Producing Publication - Quality Mass Spectra

Fatty Acids and Mass Spectrometry

Here I describe how all the mass spectra on this website were produced from the raw data files produced by Agilent/HP gas chromatography-mass spectrometry software. Note: some details of the Agilent software are modified from time to time, so the command structure on some versions may differ from that described below. The process I describe could no doubt be adapted for instruments from other manufacturers, but I have no relevant experience. Similarly, I only have experience of programs running under Microsoft Windows.

The first step is to obtain the best possible spectrum from the raw data files by averaging the spectrum over the selected GC-MS peak and subtracting noise from an appropriate adjacent area. In the example, below, I have selected a mass spectrum of methyl oleate. The basic spectrum output from the instrument is –

Mass spectrum of methyl oleate - first step

Next, we must remove any extension to the spectrum due to noise in the high molecular weight range (and if required below m/z = 50) and normalize the spectrum to make the base peak at 100%. This is done from the command line in the instrument software.

To eliminate high molecular weight noise, type -

msclip x,a:600       [enter]       where a = MW of compound +10

To eliminate low molecular weight fragments, type -

msclip x,0:50       [enter]       (for example)

To normalize to 100%, type -

norm 100       [enter]

To redraw the amended spectrum on the computer screen, type -

draw 1,x       [enter]

The spectrum will now look like this -

Mass spectrum of methyl oleate - second step

Go to the OPTIONS menu, and select Copy Window. At the prompt, type 1 for the spectrum window. The spectrum will be copied to the clipboard and can be pasted into Word, Access, Powerpoint, etc. However, the most elegant option is to copy into Metafile CompanionTM to change fonts, colours and line thickness, and generally tidy up for presentation purposes. This is a small inexpensive (currently $29 US) program, available online at It is available free for trial purposes.

Copy the required spectrum from the clipboard into Metafile CompanionTM.

Use the selection arrow tool to select the whole figure, or better go to the ‘Select’ menu, and click on ‘All’.

In the Format menu, select ‘Line’ and change the line width to 10. Select Colour, and change to black (bottom left-hand corner). Then go to ‘Text’ and click on Font: select ‘Arial’ and adjust the size to 8. As before, go to the Colour menu and change to black. Go to ‘Other’, and highlight ‘transparent’ under ‘Background Mode’. Exit the Format menu.

The spectrum is now –

Mass spectrum of methyl oleate - third step

Tidy up the spectrum by removing unwanted text items. Select with the arrow tool and press ‘delete’. For example, on the y-axis, remove intermediate numbers - 5, 15, 25, etc (and 0) – if present. Numbers can be changed by double clicking with the arrow tool to bring up a dialogue box that permits editing. Tidy up the m/z box by removing extra characters and moving along the x-axis to the end (delete the last number on the axis if necessary); italicise it. Move ‘Abundance’ closer to the y-axis and add ‘%’ below this. Add appropriate numbers above unmarked ions where required.

Convert the legends to the x- and y-axis to a bold typeface.

Use the selection arrow tool again to select the whole figure, or go to the ‘Select’ menu, and click on ‘All’, then centre the figure on the page. The file should now be saved to disk with an appropriate name in the Windows Metafile format (.wmf).

For many purposes, the spectrum below would now be considered complete and ready for publication.

Mass spectrum of methyl oleate - fourth step

However, it is also possible to add further information.

To create new text boxes, click on the text-tool (letter A on the left menu), and then at the approximate point where it is required. A menu will appear in which the additional text can be entered. It can be positioned using the selection tool, and the font size determined by using the Font tools on the main tool bar. For example, it is useful to label the molecular ion by adding ‘M+’ above the appropriate ion.

To enter a structural formula or other figure from ChemWindowsTM, ChemDrawTM or other chemical drawing software, it is first necessary to reduce the scale of the figure to the approximate size required (by moving an ‘anchor’ on one corner of the figure), then copy and paste it onto the mass spectrum. If the size is wrong, delete it or ‘undo’ from the ‘edit’ menu, re-size and repeat the process. Use the Select arrow to move the figure to a suitable place within the spectrum.

It is also possible to change the colour of any of the text (or of the graphics) to highlight important aspects of the spectrum, for example for a Web document or for a Powerpoint presentation.

The final spectrum below has been modified from the previous to illustrate the kind of changes that are possible.

Mass spectrum of methyl oleate - final step

When multiple mass spectra on one figure are required, I find the simplest method is to copy them consecutively to Microsoft Word or Powerpoint and resize as appropriate.

Total ion current traces from Agilent mass spectrometers can be annotated in the same way, but because these may potentially contain a very large number of data points, they can be slow to load into Metafile Companion.

To convert to a format suitable for the web. First copy into Word and re-size as appropriate. Then hold down the [Ctrl] and [Alt] keys and press the [Prt Scrn] key. This captures the active window, which can be pasted into a program such as the free Microsoft Paint. The surplus material is removed by using the cropping tool, when the figure can be saved as a .png or .gif file.

Updated March 3, 2014