The Perfinity iDP system automates key proteomics workflow steps including protein digestion, desalting and reversed phase chromatography to significantly reduce sample preparation times and enhance reproducibility. The automated process removes much of the equipment and labor associated with protein sample preparation for LCMS analyses, minimizing a potential source of error and improving laboratory productivity. Additionally, the Perfinity trypsin immobilized enzyme reaction (IMER) columns reduce digestion times from eighteen hours to between one and eight minutes with greatly improved digest efficiency over benchtop digestion.