Subregion-Specific Proteomic Signature in the Hippocampus for Recognition Processes in Adult Mice

Abstract

The hippocampal formation is a brain structure essential for higher-order cognitive functions. It has a complex anatomical organization and cellular composition, and hippocampal subregions have different properties and functional roles. In this study, we used SWATH-MS to determine whether the proteomes of hippocampus areas CA1 and CA3 can explain the commonalities or specificities of these subregions in basal conditions and after recognition memory. We show that the proteomes of areas CA1 and CA3 are largely different in basal conditions and that differential changes and dynamics in protein expression are induced in these areas after recognition of an object or object location. While changes are consistent across both recognition paradigms in area CA1, they are not in area CA3, suggesting distinct proteomic responses in areas CA1 and CA3 for memory formation.

A mouse SWATH-MS reference spectral library enables deconvolution of species-specific proteomic alterations in human tumour xenografts

“…BAT is brown adipocyte tissue and quad is quadriceps. G) Venn diagram depicting overlap of hippocampal proteins detected by the MouseRefSWATH library and study-specific library based on analysis of the PXD006382 dataset [22]. H) Similarity matrix showing Pearson’s correlation coefficient of the 943 overlapping hippocampal proteins which were quantified by either the MouseRefSWATH library or the study-specific library.…”

“…To demonstrate the utility of the MouseRefSWATH library and benchmark its performance against study-specific libraries generated as part of published SWATH-MS studies, we applied the reference spectral library to 2 publicly available SWATH-MS datasets focused on mitochondrial [21] and hippocampal [22] proteins (Figure 1). Each dataset was analysed using either the original study-specific library generated by the authors or the MouseRefSWATH library.…”

“…We undertook a similar comparative analysis on the study by von Ziegler et al [22] where the basal mouse hippocampal proteome was analysed utilising a study-specific spectral library built from DDA data generated from the mouse hippocampus. For this analysis, the SWATH-MS experimental data of hippocampal area CA1 and CA3 from 6 different animals were analysed (Figure 2G & H).…”

Data-independent acquisition mass spectrometry (DIA-MS) for proteomic applications in oncology

“…2B). [21][22][23] However, study-specific libraries can vary between laboratories due to the lack of consistency in DDA experiments and spectral library generation. This can result in wide variations in the number and type of proteins identified and quantified between studies.…”

A mouse SWATH-MS reference spectral library enables deconvolution of species-specific proteomic alterations in human tumour xenografts

“…To demonstrate the utility of the MouseRefSWATH library and benchmark its performance against study-specific libraries generated as part of published SWATH-MS studies, we applied the reference spectral library to two publicly available SWATH-MS datasets focused on mitochondrial (Williams et al, 2018) and hippocampal (von Ziegler et al, 2018) proteins (Fig. 1).…”