4 research outputs found
Brain Region-Specific Dynamics of On-Tissue Protein Digestion Using MALDI Mass Spectrometry Imaging
In mass spectrometry imaging (MSI),
on-tissue proteolytic digestion
is performed to access larger protein species and to assign protein
identities through matching the detected peaks with those obtained
by LCāMS/MS analyses of tissue extracts. The on-tissue proteolytic
digestion also allows the analysis of proteins from formalin-fixed,
paraffin-embedded tissues. For these reasons, on-tissue digestion-based
MSI is frequently used in clinical investigations, for example, to
determine changes in protein content and distribution associated with
a disease. In this work, we sought to investigate the completeness
and uniformity of the digestion in on-tissue digestion MSI. On the
basis of an extensive experiment investigating three groups with varying
incubation times: (i) 1.5 h, (ii) 3 h, and (iii) 18 h, we have found
that longer incubation times improve the repeatability of the analyses.
Furthermore, we discovered morphology-associated differences in the
completeness of the proteolysis for short incubation times. These
results support the notion that a more complete proteolysis allows
better quantitation
Comprehensive Analysis of the Mouse Brain Proteome Sampled in Mass Spectrometry Imaging
On-tissue enzymatic digestion is
performed in mass spectrometry
imaging (MSI) experiments to access larger proteins and to assign
protein identities. Most on-tissue digestion MSI studies have focused
on method development rather than identifying the molecular features
observed. Herein, we report a comprehensive study of the mouse brain
proteome sampled by MSI. Using complementary proteases, we were able
to identify 5337 peptides in the matrix-assisted laser desorption/ionization
(MALDI) matrix, corresponding to 1198 proteins. 630 of these peptides,
corresponding to 280 proteins, could be assigned to peaks in MSI data
sets. Gene ontology and pathway analyses revealed that many of the
proteins are involved in neurodegenerative disorders, such as Alzheimerās,
Parkinsonās, and Huntingtonās disease
Automatic Registration of Mass Spectrometry Imaging Data Sets to the Allen Brain Atlas
Mass
spectrometry imaging holds great potential for understanding
the molecular basis of neurological disease. Several key studies have
demonstrated its ability to uncover disease-related biomolecular changes
in rodent models of disease, even if highly localized or invisible
to established histological methods. The high analytical reproducibility
necessary for the biomedical application of mass spectrometry imaging
means it is widely developed in mass spectrometry laboratories. However,
many lack the expertise to correctly annotate the complex anatomy
of brain tissue, or have the capacity to analyze the number of animals
required in preclinical studies, especially considering the significant
variability in sizes of brain regions. To address this issue, we have
developed a pipeline to automatically map mass spectrometry imaging
data sets of mouse brains to the Allen Brain Reference Atlas, which
contains publically available data combining gene expression with
brain anatomical locations. Our pipeline enables facile and rapid
interanimal comparisons by first testing if each animalās tissue
section was sampled at a similar location and enabling the extraction
of the biomolecular signatures from specific brain regions
Automatic Generic Registration of Mass Spectrometry Imaging Data to Histology Using Nonlinear Stochastic Embedding
The
combination of mass spectrometry imaging and histology has
proven a powerful approach for obtaining molecular signatures from
specific cells/tissues of interest, whether to identify biomolecular
changes associated with specific histopathological entities or to
determine the amount of a drug in specific organs/compartments. Currently
there is no software that is able to explicitly register mass spectrometry
imaging data spanning different ionization techniques or mass analyzers.
Accordingly, the full capabilities of mass spectrometry imaging are
at present underexploited. Here we present a fully automated generic
approach for registering mass spectrometry imaging data to histology
and demonstrate its capabilities for multiple mass analyzers, multiple
ionization sources, and multiple tissue types