
0.967780277	52925	113	0.002066305	N6,N6-dimethyllysine
0.969645437	53027	102	0.00186516	4-carboxyglutamate
0.971400881	53123	96	0.001755445	Hydroxyproline
0.973064897	53214	91	0.001664015	Pyrrolidone carboxylic acid
0.974546053	53295	81	0.001481156	N-acetylthreonine
0.975972352	53373	78	0.001426299	5-hydroxylysine
0.977270649	53444	71	0.001298298	Dimethylated arginine
0.978568947	53515	71	0.001298298	S-nitrosocysteine
0.979702672	53577	62	0.001133725	N6-butyryllysine
0.98081811	53638	61	0.001115439	3'-nitrotyrosine
0.981805548	53692	54	0.000987438	Symmetric dimethylarginine
0.9827747	53745	53	0.000969152	N6-(pyridoxal phosphate)lysine
0.983597564	53790	45	0.000822865	N6-malonyllysine
0.984347285	53831	41	0.000749721	Allysine
0.985023863	53868	37	0.000676578	ADP-ribosylserine
0.985627297	53901	33	0.000603434	Deamidated asparagine
0.986175874	53931	30	0.000548576	N-acetylglycine
0.986687878	53959	28	0.000512005	N6-methylated lysine
0.987181597	53986	27	0.000493719	(3S)-3-hydroxyasparagine
0.98765703	54012	26	0.000475433	N5-methylglutamine
0.988095891	54036	24	0.000438861	3-hydroxyproline
0.988516466	54059	23	0.000420575	S-(2-succinyl)cysteine
0.988918756	54081	22	0.000402289	N-acetylproline
0.989284473	54101	20	0.000365718	ADP-ribosylarginine
0.989631905	54120	19	0.000347432	5-glutamyl polyglutamate
0.989979337	54139	19	0.000347432	ADP-ribosylcysteine
0.990290197	54156	17	0.00031086	3-oxoalanine (Cys)
0.990601057	54173	17	0.00031086	PolyADP-ribosyl glutamic acid
0.990911917	54190	17	0.00031086	Iodotyrosine
0.991204491	54206	16	0.000292574	Methionine (R)-sulfoxide
0.991497065	54222	16	0.000292574	ADP-ribosyl glutamic acid
0.991753067	54236	14	0.000256002	N-acetylvaline
0.991990784	54249	13	0.000237716	(Microbial infection) O-acetylthreonine
0.9922285	54262	13	0.000237716	Deamidated glutamine
0.992466217	54275	13	0.000237716	Phenylalanine amide
0.992667362	54286	11	0.000201145	N6-propionyllysine
0.992868506	54297	11	0.000201145	N-acetylcysteine
0.993069651	54308	11	0.000201145	Pros-methylhistidine
0.993270796	54319	11	0.000201145	N6-(retinylidene)lysine
0.99347194	54330	11	0.000201145	5-glutamyl serotonin
0.993654799	54340	10	0.000182859	(3R)-3-hydroxyasparagine
0.993837658	54350	10	0.000182859	Cysteine sulfenic acid (-SOH)
0.994020517	54360	10	0.000182859	S-glutathionyl cysteine
0.994203376	54370	10	0.000182859	(Microbial infection) O-acetylserine
0.994367949	54379	9	0.000164573	Cysteine sulfonic acid (-SO3H)
0.994532521	54388	9	0.000164573	Diiodotyrosine
0.994678808	54396	8	0.000146287	N,N,N-trimethylalanine
0.994825096	54404	8	0.000146287	Methionine amide
0.994971383	54412	8	0.000146287	5-glutamyl dopamine
0.99511767	54420	8	0.000146287	Methionine sulfoxide
0.995263957	54428	8	0.000146287	2',4',5'-topaquinone
0.995410244	54436	8	0.000146287	Tele-methylhistidine
0.995556531	54444	8	0.000146287	(3R)-3-hydroxyaspartate
0.995702818	54452	8	0.000146287	Proline amide
0.995830819	54459	7	0.000128001	ADP-ribosyl aspartic acid
0.99595882	54466	7	0.000128001	N6-(ADP-ribosyl)lysine
0.996068535	54472	6	0.000109715	Tyrosine amide
0.996178251	54478	6	0.000109715	S-methylcysteine
0.996287966	54484	6	0.000109715	N6-lipoyllysine
0.996397681	54490	6	0.000109715	5-glutamyl glycerylphosphorylethanolamine
0.996489111	54495	5	9.14294E-05	ADP-ribosylasparagine
0.99658054	54500	5	9.14294E-05	Omega-N-methylated arginine
0.99667197	54505	5	9.14294E-05	Glycine amide
0.996763399	54510	5	9.14294E-05	Leucine amide
0.996854828	54515	5	9.14294E-05	O-(pantetheine 4'-phosphoryl)serine
0.996946258	54520	5	9.14294E-05	N,N,N-trimethylglycine
0.997037687	54525	5	9.14294E-05	N6-biotinyllysine
0.997129117	54530	5	9.14294E-05	5-glutamyl glycine
0.997220546	54535	5	9.14294E-05	Thyroxine
0.99729369	54539	4	7.31435E-05	(Microbial infection) O-AMP-tyrosine
0.997366833	54543	4	7.31435E-05	O-AMP-tyrosine
0.997439977	54547	4	7.31435E-05	ADP-ribosylglycine
0.99751312	54551	4	7.31435E-05	(3S)-3-hydroxyhistidine
0.997586264	54555	4	7.31435E-05	(Microbial infection) Deamidated asparagine
0.997659407	54559	4	7.31435E-05	Phosphohistidine
0.997732551	54563	4	7.31435E-05	Arginine amide
0.997805694	54567	4	7.31435E-05	Triiodothyronine
0.997878838	54571	4	7.31435E-05	S-(2,3-dicarboxypropyl)cysteine
0.997933695	54574	3	5.48576E-05	(Microbial infection) O-(2-cholinephosphoryl)serine
0.997988553	54577	3	5.48576E-05	(Microbial infection) O-AMP-threonine
0.998043411	54580	3	5.48576E-05	(Microbial infection) S-methylcysteine
0.998098268	54583	3	5.48576E-05	Cysteine persulfide
0.998153126	54586	3	5.48576E-05	Tele-8alpha-FAD histidine
0.998207984	54589	3	5.48576E-05	S-8alpha-FAD cysteine
0.998262841	54592	3	5.48576E-05	Isoleucine amide
0.998317699	54595	3	5.48576E-05	(Microbial infection) Deamidated glutamine
0.998372557	54598	3	5.48576E-05	O-AMP-threonine
0.998427414	54601	3	5.48576E-05	3-hydroxyasparagine
0.998482272	54604	3	5.48576E-05	Valine amide
0.998537129	54607	3	5.48576E-05	Aspartate 1-(chondroitin 4-sulfate)-ester
0.998591987	54610	3	5.48576E-05	Asparagine amide
0.998646845	54613	3	5.48576E-05	N6-carboxylysine
0.998701702	54616	3	5.48576E-05	Leucine methyl ester
0.99875656	54619	3	5.48576E-05	S-cysteinyl cysteine
0.998811418	54622	3	5.48576E-05	(Microbial infection) Phosphothreonine
0.998866275	54625	3	5.48576E-05	N-acetylglutamate
0.998921133	54628	3	5.48576E-05	Hypusine
0.998957705	54630	2	3.65718E-05	1-thioglycine
0.998994277	54632	2	3.65718E-05	Cysteine sulfinic acid (-SO2H)
0.999030848	54634	2	3.65718E-05	Sulfoserine
0.99906742	54636	2	3.65718E-05	Lysine amide
0.999103992	54638	2	3.65718E-05	Alanine amide
0.999140564	54640	2	3.65718E-05	Diphosphoserine
0.999177135	54642	2	3.65718E-05	5-glutamyl histamine
0.999213707	54644	2	3.65718E-05	(3R)-3-hydroxyarginine
0.999250279	54646	2	3.65718E-05	Blocked amino end (Ser)
0.999286851	54648	2	3.65718E-05	ADP-ribosyltyrosine
0.999323422	54650	2	3.65718E-05	Pyruvic acid (Ser)
0.999359994	54652	2	3.65718E-05	(3S)-3-hydroxylysine
0.99937828	54653	1	1.82859E-05	N,N-dimethylproline
0.999396566	54654	1	1.82859E-05	(Microbial infection) ADP-ribosylasparagine
0.999414852	54655	1	1.82859E-05	5-glutamyl glutamate
0.999433138	54656	1	1.82859E-05	2,3-didehydroalanine (Ser)
0.999451424	54657	1	1.82859E-05	Pyrrolidone carboxylic acid (Glu)
0.999469709	54658	1	1.82859E-05	O-AMP-serine
0.999487995	54659	1	1.82859E-05	Glutamic acid 1-amide
0.999506281	54660	1	1.82859E-05	S-(dipyrrolylmethanemethyl)cysteine
0.999524567	54661	1	1.82859E-05	(Microbial infection) ADP-riboxanated arginine
0.999542853	54662	1	1.82859E-05	4-hydroxylysine
0.999561139	54663	1	1.82859E-05	(Microbial infection) N6-acetyllysine
0.999579425	54664	1	1.82859E-05	Beta-decarboxylated aspartate
0.999597711	54665	1	1.82859E-05	N,N-dimethylglycine
0.999615996	54666	1	1.82859E-05	N-methylglycine
0.999634282	54667	1	1.82859E-05	N6-1-carboxyethyl lysine
0.999652568	54668	1	1.82859E-05	N-pyruvate 2-iminyl-valine
0.999670854	54669	1	1.82859E-05	Thiazolidine linkage to a ring-opened DNA abasic site
0.99968914	54670	1	1.82859E-05	Hydroxyarginine
0.999707426	54671	1	1.82859E-05	(3S)-3-hydroxyaspartate
0.999725712	54672	1	1.82859E-05	Glutamine amide
0.999743998	54673	1	1.82859E-05	Blocked amino end (Thr)
0.999762284	54674	1	1.82859E-05	PolyADP-ribosyl aspartic acid
0.999780569	54675	1	1.82859E-05	N4,N4-dimethylasparagine
0.999798855	54676	1	1.82859E-05	O-acetylserine
0.999817141	54677	1	1.82859E-05	O-(2-cholinephosphoryl)serine
0.999835427	54678	1	1.82859E-05	N,N,N-trimethylserine
0.999853713	54679	1	1.82859E-05	N,N-dimethylserine
0.999871999	54680	1	1.82859E-05	N-methylserine
0.999890285	54681	1	1.82859E-05	S-cGMP-cysteine
0.999908571	54682	1	1.82859E-05	Glycyl adenylate
0.999926856	54683	1	1.82859E-05	(4R)-5-hydroxyleucine
0.999945142	54684	1	1.82859E-05	(4R)-5-oxoleucine
0.999963428	54685	1	1.82859E-05	(Microbial infection) ADP-ribosyldiphthamide
0.999981714	54686	1	1.82859E-05	Diphthamide
1	54687	1	1.82859E-05	N-acetylaspartate

[Apirog9]

Hi, What is the data source?

[trishorts]

It's from the human uniprot xml. I mined the info from it using text manipulation.