PlotMS for QCxMS

Plot Mass Spectra (PlotMS) plotting program for the QCxMS program.

Installation

Put the plotms executable and the .mass_raw.agr files into the $HOME folder.

Compiling

Using meson as build system requires you to install a fairly new version like 0.57.2 or newer. To use the default backend of meson you have to install ninja version 1.10 or newer.

export FC=ifort CC=icc
meson setup build -Dfortran_link_args=-static
ninja -C build 

Copy the binary from the build/plotms file into a directory in your path, e.g. ~/bin/.

Running the script

The files qcxms.res and qcxms_cid.res are produced then QCxMS is finished with the last run. Run plotms in your working directory. From version 6.0 and higher, exact masses are produced.

The following files are produced:

1. mass.agr - output in the XMGRACE format. The m/z and relative intensities can be found at the bottom of the file.
2. result.jdx - output in the JCAMP format.
3. result.csv - output in the CSV format. the m/z and the abundances values can be found.

For the older QCEIMS program, use plotms version 4.2. Calculations done with QCEIMS can still be used with newer versions by renaming the qceims.res to qcxms.res or qceims_cid.res to qcxms_cid.res .

Documentation

Find the documentation and other useful information for visualization at the PlotMS docs.