Software to aid in modeling and analyzing mass-spectrometry-based
proteome melting data. Quantitative data is imported and normalized and
thermal behavior is modeled at the protein level. Methods exist for
normalization, modeling, visualization, and export of results. For a
general introduction to MS-based thermal profiling, see Savitski et al.
MSTherm is an R package to aid in modeling and analyzing mass spectrometry-based protein melting data. Quantitative data is imported and normalized and thermal behavior is modeled at the protein level. Methods exist for normalization, visualization, exploratory analysis, and data export.
In Linux, do:
git clone https://github.com/jvolkening/r-MSTherm.git cd r-MSTherm R CMD INSTALL
You may need to install some prerequisites first depending on your environment -- the installer will notify you of this.
Once you have produced spectral quantification tables and created the necessary metadata files describing the experimental setup (as described in the vignette), a modeling session can be a simple as:
library(mstherm) expt <- MSThermExperiment("control.tsv", "annotations.tsv") expt <- normalize_to_std(expt, "BOVINE_SERUM_ALBUMIN") res <- model_experiment(expt) tbl <- as.data.frame(res) pdf("plots.pdf", 5, 5, pointsize=10) plot(res) dev.off()
(Of couse, you will likely want to experiment with the various options available to the modeling and plotting methods).
Further details of the required input files and available methods are available in the package vignette.