A Semiautomated Paramagnetic Bead-Based Platform for Isobaric Tag Sample Preparation

The development of
streamlined and high-throughput sample processing
workflows is important for capitalizing on emerging advances and innovations
in mass spectrometry-based applications. While the adaptation of new
technologies and improved methodologies is fast paced, automation
of upstream sample processing often lags. Here we have developed and
implemented a semiautomated paramagnetic bead-based platform for isobaric
tag sample preparation. We benchmarked the robot-assisted platform
by comparing the protein abundance profiles of six common parental
laboratory yeast strains in triplicate TMTpro16-plex experiments against
an identical set of experiments in which the samples were manually
processed. Both sets of experiments quantified similar numbers of
proteins and peptides with good reproducibility. Using these data,
we constructed an interactive website to explore the proteome profiles
of six yeast strains. We also provide the community with open-source
templates for automating routine proteomics workflows on an opentrons
OT-2 liquid handler. The robot-assisted platform offers a versatile
and affordable option for reproducible sample processing for a wide
range of protein profiling applications.