README.md

In mooredf22/protlocassign: Estimation of protein distribution from quantitative subcellular fractionation experiments using a constrained proportional assignment model

protlocassign: A method for proportionally assigning protein residence among subcellular organelles

Introduction

This package implements constrained proportional assignment to assign proteins proportionately to their subcellular organelle residences. It uses quantitative mass spectrometry data from subcellular fractionation experiments to create profiles describing the distribution of proteins and peptides across centrifugation fractions. The package identifies outlier spectra and computes weighted means across peptides using random effects models. Then, using reference proteins that reside in single compartments, it estimates the distribution of each protein across these compartments by obtaining optimal mixtures of the reference profiles.

Installation

Start by installing the package from Bioconductor. For this you will need the Bioconductor installation facility BiocManager, which may be installed from CRAN as follows:

install.packages("BiocManager")

Then obtain the protlocassign package as follows:

BiocManager::install("protlocassign")

Alternatively, one may install a development version directly from Github by first installing the devtools package from CRAN:

install.packages("devtools")

and then installing the github version of protlocassign:

devtools::install_github("mooredf22/protlocassign")

Next, install other required packages:

BiocManager::install(c("BB", "pracma", "lme4", "outliers", "BiocParallel"))

Finally, load the package:

library(protlocassign)

This will make the programs and datasets available. Instructions for use of the package are in the vignette.

References

Jadot, M.; Boonen, M.; Thirion, J.; Wang, N.; Xing, J.; Zhao, C.; Tannous, A.; Qian, M.; Zheng, H.; Everett, J. K., Accounting for protein subcellular localization: A compartmental map of the rat liver proteome. Molecular & Cellular Proteomics 2017, 16, (2), 194-212.

Moore DF, Sleat D, Lobel P. A method to estimate the distribution of proteins across multiple compartments using data from quantitative proteomics subcellular fractionation experiments. Journal of Proteome Research, 2022, 21, 6, 1371-1381 https://doi.org/10.1021/acs.jproteome.1c00781

Tannous, A.; Boonen, M.; Zheng, H.; Zhao, C.; Germain, C. J.; Moore, D. F.; Sleat, D. E.; Jadot, M.; Lobel, P., Comparative analysis of quantitative mass spectrometric methods for subcellular proteomics. J Proteome Res 2020, 19, (4), 1718-1730.

mooredf22/protlocassign documentation built on Sept. 13, 2023, 3:57 p.m.