Island clustering analysis for the comparison of the membrane and the soluble protein fractions of human brain proteome.
A protein identified in multiple separate bands of a 1-D gel reflects variation in the molecular weight caused by alternative splicing, endoproteolytic cleavage, or PTMs, such as glycosylation or ubiquitination. To characterize such a protein distribution over the bands, we defined an entity called an 'island' as the band region including the bands of the same protein identified sequentially. We quantified the island distribution using a new variable called an Iscore. Previously, as described in Park et al.. (Proteomics 2006, 6, 4978-4986.), we analyzed human brain tissue using a multidimensional MS/MS separation method. Here, the new method of island analysis was applied to the previous proteome data. The soluble and membrane protein fractions of human brain tissue were reanalyzed using the island distribution. The proteome of the soluble fraction exhibited more variation in island positions than that of the membrane fraction. Through the island analysis, we identified protein modifications and protein complexes over the 1-D gel bands.
Kwon
Kyung-Hoon
KH
Korea Basic Science Institute, Daejeon, Republic of Korea.
Park
Gun Wook
GW
Kim
Jin Young
JY
Lee
Sang Kwang
SK
Lee
Jeong Hwa
JH
Kim
Young Hye
YH
Kim
Se-Young
SY
Park
Young Mok
YM
Yoo
Jong Shin
JS
D001921:Brain / Q000378:metabolism*; D016000:Cluster Analysis; D004591:Electrophoresis, Polyacrylamide Gel; D006801:Humans; D008565:Membrane Proteins / Q000032:analysis* / Q000737:chemistry; D020543:Proteome / Q000032:analysis* / Q000737:chemistry; D040901:Proteomics / Q000379:methods*; D012995:Solubility; D053719:Tandem Mass Spectrometry
D008565:Membrane Proteins; D020543:Proteome