Hierarchical Biclustering of Mouse Pancreas Mass Spectrometry Imaging Data Using Recursive Rank-2 Non-negative Matrix Factorization

One of the main challenges in mass spectrometry imaging data analysis remains the analysis of <i>m</i>/<i>z</i>-spectra displaying a low signal-to-noise ratio caused by their low abundance, sample preparation, matrix effects, fragmentation, and other artifacts. Additionally, we observe that molecules with a high abundance suppress those with lower intensities and misdirect classical tools for MSI data analysis, such as principal component analysis. As a result, the observed significance of a molecule may not always be directly related to its abundance. In this work, we present a recursive rank-2 non-negative matrix factorization (rr2-NMF) algorithm that automatically returns spectral and spatial visualization of colocalized molecules, both highly and lowly abundant. Using this hierarchical decomposition, our method finds spatial and spectral correlations on different levels of abundances. The quality of the analysis is evaluated on MALDI-TOF data of healthy mouse pancreatic tissue for the annotation of molecules of interest in the lower abundances. The results show interesting findings regarding the functioning and colocalization of certain molecules.