title: Island clustering analysis for the comparison of the membrane and the soluble protein fractions of human brain proteome.
abstract: 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.
authors.affiliation: Korea Basic Science Institute, Daejeon, Republic of Korea.
authors.forename: Kyung-Hoon
authors.initials: KH
authors.lastname: Kwon
authors.forename: Gun Wook
authors.initials: GW
authors.lastname: Park
authors.forename: Jin Young
authors.initials: JY
authors.lastname: Kim
authors.forename: Sang Kwang
authors.initials: SK
authors.lastname: Lee
authors.forename: Jeong Hwa
authors.initials: JH
authors.lastname: Lee
authors.forename: Young Hye
authors.initials: YH
authors.lastname: Kim
authors.forename: Se-Young
authors.initials: SY
authors.lastname: Kim
authors.forename: Young Mok
authors.initials: YM
authors.lastname: Park
authors.forename: Jong Shin
authors.initials: JS
authors.lastname: Yoo
mesh_terms: 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
chemical_list: D008565:Membrane Proteins; D020543:Proteome