Flexible Automated Sample Preparation Workflows: Modified Automated Systems for Specific Immuno-MS and MS Workflows

The automation of sample preparation has become an increasingly important component for reproducible and operator-independent experiments. The Perfinity Workstation has provided researchers established applications in affinity capture and digestion for targeted proteomic workflows, utilizing specific affinity, IMER and reversed phase components coupled directly to a mass spectrometer. This approach offers the benefits of both specificity and resolution. However, utilizing alternative existing chemistries and multi-dimensional approaches, it is possible to reconfigure systems with a great deal of flexibility (e.g, pepsin digestion, HILIC, fraction collectors (FRC) or intact protein separation). The automated systems can then be utilized for a host of applications including targeting post-translationally modified proteins, non-tryptic peptides, and intact proteins. This work outlines novel strategies that are being utilized for automated online and offline sample preparation to achieve these specific goals.