Table I. Summary of protein discovery results.

The total number of unique peptide spectrum matches (PSM), unique stripped peptides (unique peptide sequence disregarding variable modifications and charge state), and unique proteins identified are given for each of the nanoLC-MS experiments described here. The percent composition of each protein source (e.g. Plasmodium, mosquito, etc.) is given. Entries labeled as “Chimera” are peptides or protein inferences that correspond equally well to distinct proteins from different genera (e.g. both mosquito and Plasmodium). The row labeled “Contaminants” indicates the portion of the sample identified as common lab contaminants (e.g. keratin). Trypsin and BSA are listed separately from other contaminants because they are endogenous interferants rather than exogenous contaminants. The P. yoelii spectra were searched separately against a P. yoelii database and a P. berghei database. Two separate P. falciparum whole cell lysates were analyzed. The proteins identified by the second attempt constitute the P. falciparum proteome described in this paper. The results of the first attempt are summarized in this table to illustrate the negative effect of extensive contamination by mosquito debris.

	Whole cell lysate								Affinity capture
	P. yoelii				P. falciparum				P. yoelii				P. falciparum
	P. yoelii search		P. berghei search		1st attempt		2nd attempt		P. yoelii search		P. berghei search
	PSM	%	PSM	%	PSM	%	PSM	%	PSM	%	PSM	%	PSM	%
Peptide spectrum matches
Plasmodium	89,752	63.0	64,200	54.9	49,490	19.5	120,668	65.0	283	2.4	96	0.8	237	2.9
Mosquito	16,051	11.3	16,005	13.7	178,687	70.4	39,213	21.1	4466	37.5	4399	37.9	2517	31.0
Chimera	2476	1.7	2551	2.2	4642	1.8	3521	1.9	114	1.0	118	1.0	108	1.3
Trypsin	4548	3.2	4507	3.9	5167	2.0	7430	4.0	3565	29.9	3510	30.2	2777	34.2
BSA	21,730	15.3	21,767	18.6	11,861	4.7	6264	3.4	782	6.6	789	6.8	814	10.0
Contaminants	7869	5.5	7895	6.8	3923	1.5	8593	4.6	2709	22.7	2695	23.2	1658	20.4
TOTAL	142,426		116,926		253,770		185,689		11,919		11,607		8111

	Peptides	%	Peptides	%	Peptides	%	Peptides	%	Peptides	%	Peptides	%	Peptides	%
Unique stripped peptides
Plasmodium	14,523	80.1	9631	73.2	6615	40.8	19,440	79.2	66	3.6	41	2.3	57	4.6
Mosquito	2973	16.4	2911	22.1	9106	56.2	4401	17.9	1427	77.9	1404	78.6	799	64.8
Chimera	185	1.0	183	1.4	164	1.0	264	1.1	31	1.7	33	1.8	25	2.0
Trypsin	39	0.2	39	0.3	30	0.2	78	0.3	64	3.5	64	3.6	62	5.0
BSA	170	0.9	163	1.2	149	0.9	139	0.6	54	2.9	54	3.0	57	4.6
Contaminants	233	1.3	226	1.7	135	0.8	217	0.9	191	10.4	191	10.7	233	18.9
TOTAL	18,123		13,153		16,199		24,539		1833		1787		1233

	Proteins	%	Proteins	%	Proteins	%	Proteins	%	Proteins	%	Proteins	%	Proteins	%
Proteins
Plasmodium	1749	72.6	1466	69.3	861	39.5	1991	70.5	27	6.0	24	5.4	22	8.0
Mosquito	642	26.7	628	29.7	1311	60.1	820	29.0	411	90.7	403	91.2	227	82.8
Chimera	1	0.04	2	0.09	1	0.05	0	0.00	1	0.2	1	0.2	0	0.0
Other	17	0.7	18	0.9	9	0.4	15	0.5	14	3.1	14	3.2	25	9.1
TOTAL	2409		2114		2182		2826		453		442		274