stekhoven2014: Data from Stekhoven et al. 2014

In lgatto/pRolocdata: Data accompanying the pRoloc package

Data from Stekhoven et al. 2014

Description

Proteomics data provide unique insights into biological systems, including the predominant subcellular localization (SCL) of proteins, which can reveal important clues about their functions. Here we analyzed data of a complete prokaryotic proteome expressed under two conditions mimicking interaction of the emerging pathogen Bartonella henselae with its mammalian host. Normalized spectral count data from cytoplasmic, total membrane, inner and outer membrane fractions allowed us to identify the predominant SCL for 82 proteins. The spectral count proportion of total membrane versus cytoplasmic fractions indicated the propensity of cytoplasmic proteins to co-fractionate with the inner membrane, and enabled us to distinguish cytoplasmic, peripheral inner membrane and bona fide inner membrane proteins. Principal component analysis and k-nearest neighbor classification training on selected marker proteins or predominantly localized proteins, allowed us to determine an extensive catalog of at least 74 expressed outer membrane proteins, and to extend the SCL assignment to 94% of the identified proteins, including 18 silico methods gave no prediction. Suitable experimental proteomics data combined with straightforward computational approaches can thus identify the predominant SCL on a proteome-wide scale. Finally, we present a conceptual approach to identify proteins potentially changing their SCL in a condition-dependent fashion.

Usage

data("stekhoven2014")

References

Stekhoven DJ, Omasits U, Quebatte M, Dehio C, Ahrens CH. Proteome-wide identification of predominant subcellular protein localizations in a bacterial model organism. J Proteomics. 2014 Mar 17;99:123-37. doi:10.1016/j.jprot.2014.01.015. Epub 2014 Jan 28. PubMed PMID: 24486812.

Examples

data(stekhoven2014)
library("pRoloc")
plot2D(stekhoven2014)

lgatto/pRolocdata documentation built on Oct. 17, 2024, 10:16 p.m.