Seagrass Omics: How to Short the Workflow for Protein Expression Analyses

When planning a differential protein expression trial in seagrass populations, time consuming and expensive workflow is the main issue to be addressed. Here we reported a faster procedure from the electrophoretic separation to the mass spectrometric analysis of Posidonia oceanica leaf proteins, selected among three different acrylamide/diacrylamide concentrations, three different running times of denaturing electrophoresis followed by in-gel digestion reactions, three total mass spectrometry run times. We demonstrated that the procedure using 12 or 10% polyacrylamide gel, the SDS-PAGE duration of 15 min and the total LC-MS/MS run of 120 min, did not affect the proteolytic efficiency of trypsin, improved the quality of the generated peptides, increased the number of identified proteins belonging to many functional categories per sample, compared to those of a standard workflow and of the other tested conditions.