Improved Reproducibility of Protein Detection in Neuromelanin-containing Human Substantia Nigra Tissue enriched by Laser Microdissection

Abstract Background: Processing of post-mortem human brain tissue samples like Neuromelanin-containing substantia nigra is a challenging task in proteomics research in the context of neurodegenerative diseases such as Parkinson’s disease, due to the availability of only limited sample amounts. Therefore, a highly efficient lysis and digestion approach is needed to guarantee high reproducibility and a good quantification performance. We conducted a systematic study in order to compare qualitatively and quantitatively six different sample preparation protocols for substantia nigra brain tissue collected by laser microdissection.Results: LC-MS/MS analysis revealed that the combination of formic acid and in-solution digestion with trypsin leads to an enhanced peptide and protein identification as well as a robust and reliable protein quantification with a very good reproducibility.Conclusion: We recommend this protocol for future studies of human substantia nigra tissue as well as NM granules in the context of neurodegenerative disorders like Parkinson syndrome.