Plotting Mass Spectra (PlotMS)

The PlotMS utility was developed to visualize the results of QCxMS calculations. The newest version can be found in the PlotMS repository.

The program analyzes the qcxms.res or qcxms_cid.res file and provides the results as m/z-values and abundances. Versions 6.0 and higher provide exact masses of the fragments.

To run the program, change into your working directory and run plotms. This generates three files:
  • mass.agr -> XMGRACE file using the ~/.mass_raw.agr template file

  • results.jdx -> JCAMP-DX ( Joint Committee on Atomic and Molecular Physical data) file

  • results.csv -> CSV (comma seperated values) file for spreadsheet programs (e.g. Excel)

The spectra can be plotted as soon as the production run has started by using the getres script, which creates an tmpqcxms.res file. The file has to be deleted before getres is used a second time.

For a comparison to experimental EI spectra, a spectrum can be downloaded from the NIST database if available (JCAMP-DX format). Copy it to the working directory as exp.dat. PlotMS reads the exp.dat and compares your calculated spectrum directly to the experiment (inverted). A matching score is printed at the end of the program output.


There is currently no feature to do this for the CID spectrum as well.


In PlotMS version 6.0, the automatic matching score calculation is not supported!

Program flags and command-line options

There are some useful command-line options to manipulate your results.


print spectra “mass % intensity counts Int. exptl” to stdout with “Int. exptl” (experimental) taken from exp.dat but not all exp peaks are exported, if no theoretical counterpart exists

-f <filename> or -f <name_of_res_file>

provide .res file for plotting the spectrum

-t <x> <y>

couting ions with charge x to y (give the value, e.g. “-t 1 2” for charge 1 to 2)

-w <real>

broadening the charges by an standard distribution (given in decimal numbers between 0 and 1)

-s <integer>

account only for only secondary and tertiary fragmentations (give the value, e.g. “-s 2” for secondary)

-m <integer>

set minimum value for m/z, so rel. 100% value will be calculated for higher masses (x-axis)

-i <real>

set the minimum rel. intensity from which the signals are counted (y-axis)


do not calculate the isotope pattern

Visualization of Trajectories

Trajectories are saved in the TMPQCXMS/TMP.XXX directories, where NUM is the first number of the specific trajectory track to be visualized. There are two programs that can easily display the trajectories, which are saved in the files. One is (g)molden, the other is VMD. Obtaining a video (.avi) of a given trajectory is possibly most easily done by loading the trajectory of choice into VMD (file type .xyz).

The msmovie and movie.tcl scripts for VMD generate a visualization using the dynamic bonds graphical representations setting. This allows for movie generation employing the VMD movie maker plug-in. Simply type msmovie X Y in the working directory to load the trajectory TMPQCEIMS/TMP.X/trj.X.Y. For instance, msmovie 1 1 loads the first trajectory of the first folder. Some adjustments according to personal preferences for movie-making may have to be made in these scripts.