Shin2020: Spatial proteomics defines the content of trafficking...

In lgatto/pRolocdata: Data accompanying the pRoloc package

Spatial proteomics defines the content of trafficking vesicles captured by golgin tethers

Description

Data from 'Spatial proteomics defines the content of trafficking vesicles captured by golgin tethers'

Intracellular traffic between compartments of the secretory and endocytic pathways is mediated by vesicle-based carriers. The precise and complete proteomes of carriers destined for many organelles are ill-defined because the vesicular intermediates are transient, low-abundance and difficult to purify. Here, we combine vesicle relocalisation with organelle proteomics and Bayesian analysis to define the content of different endosome-derived vesicles destined for the trans-Golgi network (TGN). The golgin coiled-coil proteins golgin-97, golgin-245 and GCC88, shown previously to capture endosome-derived vesicles at the TGN, were individually relocalised to mitochondria and the content of subsequently re-routed vesicles was determined by organelle proteomics. Our findings revealed 45 integral and 51 peripheral membrane proteins re-routed by golgin-97, evidence for a distinct class of vesicles shared by golgin-97 and GCC88, and various cargoes specific to individual golgins. These results illustrate a general strategy for analysing intracellular sub-proteomes by combining acute cellular re-wiring with high-resolution spatial proteomics.

Usage

  data("Shin2019MitoControlrep1")
  data("Shin2019MitoGcc88rep1")
  data("Shin2019MitoGol97rep1")

Format

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

References

Spatial proteomics defines the content of trafficking vesicles captured by golgin tethers. John J.H. Shin, Oliver M. Crook, Alicia C. Borgeaud, Jerome Cattin-Ortola, Sew-Yeu Peak- Chew, Jessica Chadwick, Kathryn S. Lilley, Sean Munro.

Examples

  data(Shin2019MitoControlrep1)
  Shin2019MitoControlrep1
  pData(Shin2019MitoControlrep1)
  exprs(Shin2019MitoControlrep1)[1:3,1:3]
  
  library("pRoloc")
  plot2D(Shin2019MitoControlrep1, main = "Shin 2019 HeK 293T WT")

lgatto/pRolocdata documentation built on April 7, 2023, 1:56 a.m.