Analyze MS/MS Protein Melting Data

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. (2014) .


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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.

Installation

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.

Usage

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.

News

mstherm 0.4.7

  • Added additional method parameters related to filtering of protein results

mstherm 0.4.6

  • Fixed conversion of MSThermResultSet to data frame

mstherm 0.4.5

  • Added export to SQLite database
  • Added RMSD as measure of fit
  • Various modifications to satisfy R CMD check
  • Renaming of some methods for the sake of clarity
  • Package name to lowercase

MSTherm 0.4.3

  • Additional normalization method (by Tm distribution)
  • Fixed warnings due to missing 'score' column (should be optional)
  • Fixed bug due to spectra with all missing quant values (from some quant software)

MSTherm 0.4.1

  • The plot.MSThermResult method has two additional arguments (CI.points and CI.Tm) which control whether to plot the confidence intervals if present. Previously these were always plotted if present. The default of both is still TRUE.

Reference manual

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install.packages("mstherm")

0.4.7 by Jeremy Volkening, 2 years ago


Browse source code at https://github.com/cran/mstherm


Authors: Jeremy Volkening [aut, cre]


Documentation:   PDF Manual  


GPL-3 license


Imports foreach, parallel, doParallel, nls2, RColorBrewer, plotrix

Suggests RSQLite, testthat, knitr, rmarkdown


See at CRAN