Comparison of two label-free global quantitation methods, APEX and 2D gel electrophoresis, applied to the Shigella dysenteriae proteome

Table 2 Comparison of proteins quantitated by 2D-LC-MS/MS-APEX vs. 2-DE

	2D-LC-MS/MS-APEX	2-DE
Cytoplasmic	883	234
Periplasmic	52	17
Cytoplasmic membrane	132	14
Outer membrane	80	6
Extracellular	1	-
Plasmid proteins	35	5
Hypothetical proteins	257	35
Abundance range (molecules/cell)	~20 to ~45000	~500 to ~52000
M_r range (kDa)	6.4 – 163.3	8.3 – 99.7
pI range	3.59 – 11.81	4.52 – 8.48
Net charge range	33.74 to -50	3.65 to -40
Hydropathy range	1.36 to -1.53	0.31 to -1.53
Aromaticity range	0.01 to 0.18	0.01 to 0.14

1148 SD1 proteins quantitated by 2D-LC-MS/MS-APEX were compared with 271 proteins quantitated in 2D gels based on physicochemical properties and protein subcellular localizations. APEX data revealed less constraints than 2D gel data in quantitation of proteins with physicochemical characteristics very different from mean values, including high hydrophobicity, very low M_r, high net charge and high pI values.

ISSN: 1477-5956