pRolocGUI package is an interactive interface to explore and visualise experimental mass spectrometry-based spatial proteomics data. It relies on the
shiny framework for interactive visualisation, the
MSnbase package to handle data and metadata and the
pRoloc software for spatial proteomics specific data matters. Example spatial data is available in the
pRolocdata experiment package.
pRoloc suite set of software are distributed as part of the
R/Bioconductor project and are developed at the Computational Proteomics Unit at the Cambridge Centre for Proteomics labs, at the University of Cambridge.
This document describes the installation of the software, followed by a basic quick start guide for using
pRolocGUI to search and visualise the organelle map. Please refer to the respective documentation and vignettes for full details about the software.
If you use these open-source software for your research, please cite:
Gatto L, Breckels LM, Wieczorek S, Burger T, Lilley KS. Mass-spectrometry-based spatial proteomics data analysis using pRoloc and pRolocdata. Bioinformatics. 2014 May 1;30(9):1322-4. doi:10.1093/bioinformatics/btu013. Epub 2014 Jan 11. PMID:24413670; PMCID:PMC3998135.
Breckels LM, Gatto L, Christoforou A, Groen AJ, Lilley KS, Trotter MW. The effect of organelle discovery upon sub-cellular protein localisation. J Proteomics. 2013 Mar 21. doi:pii: S1874-3919(13)00094-8. 10.1016/j.jprot.2013.02.019. PMID:23523639.
Gatto L., Breckels L.M., Burger T, Nightingale D.J.H., Groen A.J., Campbell C., Mulvey C.M., Christoforou A., Ferro M., Lilley K.S. ‘A foundation for reliable spatial proteomics data analysis’ Mol Cell Proteomics. 2014 May 20.
pRolocGUI is written in the
R programming language. Before installing the software you need to download
R and (optionally)
1) Download the latest
R release for your operating system from the R website and install it.
2) Optional, but recommended. Download and install the RStudio IDE.
RStudio provides a good code editor and excellent integration with the
4) Install the Bioconductor packages
R >= 3.1.1 and Bioconductor version
>= 3.0. In an
R console, type
if (!requireNamespace("BiocManager", quietly=TRUE)) install.packages("BiocManager") BiocManager::install(c("pRoloc", "pRolocdata", "pRolocGUI"))
The development code on github can also be installed using
install_github). New pre-release features might not be documented or thoroughly tested and could substantially change prior to release. Use at your own risks.
Before using a package’s functionality, it needs to be loaded:
We first load data from Christoforou et al 2016 distributed in the
There are 3 different visualisation applications currently available:
compare. These apps are launched using the
pRolocVis function and passing
object, which is an
MSnSet containing the data one wishes to interrogate. One may also specify which app they wish to use by using the
app argument, see
?pRolocVis for more details. The default app that is loaded if
app is not specified is the
The graphical interface is described in details in the package vignette that is included in the package itself (get it by typing
R), available by clicking the
? once the interface is loaded or can be consulted online.
pRolocGUI- This tutorial is for the older legacy applications. New videos will appear shortly for the new applications.
pRolocGUIto explore and visualise experimental spatial proteomics data - This tutorial is for the older legacy applications. New videos will appear shortly for the new applications.