Averaging Mass Spectra

There are several reasons for averaging individual mass spectra. First and foremost, averaging allows the spectral signal-to-noise ratio (SNR) to be improved. A second purpose of averaging spectra is to eliminate the degree of spectral variability when measuring spatially inhomogeneous samples from different sample spots. Finally, spectral averaging can be useful when preparing illustrations for presentations or scientific publications.

IMPORTANT: Average spectra should not be used as inputs for identification algorithms. For this purpose please use the function create database spectra from individual microbial mass spectra.

Producing average spectra

1. Load the mass spectral data files via the load spectra (Bruker data file format), import spectra from mzXML data, or the load MS multifile options of the File pull down menu.

2. To produce an average spectrum select the respective mass spectra in the list box at the top left corner (the list box is labeled by MicrobeMS spectra ID`s). To select multiple spectra hold the <shift> key while selecting.

3. Start the procedure by selecting average spectra --> from selection from the Analysis pull down menu. Average spectra can be also created from labeled spectra, i.e. from spectra with a class assignment. Labeling, or class assignment, can be carried out by selecting the appropriate spectra and choosing class assignments --> class X from the Edit pull down menu.

4. Average spectra are created by a simple averaging procedure, either from original, or from pre-processed mass spectra (depending on the status of the checkbox org.spectra in the VIEW tab). When averaging is finished a new file id in the format avrgspec-DD-MON-YEAR-HR-MI-SE.XXX is created. Note that the metadata from the first spectrum are automatically adopted as the metadata of the average spectrum.