plot-mass-error

For tandem mass spectrometry data (MS2) searched with Comet, plot the mass error

This describes how to install the software needed to create plots using the R script plot-mass-error.R, and how to run this script. This script can only be used with search results of Comet.

Installation

Note: installation must be executed with root (Linux)/ Administrator (Windows) privileges.

Install R from https://cran.r-project.org/
Start R:
```
cd "\Program Files\R\R-4.3.0"
R
```

Install standard R packages, install BioConductor and install MSnbase. From the R command prompt:

install.packages(c("stringr", "futile.logger", "optparse", "ggplot2", "gridExtra"))
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install(version = "3.17")
BiocManager::install("MSnbase")

Execution

After the above software is installed, plots can be generated by running from the command prompt:

Rscript plot-mass-error.R -e 0.01 -m 10 --outfile=recalplot --name="Mass error" somefile.mzid

Where option -e is the cutoff value for the Comet expect score and option -m is the maximum ppm error included in the plot, and the final arguments are the mzID file of the data.

524D/plot-mass-error

plot-mass-error

Installation

Execution