Towards a membrane proteome in Drosophila: a method for the isolation of plasma membrane

BMC Genomics

Table 2 Membrane and compartment assignments for identified proteins.

Category	Compartment	Flybase annotation	Percent integral¹	Number of proteins in category	Percentage of all proteins
Plasma Membrane	Plasma membrane	Plasma membrane	60% (57/95)	95	22%
Candidate Plasma Membrane Residents (Integral)	Not assigned	Membrane	50% (10/21)	74	17%
		Integral to membrane	100% (21/21)
		None but we predict ≥ 1 transmembrane domain	100% (43/43)
Candidate Plasma Membrane Residents (Peripheral)	Not assigned	Membrane	N/A² 11 proteins	74	17%
		None with no predicted transmembrane domains	N/A² 63 proteins
Lipid particles	Lipid particles	Lipid particles	22% (16/74)	74	17%
Other	Cytoplasm and Nucleus	Cytoplasm Cytoskeleton Nucleus Ribosomes	6% (4/69)	69	16%
Mitochondrial	Mitochondrial	Mitochondrial	18% (5/38)	38	9%
Endoplasmic reticulum and Golgi	Endoplasmic reticulum and Golgi	Endoplasmic reticulum and Golgi	38% (3/8)	8	2%
All compartments			37% (159/432)	432	100%

¹Proteins predicted by hydropathy analysis to have ≥ 1 transmembrane domain
²Not Applicable - neither category has any predicted integral membrane proteins.
The table shows the number of proteins assigned to compartments based on their Flybase annotation in conjunction with our hydropathy analysis. The biggest single category has been annotated in Flybase as 'Plasma membrane'. The next two categories we predict will also contain a substantial fraction, which are in the PM compartment; however, this will obviously require experimental verification by interested investigators (see text for discussion).

ISSN: 1471-2164