Mass spectrometry image normalization

Mass spectrometry image normalization rescales the spectra associated with individual image pixels to make a specified comparison more meaningful. In mass spectrometry imaging, raw intensity depends on both the sample and measurement conditions; MALDI matrix distribution can change the recorded intensity. A normalization rule therefore embodies an assumption about which variation should be removed.^[ref]

For example, total ion current normalization divides each nonzero spectrum by the sum of its included intensities. Write pixel $p$ as values $I_{p,k}$ and setIn an invented two-feature example, spectra $(2,6)$ and $(4,12)$ both become $(1/4,3/4)$. This removes a common multiplicative change. But $(2,14)$ becomes $(1/8,7/8)$: the first feature now appears half as strong as in $(2,6)$ even though its raw intensity is unchanged. The normalized image represents a relative share of the included signal. It answers a different question from an image of raw intensity or calibrated molecular abundance.

In actual MALDI datasets, Deininger and colleagues found that locally dominant signals could introduce artifacts under total-signal normalization; they compared median and noise-based alternatives. Their examples motivate inspecting the denominator as well as the selected ion image.^[ref] Specify the mass range, excluded peaks and zero-signal handling. Neither total ion current normalization nor another single scalar correction can, in general, undo selective suppression of one molecular signal.