Incorrect masses/formulas for several terms

[pgarrett-scripps]

Mass Discrepancies in PSI-MOD Ontology

While parsing the current PSI-MOD ontology file, I identified several mass mismatches between the reported values and recalculated values based on the molecular formulas. These discrepancies primarily affect average masses for modifications containing elements with multiple isotopes (e.g., S, Cl, Br).

I cross-referenced several of these entries against Unimod, which reports values matching my recalculated masses rather than the PSI-MOD reported values, suggesting the PSI-MOD entries may need correction. Additionally, I think that the formula for dihydroxyphenylalanine should be O2?

Happy to submit a PR if these are indeed issues and need addressing.

mod_id	modification_name	mass_type	calculated	reported	delta	formula	unimod
00402	Gygi ICAT(TM) d8 modified cysteine	Average	494.671785	494.3	0.371785	C22[1H30][2H8]N4O6S	494.6746
00405	Applied Biosystems original ICAT(TM) d8 modified cysteine	Average	450.619608	450.28	0.339608	C20[1H26][2H8]N4O5S	450.6221
00406	Applied Biosystems original ICAT(TM) d0 modified cysteine	Average	442.569394	442.22	0.349394	C20[1H34]N4O5S	442.5728
00469	ESP-Tag heavy d10	Average	348.528403	348.24	0.288403	C16[1H16][2H10]N4O2S	348.5299
00495	N-iodoacetyl, p-chlorobenzyl-13C6-glucamine	Average	351.635014	351.12	0.515014	[12C9][13C6]ClH20NO6	351.7313
00880	6x(13)C labeled 4-sulfophenyl isothiocyanate derivatized residue	Average	221.194326	220.99	0.204326	[12C][13C6]H5NO3S2	NA
00932	IDBEST tag for quantitation	Average	299.025684	298.02	1.005684	Br[12C10][13C2]H13N2O2	299.1331
01335	6x(13)C labeled 4-sulfophenyl isothiocyanate derivatized lysine	Average	221.194326	220.99	0.204326	[12C][13C6]H5NO3S2	348.5299
01340	ESP-Tag heavy d10 - site K	Average	348.528403	348.24	0.288403	C16[1H16][2H10]N4O2S
01909	6x(13)C labeled 4-sulfophenyl isothiocyanate alpha-amino derivatized residue	Average	221.194326	220.99	0.204326	[12C][13C6]H5NO3S2
02105	L-2,5-dihydroxyphenylalanine (Phe)	Monoisotopic	15.994915	31.989828	-15.994913	O	31.989829
02105	L-2,5-dihydroxyphenylalanine (Phe)	Average	15.999405	32.0	-16.000595	O	31.9988

[pgarrett-scripps]

Some more mismatches with a lower tolerance threshold (diff > 0.05 da). I checked a few of these against unimod and they seem to differ as well. I would expect that the unimod and psi mods would agree with each other, as currently you will get slightly different masses depending on the ontology you reference.

For example:

Shimadzu 13CNBS

• PSI avg mass: 159.01
• unimod avg mass: 159.1144
• Calc avg mass: 159.114252

mod_id	modification_name	mass_type	calculated	reported	delta	formula
00150	L-cysteinyl-L-histidino-homocitryl molybdenum heptairon nonasulfide	Average	991.58422	991.53	0.05422	C7Fe7H6MoNO7S9
00402	Gygi ICAT(TM) d8 modified cysteine	Average	494.671785	494.3	0.371785	C22[1H30][2H8]N4O6S
00405	Applied Biosystems original ICAT(TM) d8 modified cysteine	Average	450.619608	450.28	0.339608	C20[1H26][2H8]N4O5S
00406	Applied Biosystems original ICAT(TM) d0 modified cysteine	Average	442.569394	442.22	0.349394	C20[1H34]N4O5S
00454	quaternary amine labeling reagent heavy form (+3amu) (N-term & K)	Average	130.201815	130.12	0.081815	C7[1H10][2H3]NO
00455	quaternary amine labeling reagent heavy form (+6amu) (N-term & K)	Average	133.221455	133.14	0.081455	C7H7[2H6]NO
00456	quaternary amine labeling reagent heavy form (+9amu) (N-term & K)	Average	136.239476	136.16	0.079476	C7[1H4][2H9]NO
00458	4x(2)H labeled alpha-amino succinylated residue	Average	104.097565	104.04	0.057565	C4[2H4]O3
00469	ESP-Tag heavy d10	Average	348.528403	348.24	0.288403	C16[1H16][2H10]N4O2S
00495	N-iodoacetyl, p-chlorobenzyl-13C6-glucamine	Average	351.635014	351.12	0.515014	[12C9][13C6]ClH20NO6
00532	Shimadzu 13CNBS	Average	159.114252	159.01	0.104252	[13C6]H3NO2S
00533	Shimadzu 12CNBS	Average	153.094123	152.99	0.104123	[12C6]H3NO2S
00549	APTA d3	Average	174.27694	174.17	0.10694	C9[1H16][2H3]N2O
00551	EAPTA d5	Average	189.308055	189.19	0.118055	C10[1H15][2H5]N2O
00562	N-ethyl iodoacetamide-d5	Average	90.135211	90.08	0.055211	C4[1H2][2H5]NO
00605	Sulfanilic Acid (SA), light C12	Average	155.110004	155.0	0.110004	[12C6]H5NO2S
00606	Sulfanilic Acid (SA), heavy C13	Average	161.130133	161.02	0.110133	[13C6]H5NO2S
00871	(2)H5-phenyl isocyanate derivatized residue	Average	124.151768	124.07	0.081768	C7[2H5]NO
00880	6x(13)C labeled 4-sulfophenyl isothiocyanate derivatized residue	Average	221.194326	220.99	0.204326	[12C][13C6]H5NO3S2
00932	IDBEST tag for quantitation	Average	299.025684	298.02	1.005684	Br[12C10][13C2]H13N2O2
00944	d9-4-trimethylammoniumbutanoyl derivatized residue	Average	137.247301	137.16	0.087301	C7[1H5][2H9]NO
01188	N-ethyl iodoacetamide-d5 - site Y	Average	90.135211	90.08	0.055211	C4[1H2][2H5]NO
01189	N-ethyl iodoacetamide-d5 - site C	Average	90.135211	90.08	0.055211	C4[1H2][2H5]NO
01217	Sulfanilic Acid (SA), light C12 - site D	Average	155.110004	155.0	0.110004	[12C6]H5NO2S
01218	Sulfanilic Acid (SA), light C12 - site E	Average	155.110004	155.0	0.110004	[12C6]H5NO2S
01219	Sulfanilic Acid (SA), heavy C13 - site D	Average	161.130133	161.02	0.110133	[13C6]H5NO2S
01220	Sulfanilic Acid (SA), heavy C13 - site E	Average	161.130133	161.02	0.110133	[13C6]H5NO2S
01315	4x(2)H labeled N6-succinyl-L-lysine	Average	104.097565	104.04	0.057565	C4[2H4]O3
01335	6x(13)C labeled 4-sulfophenyl isothiocyanate derivatized lysine	Average	221.194326	220.99	0.204326	[12C][13C6]H5NO3S2
01340	ESP-Tag heavy d10 - site K	Average	348.528403	348.24	0.288403	C16[1H16][2H10]N4O2S
01358	Bruker Daltonics SERVA-ICPL(TM) quantification chemistry, medium form - site N-term	Average	109.119106	109.05	0.069106	C6[1H-1][2H4]NO
01359	Bruker Daltonics SERVA-ICPL(TM) quantification chemistry, medium form - site K	Average	109.119106	109.05	0.069106	C6[1H-1][2H4]NO
01822	cysTMT6plex-zero reporter+balance reagent cysteine disulfide	Average	299.271338	299.17	0.101338	[12C14]H25[14N3]O2S
01823	cysTMT6plex-126 reporter+balance reagent cysteine disulfide	Average	304.281792	304.18	0.101792	[12C10][13C4]H25[14N2][15N]O2S
01824	cysTMT6plex-127 reporter+balance reagent cysteine disulfide	Average	304.281792	304.18	0.101792	[12C10][13C4]H25[14N2][15N]O2S
01825	cysTMT6plex-128 reporter+balance reagent cysteine disulfide	Average	304.281792	304.18	0.101792	[12C10][13C4]H25[14N2][15N]O2S
01826	cysTMT6plex-129 reporter+balance reagent cysteine disulfide	Average	304.281792	304.18	0.101792	[12C10][13C4]H25[14N2][15N]O2S
01827	cysTMT6plex-130 reporter+balance reagent cysteine disulfide	Average	304.281792	304.18	0.101792	[12C10][13C4]H25[14N2][15N]O2S
01828	cysTMT6plex-131 reporter+balance reagent cysteine disulfide	Average	304.281792	304.18	0.101792	[12C10][13C4]H25[14N2][15N]O2S
01909	6x(13)C labeled 4-sulfophenyl isothiocyanate alpha-amino derivatized residue	Average	221.194326	220.99	0.204326	[12C][13C6]H5NO3S2
02022	N6-cervonoyl-L-lysine	Average	310.473817	310.53	-0.056183	C22H30O
02023	N-cervonoylated residue	Average	310.473817	310.53	-0.056183	C22H30O
02024	cervonoylated residue	Average	310.473817	310.53	-0.056183	C22H30O
02105	L-2,5-dihydroxyphenylalanine (Phe)	Monoisotopic	15.994915	31.989828	-15.994913	O
02105	L-2,5-dihydroxyphenylalanine (Phe)	Average	15.999405	32.0	-16.000595	O

[pgarrett-scripps]

Average Mass Calculation

All atomic masses and isotopic abundances were sourced from NIST, parsed using tacular.
The full elemental dataset used is available as a JSON file.

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Elements without an isotope prefix (e.g., C, N, O, S) contribute their natural abundance-weighted average mass:

$$avgmass = \frac{\sum (isotopemass \times abundance)}{\sum abundance}$$

For example, sulfur: (31.972 × 0.9499) + (32.971 × 0.0075) + (33.968 × 0.0425) + (35.967 × 0.0001) = 32.064787 Da

Elements with an isotope prefix (e.g., [2H], [13C], [12C]) contribute their exact isotope mass

For example, the avg mass for formula [13C]C is calculated as follows:

13.003355 ([13C]) + 12.010736 (C) = 25.014091 Da