# This file contains OpenMS- and user-defined RNA modifications.
# It is read in addition to the Modomics data file ("Modomics.tsv") and uses the same format (except for the optional "alternatives" column).
# For terminal modifications, the "new_nomenclature" value has to end in "N" and contain either "33" (3'-terminal mod.) or "55" (5'-terminal mod.).
# An "ambiguous" modification represents two isobaric modifications with a methyl group on either the base or the ribose, that could be distinguished based on a-B ions. Its code ("short_name") must end in "?" and the codes of the two alternatives must be given in the last column.
name	short_name	new_nomenclature	originating_base	rnamods_abbrev	html_abbrev	formula	monoisotopic_mass	average_mass	alternatives
3' terminal phosphate	3'-p	33N	pppN	p	p	H2PO3	0.0	0.0
5' terminal phosphate	5'-p	55N	pppN	p	p	H2PO3	0.0	0.0
5' terminal phsophorothioate	5'-p*	55N	pppN	p	p	H2PO2S	0.0	0.0
2',3' terminal cyclophosphate	3'-c	33cN	pppN	p	p	PO2	0.0	0.0
generic methyladenosine ("m_A")	mA		A	a	a	C11O4N5H15	281.1124	281.2719
generic methylcytidine ("m_C")	mC		C	c	c	C10O5N3H15	257.1012	257.2467
generic methylguanosine ("m_G")	mG		G	g	g	C11O5N5H15	297.1073	297.2712
generic methyl[pseudo]uridine ("m_U")	mU		U	u	u	C10O6N2H14	258.0852	258.2313
generic thiouridine ("s_U")	sU		U	s	s	C9O5N2H12S1	260.0467	260.2694
generic dimethyladenosine ("m_,_A")	mmA		A	Ä	&Auml;	C12O4N5H17	295.1281	295.2989
generic 2'-O-dimethyladenosine ("m_Am")	mAm		A	ä	&auml;	C12O4N5H17	295.1281	295.2989
generic 2'-O-dimethylcytidine ("m_Cm")	mCm		C	ë	&euml;	C11O5N3H17	0.0	0.0
generic 2'-O-dimethylguanosine ("m_Gm")	mGm		G	ö	&ouml;	C12O5N5H17	311.123	311.2977
generic 2'-O-dimethyluridine ("m_Um")	mUm		U	ü	&uuml;	C11O6N2H16	272.1008	272.2583
5-carboxyhydroxymethyluridine or uridine 5-oxyacetic acid  	cmo5U/chm5U		U	V	V	C11O9N2H14	318.0699	318.2403
5-(carboxyhydroxymethyl)uridine methyl ester or uridine 5-oxyacetic acid methyl ester	mchm5U/mcmo5U		U	,	,	C12O9N2H16	332.0856	332.2672
5-(carboxyhydroxymethyl)-2'-O-methyluridine methyl ester or 2'-O-methyluridine 5-oxyacetic acid methyl ester	mchm5Um/mcmo5Um		U	b	b	C13O9N2H18	346.1012	346.2940
N6-methyl-N6-threonylcarbamoyladenosine or N6-hydroxynorvalylcarbamoyladenosine	m6t6A/hn6A		A	E	E	C16O8N6H22	426.1499	426.3868
galactosyl- or mannosyl-queuosine	galQ/manQ		preQ0base	9	9	C23O12N5H33	571.2126	571.5423
ambiguous methyladenosine ("m_A" or "Am")	mA?		A	á	&aacute;	C11O4N5H15	281.1124	281.2719	mA Am
ambiguous methylcytidine ("m_C" or "Cm")	mC?		C	é	&eacute;	C10O5N3H15	257.1012	257.2467	mC Cm
ambiguous methylguanosine ("m_G" or "Gm")	mG?		G	ó	&oacute;	C11O5N5H15	297.1073	297.2712	mG Gm
ambiguous methyl[pseudo]uridine ("m_U" or "Um")	mU?		U	ú	&uacute;	C10O6N2H14	258.0852	258.2313	mU Um
ambiguous methylinosine ("m1I" or "Im")	mI?		A	í	&iacute;	C11O5N4H14	282.0964	282.2565	m1I Im
ambiguous methylthiouridine ("m5s2U" or "s2Um")	msU?		U	ß	&szlig;	C10O5N2H14S1	274.0623	274.2964	m5s2U s2Um
ambiguous dimethyladenosine ("m_,_A" or "m_Am")	mmA?		A	Á	&Aacute;	C12O4N5H17	295.1281	295.2989	mmA mAm
ambiguous dimethylcytidine ("m4,4C" or "m_Cm")	mmC?		C	É	&Eacute;	C11O5N3H17	271.1168	271.2737	m4,4C mCm
ambiguous dimethylguanosine ("m2,2G" or "m_Gm")	mmG?		G	Ó	&Oacute;	C12O5N5H17	311.123	311.2977	m2,2G mGm
ambiguous trimethylguanosine ("m2,2,7G" or "m2,7Gm")	mmmG?		G	Ô	&Ocirc;	C13O5N5H21	327.1543	327.3404	m2,2,7G m2,7Gm
N4-acetylcytidine or 5-formyl-2'-O-methylcytidine	ac4C/f5Cm?		C	M	M	C11O6N3H15	285.0961	285.257	ac4C f5Cm
3-(3-amino-3-carboxypropyl)uridine or 5-carboxymethylaminomethyl-2'-O-methyluridine	acp3U/cmnm5Um?		U	X	X	C13O8N3H19	345.1172	345.3096	acp3U cmnm5Um
deoxyadenosine	dA	dA	A			C10O3N5H13	251.1018	251.2424
deoxycytidine	dC	dC	C			C9O4N3H13	227.0906	227.2176
deoxyguanosine	dG	dG	G			C10O4N5H13	267.0968	267.2418
deoxyuridine	dU	dU	U			C9O5N2H12	228.0746	228.2024
thymidine	dT	dT	U			C10O5N2H14	242.0903	242.2290
thio-adenosine	A*	A*	A	A	A	C10O4N5H13	267.0968	267.2449
thio-cytidine	C*	C*	C	C	C	C9O5N3H13	243.0855	243.2197
thio-guanosine	G*	G*	G	G	G	C10O5N5H13	283.0917	283.2442
thio-uridine	U*	U*	U	U	U	C9O6N2H12	244.0695	244.2043
thio-deoxyadenosine	dA*	dA*	A			C10O3N5H13	251.1018	251.2424
thio-deoxycytidine	dC*	dC*	C			C9O4N3H13	227.0906	227.2176
thio-deoxyguanosine	dG*	dG*	G			C10O4N5H13	267.0968	267.2418
thio-deoxyuridine	dU*	dU*	U			C9O5N2H12	228.0746	228.2024
thio-thymidine	dT*	dT*	U			C10O5N2H14	242.0903	242.2290