Fragmentation trees reloaded

Böcker, Sebastian; Dührkop, Kai

doi:10.1186/s13321-016-0116-8

Journal of Cheminformatics

Table 3 Priors \(P_{\text{loss-comm}}(l)\) for common losses l

From: Fragmentation trees reloaded

Mol. formula	Mass	Loss name	Known	Intensity GNPS		Intensity Agilent		\(P_{\text{loss-comm}}\)
Mol. formula	Mass	Loss name	Known	Total	Expected	Total	Expected	\(P_{\text{loss-comm}}\)
H^a	1.0078	Hydrogen radical		110	0.00	77	0.00	^a
\(\hbox {H}_{2}^{\mathrm{a}}\)	2.0157	Hydrogen	A, B	1799	0.00	890	0.00	^a
\(\hbox {CH}_{2}\)	14.0157	Methylene		33	17.47	71	37.35	1.92
\(\hbox {CH}_{3}\)	15.0235	Methyl	A	3231	46.48	1481	21.31	69.53
\(\hbox {CH}_{4}\)	16.0313	Methane	A, B, C	2011	75.23	929	34.76	26.73
\(\hbox {H}_{3}\hbox {N}\)	17.0265	Ammonia	A, B, C	1409	62.73	1481	65.92	22.47
\(\hbox {H}_{2}\hbox {O}\)	18.0106	Water	A, B, C	5548	85.53	4014	61.88	64.87
HF	20.0062	Hydrogen fluoride		266	13.43	365	18.36	19.88
\(\hbox {C}_{2}\hbox {H}_{2}\)	26.0157	Ethine	B, C	2434	133.98	2324	127.90	18.17
CHN	27.0109	Hydrogen cyanide		1117	139.90	1078	134.94	7.99
CO	27.9949	Carbon monoxide	B, C	4232	177.14	2614	109.45	23.89
\(\hbox {C}_{2}\hbox {H}_{4}\)	28.0313	Ethene	A, B, C	483	87.19	1108	199.82	5.55
\(\hbox {CH}_{3}\hbox {N}\)	29.0265	Methyleneimine	B	347	158.43	305	139.34	2.19
S	31.9721	Sulfur	B, C	79	38.60	179	87.07	2.06
\(\hbox {CH}_{4}\hbox {O}\)	32.0262	Methyl esters		202	127.42	341	214.18	1.59
Cl	34.9689	Chlorine		296	45.18	394	60.27	6.55
HCl	35.9767	Hydrogen chloride		462	45.88	613	60.95	10.07
\(\hbox {C}_{2}\hbox {H}_{2}\hbox {O}\)	42.0106	Ketene	B, C	811	246.67	584	177.75	3.29
\(\hbox {C}_{3}\hbox {H}_{6}\)	42.0470	Propene		207	101.85	656	322.40	2.03
\(\hbox {C}_{2}\hbox {H}_{5}\hbox {N}\)	43.0422	Aminoethylene		332	177.18	454	242.22	1.88
\(\hbox {CO}_{2}\)	43.9898	Carbon dioxide	B, C	281	199.41	215	153.06	1.41
Br	78.9183	Bromine		20	0.91	95	4.23	22.51
HBr	79.9262	Hydrogen bromide		9	0.63	65	4.38	14.98
\(\hbox {HO}_{3}\hbox {P}\)	79.9663	Metaphosphoric acid	B, C	3	0.78	25	6.55	3.93
\(\hbox {HO}_{2}\hbox {PS}\)	95.9435	Phosphenothioic acid		0	0.11	26	4.60	5.65
I	126.9045	Iodine		29	0.25	60	0.52	116.53
HI	127.9123	Hydrogen iodide		11	0.15	45	0.61	74.61
CIO	154.8994	Iodomethanone		0	0.04	3	0.32	10.28
\(\hbox {C}_{10}\hbox {H}_{9}\hbox {NO}_{3}\hbox {S}^{\mathrm{b}}\)	223.0303			20	1.12	5	0.30	18.54
\(\hbox {C}_{12}\hbox {H}_{8}\hbox {ClNS}^{\mathrm{b}}\)	233.0066	2-Chlorophenothiazine		1	0.06	25	0.83	30.72
\(\hbox {I}_{2}\)	253.8089	Iodine		0	0.00	10	0.03	357.31
\(\hbox {C}_{11}\hbox {H}_{10}\hbox {Cl}_{2}\hbox {N}_{2}\hbox {O}^{\mathrm{b}}\)	256.0170			3	0.12	9	0.40	24.93

Entry “mass” is the exact theoretical mass of the loss. Entry “known” indicates whether the loss was included in the expert-curated common loss lists in A [34], B [41], or C [42]. Entry “total” indicate the (rounded) frequency of the loss in the trees computed from the dataset, weighted by the maximum peak intensity of the two peaks that are responsible for this loss. Entries “expected” is the weighted frequency we would expect from the loss mass prior, and \(P_{\text{loss-comm}}\) is the common loss prior after correcting for the loss mass prior
^aLosses H and \(\hbox {H}_{2}\) can be interpreted as artifacts of the loss mass prior
^b \(\hbox {C}_{10}\hbox {H}_{9}\hbox {NO}_{3}\hbox {S}\), \(\hbox {C}_{12}\hbox {H}_{8}\hbox {ClNS}\) and \(\hbox {C}_{11}\hbox {H}_{10}\hbox {Cl}_{2}\hbox {N}_{2}\hbox {O}\) are artifacts, stemming from either their high mass or the small number of chlorine-containing compounds in the datasets

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ISSN: 1758-2946

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