Table 1.

Multistage sequencing results. Masses that are verified by NMR are shown in bold. PM stands for Parent Mass of the peptide. Rank 1 … 3 for the highest scoring tag of Reginamide 925 means the three high scoring tags of Reginamide 925 have equal scores, and one of them is the tag shown. Asterisk on 147Da and 113Da means if we exchange these masses, the score wouldnt change. 222 − 18 and 147 + 18 masses for Etamycin 878 means instead of returning the correct masses 222Da and 147Da, the algorithm has returned 204Da and 165Da (this alternative breakage is also reported in [24]). ⇆ between 128Da and 113Da residues of Reginamide A means the algorithm has made a mistake in the order of those two residues, compared to previous reconstructions.

Peptide	Multistage reconstruction										PM	rank
Reginamide A	71	113	128 ⇆	113	113	147	113	113			911	4 … 6
Reginamide 897	71	113	99	128	113	113	147	113			897	2 … 3
Reginamide 925	71	113	99	156	113	147*	113*	113			925	1 … 3
Reginamide 939	71	113	113	156	113	147*	113*	113			939	4 … 6
Reginamide 953	71	113	170	113	113	147	113	113			953	3 … 4
Reginamide 967	71	113	184	113	113	147	113	113			967	24 … 30
Reginamide 981	71	113	113	85	226	147	113	113			981	1 … 2
Reginamide 995	113	113	331	226	212						995	3 … 4
Reginamide 1009	113	113	297	147	113	226					1009	1 … 5
Reginamide 1023	113	113	797								1023	5 … 15
Tyrocidine A	99	114	[113+	147]	[97+	147]	147	114	128	163	1269	20 … 44
Tyrocidine A1	99	128	[113+	147]	97	147	147	114	128	163	1283	22 … 49
Tyrocidine B	99	114	[113+	147]	97	186	147	[114+	128]	163	1308	11 … 19
Tyrocidine B1	99	128	[113+	147]	97	186	147	[114+	128]	163	1322	37 … 105
Tyrocidine C	99	114	[113+	147]	97	186	[186+	114]	128	163	1347	67 … 169
Tyrocidine C1	99	128	113	147	97	186	186	114	128	163	1361	10 … 33
Etamycin 878	71	141	71	113	113	222 − 18	147 + 18				878	5 … 8
Etamycin 864	71	127	71	113	113	222 − 18	147 + 18				864	1 … 3
Etamycin 862	71	141	71	97	113	222 − 18	147 + 18				862	9 … 12
Etamycin 858	71	141	71	113	113	222 − 18	127 + 18				858	11 … 12
Dianthin F	57	97	99 ⇆	147	147						547	13 … 20
Dianthin 564	57	113	113	71	97*	113*					564	6 … 14
Dianthin E	113	87	[147+	99+	57+	97]					600	7 … 36
Dianthin 610	97	99	[97+	57]	113	147					610	7 … 11
Dianthin 624	57	97	147	113	97	113					624	5 … 9
Dianthin 640	57	113	113	[97+	147]	113					640	25 … 66
Dianthin 644	57	97	99	147	147	97					644	1
Dianthin B	113	147	[147	97	57	97]					658	1
Dianthin 672	113	559									672	1 … 6
Dianthin C	57	147 ⇆	97	163	99	113					676	5 … 7
Dianthin D	87	113	97	97	113	[147+	57]				711	13 … 18