Mass spectrometrical characterisation of mouse and rat synapsin isoforms 2a and 2b

Synapsin 2 proteins are key elements of the synaptic machinery and still hold the centre stage in neuroscience research. Although fully sequenced at the nucleic acid level in mouse and rat, structural information on amino acid sequences and post-translational modifications (PTMs) is limited. Knowledge on protein sequences and PTMs, however, is mandatory for several purposes including conformational studies and the generation of antibodies. Hippocampal proteins from rat and mouse were extracted, run on two-dimensional gel electrophoresis and multi-enzyme digestion was carried out to generate peptides for mass spectrometrical analysis [nano-LC-ESI-(CID/ETD)-MS/MS]. As much as 12 synapsin 2 proteins (6 alpha and 6 beta isoforms) in the mouse and 13 synapsin 2 proteins (6 alpha and 7 beta isoforms) were observed in the rat. Protein sequences were highly identical to nucleic acid sequences, and only few amino acid exchanges probably representing polymorphisms or sequence conflicts were detected. Mouse and rat synapsins 2a differed in three amino acids, while rat and mouse synapsins 2b differed in two amino acids. As much as 13 phosphorylation sites were determined by MS/MS data in rat and mouse hippocampus and 5 were verified by phosphatase treatment. These findings are important for interpretation of previous results and design of future studies on synapsins.