Rapid, Efficient Sample Preparation for MS-Based Proteomics Applications
Sample preparation methods for MS-based proteomics applications are not standardized with many requiring long hours to process samples and potentially resulting in low peptide yield, poor digestion efficiency, and low reproducibility. The new Thermo Scientific™ EasyPep™ sample preparation kits, provide an easy to use, out of the box solution with an optimized workflow that significantly reduces hands-on time for total sample processing time (under 4 hours) from intact cells to cleaned-up peptides. Available in multiple formats to support wide range of input amounts, these kits are ideal for sample preparation from cells, tissues, serum, and plasma for a wide range of applications including label-free quantification, targeted assays, and are compatible with downstream applications such as high-pH reversed phase fractionation, phosphopeptide enrichment and TMT™ reagent labeling.
In this application note we compare the three EasyPep formats (Mini, Maxi, and 96-well) for processing different sample types, including human cell lines, human serum/plasma, yeast, E. coli, fresh tissues, and formalin-fixed, paraffin embedded (FFPE) tissues and show that all 3 formats yielded identical protein and peptide IDs with the different sample types and scale. In addition, we demonstrate the compatibility of EasyPep MS sample preparation chemistry with downstream applications, including phosphopeptide enrichment using Fe-NTA resins and Thermo Scientific™ Tandem Mass Tag™ (TMT™) reagent labeling before or after digestion.
The optimized and standardized workflow that Thermo Scientific™ EasyPep™ sample preparation kits provides enables the rapid adoption by both novice and expert users.