In situ proteomics with imaging mass spectrometry and principal component analysis in the Scrapper‐knockout mouse brain

Abstract

Imaging MS is emerging as a useful tool for proteomic analysis. We utilized this technique to analyze gene knockout (KO) mice in addition to traditional 2-DE analysis. The Scrapper-knockout (SCR-KO) mouse brain showed two types of neurodegenerative pathologies, the spongiform neurodegeneration and shrinkage of neuronal cells. 2-DE analysis of the whole brain lysates of SCR-KO mice indicated slight changes in annexin A6, Rap1 GTPase, and glyoxalase domain containing four spots while most of the main components did not show significant changes. By imaging MS analysis based on principal component analysis (PCA), we could find numerous alterations in the KO mouse brain. Furthermore, we could also know the information on the position of altered substances all together. PCA provides information about which molecules in tissue microdomains have altered and is helpful in analyzing large dataset of imaging MS, while exact identification of each molecule from peaks in MALDI imaging MS may require additional analyses such as MS/MS. Direct imaging with PCA is a powerful tool to perform in situ proteomics and will lead to novel findings. Our study shows that imaging MS yields information complementary to conventional 2-DE analysis.

Spatial Segmentation of Imaging Mass Spectrometry Data with Edge-Preserving Image Denoising and Clustering

“…A widely used way of visualizing an IMS data set is to plot loadings derived with principal component analysis (PCA) 16 or improved variants of PCA 17 that provides images showing the main structure of the data set. However, the PCA loadings can hardly be interpreted from a mass spectrometric point of view, since certain mass spectra negatively contribute to the resulting image, that has no analytical meaning (see the paper by Deininger et al for a discussion on disadvantages of PCA in the MALDI-imaging context).…”

Selective Analysis of Lipids by Thin-Layer Chromatography Blot Matrix-Assisted Laser Desorption/Ionization Imaging Mass Spectrometry

“…Direct analysis of a tissue section with IMS allows for the detection of a wide range of molecules such as lipids 10 , peptides 11 , and nutrients 12,13 as well as administered pharmaceuticals 14 . Although IMS can be used to directly analyze the TLC surface TLC-IMS , complete retrieval of the target compound from the silica coated onto the plate is diffi cult.…”

MALDI Imaging Mass Spectrometry—A Mini Review of Methods and Recent Developments

“…Many leading edge data analyses have been introduced to IMS data analysis; Principal component analysis degenerates data dimensions and enhances the difference among data. 31,32) Hierarchical cluster analysis reveals relationships among molecules and classifies them. 31,33) Multivariate curve resolution can reveal mixed spectra from observed single spectrum.…”