nikolovski2014: LOPIMS data from Nikolovski et al. (2014)

In lgatto/pRolocdata: Data accompanying the pRoloc package

LOPIMS data from Nikolovski et al. (2014)

Description

This is the data used in Nikolovksi et al. (2014). See below for details and references.

Usage

data(nikolovski2014)

Format

The data is an instance of class MSnSet from package MSnbase.

Details

Abstract: The proteomic composition of the Arabidopsis Golgi apparatus is currently reasonably well documented; however little is known about the relative abundances between different proteins within this compartment. Accurate quantitative information of Golgi resident proteins is of great importance: it facilitates a better understanding of the biochemical processes which take place within this organelle, especially those of different polysaccharide synthesis pathways. Golgi resident proteins are challenging to quantify since the abundance of this organelle is relatively low within the cell. In this study an organelle fractionation approach, targeting the Golgi apparatus, was combined with a label free quantitative mass spectrometry (MS), data-independent acquisition (DIA) method employing ion mobility separation known as LC-IMS-MSE (or HDMSE), to simultaneously localize proteins to the Golgi apparatus and assess their relative quantity. In total 102 Golgi localised proteins were quantified. These data provide new insight into Golgi apparatus organization and demonstrate that organelle fractionation in conjunction with label free quantitative MS is a powerful and relatively simple tool to access protein organelle localisation and their relative abundances. The findings presented open a unique view on the organization of the plant Golgi apparatus, leading towards novel hypotheses centered on the biochemical processes of this organelle.

These data are a concatenation of 2 LOPIMS gradients, labelled gradient A and B, each with 10 fractions.

Source

Supplemental Data downloaded from http://www.plantphysiol.org/content/early/2014/08/13/pp.114.245589/suppl/DC1, also available in the package's extdata directory.

References

Nikolovski N, Shliaha PV, Gatto L, Dupree P, Lilley KS. Label free protein quantification for plant Golgi protein localisation and abundance. Plant Physiol. 2014 Aug 13. pii: pp.114.245589. [Epub ahead of print] PubMed PMID: 25122472.

Examples

data(nikolovski2014)
pData(nikolovski2014)
library("pRoloc")
plot2D(nikolovski2014)
addLegend(nikolovski2014, where = "topright", bty = "n", cex =.7)

A <- pData(nikolovski2014)$gradient == "A"
par(mfrow = c(1, 2))
plot2D(nikolovski2014[, A], main = "Gradient A")
plot2D(nikolovski2014[, !A], main = "Gradient B")

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