Table 1. Comparison of fragment ion annotation using NRP-Annotation or mMass.

	MC-LF1	MC-LR1	Seglitide2	CM A3	CRY-11	MG FR11
NRP-An.	23%, 13 of 57	52%, 22 of 66	74%, 38 of 53	73%, 36 of 99	32%, 10 of 36	–-
mMass *	23%, 13 of 57	52%, 22 of 66	74%, 38 of 53	73%, 36 of 99	32%, 10 of 36	–-
mMass **	96%, 51 of 57	79%, 55 of 66	98%, 51 of 53	100%, 90 of 99	80%, 21 of 36***	99%, 12 of 14

Indicated are the percentage of the ion intensity annotated as well as the number of ions matched by the software vs. the total ion number.

MC  =  Microcystin, CM  =  Cyclomarin, CRY  =  Cryptophycin, MG  =  Microginin.

^*options chosen that reflect the fragments NRP-Annotation can calculate (a- and b-ions, -NH₃ and -H₂O, Allow Scrambling, including b₁ ions).

^**all available options chosen.

^***if ³⁷Cl isotope peaks are manually deleted: 88%, 21 of 32.

m/z tolerances used for matching calculated to experimentally observed fragments: ¹0.015 Da, ²0.2 Da, ³0.1 Da.