Table 3. E. histolytica cyst proteins with more than 10 spectrum counts detected in MS/MS experiments.

E. histolytica Locus ID	*Detected in samples	Annotation	Transcriptome data**			E. dispar homolog		No. of spectrum counts in LC-MS/MS
			p-value	fold change: cyst/troph	HM-1 expr	Locus ID	% identity	Total
10.m00319	4, 5	actin	0.2720	1.1	127.75	EDI_251490	100	193
EHI_109890	1, 3, 4, 5	chitinase, putative	0.0001	87.4	0.20	EDI_120190	82	52
EHI_146120	1, 2, 4	hypothetical protein	0.0001	59.1	0.04	EDI_105270	65	36
EHI_196570	1, 2, 3, 4, 5	hypothetical protein	0.0001	37.2	0.55	EDI_039770	93	36
EHI_152170	1, 3, 4, 5	chitinase Jessie 3, putative	0.0001	43.5	0.67	EDI_038370	90	24
EHI_019630	1, 4, 5	hypothetical protein	0.0001	515.8	0.08	EDI_199570	54	15
200.m00090	1, 4, 5	clathrin heavy chain, putative	0.7530	−1.0	32.75	EDI_237980	92	11

*: Detected in samples: 1 = 8076; 2 = 4268; 3 = AM951; 4 = AM797; and 5 = CMS33-7132;

**: From [22]; NF = not found; troph = trophozoite; expr = expression; N/A = Not applicable; shown in bold fonts are those that show 90% or less identity with E. dispar proteins; ideal candidates for E. histolytica specific diagnostic tool development.

NB. Only a single spectrum was detected for a high proportion of 195 cyst proteins (137 or 70%) compared to that detected in 914/1825 (or 50%) of trophozoite MS/MS proteins deposited into the AmoebaDB database (http://amoebadb.org/amoeba/). In fact, other proteins other than E. histolytica in the cyst samples hampered an efficient identification of cyst specific proteins. The sources of these other proteins include (1) numerous bacteria that were attached to the surface of the cyst, or ingested by the cyst, and (2) the human feces, which was the original source of cyst material contributed the human proteins and diet-related (mainly rice) proteins. In contrast, the trophozoite MS/MS data in the AmoebaDB was coming from two studies that used axenically grown E. histolytica trophozoites, which should be free from all other organisms including bacteria [29], [30]. Also, note that none of the proteins listed in Table 3 could be detected in any of the 4 trophozoite-specific proteome datasets available at the AmoebaDB or EST datasets (as of February, 2012).