. Author manuscript; available in PMC: 2016 Sep 22.

Published in final edited form as: J Proteome Res. 2016 Jun 13;15(7):2309–2320. doi: 10.1021/acs.jproteome.6b00344

Table 1.

Summary of peptides identified in Alzheimer’s disease and cancer samples by the JUMPg program

Database	Dataset 1: Alzheimer’s disease brain			Dataset 2: Multiple myeloma
	Search space^*	PSMs	Peptides	Search space^*	PSMs	Peptides
	1^st stage (fully tryptic)
UniProt	5,086,244	556,551	87,806	5,086,244	723,521	129,861
Mutation	56,085	1,401	288	63,708	1,931	584
Splice junction	152,662	155	51	742,585	316	163
2^nd stage (partially tryptic)^#
UniProt	43,998,844	26,030	6,621	47,273,429	182,737	67,251
mutation	42,761	33	10	98,348	237	114
junction	14,317	0	0	51,899	14	3
3^rd stage (fully tryptic)
RNAseq 6FT	3,633,953	569	147	4,523,368	467	127

Total		584,739	94,923		909,223	198,103

The search space is indicated by the number of unique theoretical peptides in a particular database.

Only proteins/events identified in the 1^st stage are considered in partially tryptic database search.