Methodology: an optimized, high-yield tomato leaf chloroplast isolation and stroma extraction protocol for proteomics analyses and identification of chloroplast co-localizing proteins

Table 2 Comparison of deduced protein localization for the 254 co-isolating proteins, proteins detected by one unique peptide, and sporadically identified proteins

Location^a	Co-isolating proteins^b			“1 unique peptide” proteins^c			“Sporadically identified” proteins^d
Location^a	# proteins	%	% total proteins identified	# proteins	%	% total proteins identified	# proteins	%	% total proteins identified
Cytosol	92	36.22	4.21	59	34.10	2.70	52	36.11	2.38
Endomembrane	45	17.72	2.06	25	14.45	1.14	27	18.75	1.24
Mitochondrion	52	20.47	2.38	25	14.45	1.14	21	14.58	0.96
Nucleus	37	14.57	1.69	32	18.50	1.46	30	20.83	1.37
Peroxisome	19	7.48	0.87	5	2.89	0.23	4	2.78	0.18
Plasma membrane	4	1.57	0.18	9	5.20	0.41	1	0.69	0.05
Unknown/Multiple	5	1.97	0.23	17	9.83	0.78	9	6.25	0.41
Total	254	100.00	11.62	172	99.42	7.87	144	100.00	6.59

^aBased on predictions for the localization of the the tomato proteins by TargetP, ChloroP, Predotar, WoLF PSORT, and YLoc and the known localization (PPDB, plprot, SUBA4) and functions of Arabidopsis homologs proteins (TAIR); the locations of some proteins had multiple subcellular locations or their location could not be inferred
^bThe identity and putative locations of the proteins that reproducibly co-isolated (CIPs) with the tomato chloroplast stroma are found in Additional file 5: Table S5
^cThe identity and putative locations of the proteins identified by a single unique peptide are found in Additional file 3: Table S3
^dThe identity and putative locations of the proteins that were sporadically identified in the chloroplast stroma are found in Additional file 4: Table S4

ISSN: 1746-4811