Suspension TRAPping filter (sTRAP) sample preparation for quantitative proteomics in the low µg input range using a plasmid DNA micro-spin column: analysis of the hippocampus from the 5xFAD Alzheimer’s Disease mouse model

Suspension TRAPping filter (sTRAP) is an attractive sample preparation method for proteomics study. Here, we demonstrated the use of a low-cost Plasmid DNA spin column for sTRAP. We first evaluated, the reproducibility of this protocol and the low CoV using 4 replicates of 5-10 µg of a synapse enriched fraction, with 120 ng of the resulting tryptic peptides for mass spectrometry resulted in 5500 protein groups identification with CoV of 3.5%. We have also tested lower input amounts of 0.6 µg and 0.3 µg with CoV increase slightly to 5-8%. Comparing other sample preparation protocols, as the in-gel digestion and the commercial protifi sTRAP with the plasmid DNA micro-spin, the last is superior in both protein and peptide identification numbers (48523, 56714 to 60245 peptides and 5669, 6106, 6494 proteins respectively) and smaller Coefficient of Variation ( 6.7%, 3.2%, 3.1% respectively).We applied this protocol to the analysis of hippocampal proteome from a mouse model of Alzheimer’s disease, and identified about 6300 protein groups with CV of 11.6-14.6%. Protein changes in the mutant mice points to the alteration of processes related to known major AD-related pathology.