protlocassign: Constrained proportional assignment of proteins

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

Constrained proportional assignment of proteins

Description

The 'protlocassign' 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.

Value

package

References

Moore DF, Sleat DE, 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.