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ThepRoloc suite set of software offers a complete software pipelineto analyse, visualise and interpret mass spectrometry-based spatialproteomics data such, for example, as LOPIT (Localization of OrganelleProteins by Isotope Tagging), PCP (Protein Correlation Profiling) orhyperLOPIT (hyperplexed LOPIT). The suite includespRoloc,the mail software that focuses on data analysis using state-of-the-artmachine learning,pRolocdata,that distributes numerous datasets, andpRolocGUI, that offersinteractive visualisations dedicated to spatial proteomics. Thesoftware are distributed as part of theR/Bioconductor project.

ThepRoloc software comes with ampledocumentation. Themain tutorial providesa broad overview of the package and its functionality. See theArticles tab for additional manuals.

pRolocGUIalso offer several documentation files.

Here are a set ofvideo tutorialthat illustrate thepRoloc framework.

Post your questions on theBioconductor support site,tagging it with the package namepRoloc (the maintainer willautomatically be notified by email). If you identify a bug or have afeature request, please open anissue on the githubdevelopment page.

The preferred installation procedure uses the Bioconductorinfrastructure:

## unless BiocManager is already installedinstall.packages("BiocManager")## thenBiocManager::install("pRoloc")BiocManager::install("pRolocdata")BiocManager::install("pRolocGUI")

The pre-release/development code on github can also be installed usingBiocManager::install, as shown below. Note that this requires aworking R build environment (i.eRtools on Windows - seehere). Newpre-release features might not be documented not thoroughly tested andcould substantially change prior to release. Use at your own risks.

## unless BiocManager is already installedinstall.packages("BiocManager")## then, install from githubBiocManager::install("lgatto/pRoloc")BiocManager::install("lgatto/pRolocdata")BiocManager::install("lgatto/pRolocGUI")

For refences about the software, how to use it and spatial proteomicsdata analysis:

• Crook OM, Breckels LM, Lilley KS, Kirk PWD, Gatto L. A Bioconductorworkflow for the Bayesian analysis of spatial proteomics [version 1;peer review: awaiting peer review]. F1000Research 2019, 8:446(https://doi.org/10.12688/f1000research.18636.1)

• Breckels LM, Mulvey CM, Lilley KS and Gatto L. A Bioconductorworkflow for processing and analysing spatial proteomics data[version 2; peer review: 2 approved]. F1000Research 2018, 5:2926(https://doi.org/10.12688/f1000research.10411.2)

• Gatto L, Breckels LM, Burger T, Nightingale DJ, Groen AJ, CampbellC, Nikolovski N, Mulvey CM, Christoforou A, Ferro M, Lilley KS.Afoundation for reliable spatial proteomics data analysis Mol CellProteomics. 2014 Aug;13(8):1937-52. doi:10.1074/mcp.M113.036350. Epub 2014 May 20.PubMed PMID:24846987

• Gatto L, Breckels LM, Wieczorek S, Burger T, LilleyKS.Mass-spectrometry-based spatial proteomics data analysis usingpRoloc and pRolocdata Bioinformatics. 2014 May 1;30(9):1322-4. doi:10.1093/bioinformatics/btu013. Epub 2014 Jan 11.PubMed PMID:24413670.

Specific algorithms available in the software:

• Breckels LM, Gatto L, Christoforou A, Groen AJ, Lilley KS, TrotterMW.The effect of organelle discovery upon sub-cellular proteinlocalisation J Proteomics. 2013 Aug 2;88:129-40. doi:10.1016/j.jprot.2013.02.019. Epub 2013 Mar 21.PubMed PMID:23523639.

• Breckels LM, Holden S, Wojnar D, Mulvey CMM, Christoforou A, GroenAJ, Kohlbacher O, Lilley KS and Gatto L.Learning fromheterogeneous data sources: an application in spatial proteomics2015 biorXiv, doi:http://dx.doi.org/10.1101/022152

• Oliver M Crook, Claire M Mulvey, Paul D. W. Kirk, Kathryn S Lilley,Laurent GattoA Bayesian Mixture Modelling Approach For SpatialProteomics PLOS Computational Biologydoi:10.1371/journal.pcbi.1006516

• R and Bioconductor for proteomicsweb page andpackage

• Bioconductor proteomicsworkflow

Contributions to the package are more than welcome. If you want tocontribute to this package, you should follow the same conventions asthe rest of the functions whenever it makes sense to do so. Feel freeto get in touch (preferable opening agithub issue) to discussany suggestions.

Please note that this project is released with aContributor Code of Conduct.By participating in this project you agree to abide by its terms.