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.

开发流程精简且高通量的样本处理工作流，对于充分利用基于质谱法的各类新兴技术进展与创新成果至关重要。尽管新技术与改良方法的更新迭代速度极快，但上游样本处理的自动化往往相对滞后。本研究开发并搭建了一套基于顺磁磁珠（paramagnetic bead）的半自动化同量异位素标签（isobaric tag）样本制备平台。我们通过对比六株实验室常用亲本酵母菌株的蛋白质丰度谱，对该机器人辅助平台开展基准性能测试：实验组采用三次重复的TMTpro16多重标记实验（TMTpro16-plex），对照组则采用人工处理样本的平行对照实验。两组实验均定量到数量相近的蛋白质与肽段，且重现性优异。基于上述数据，我们搭建了交互式在线网站，用于探索六株酵母的蛋白质组谱。本研究还为科研共同体提供了可在Opentrons OT-2液体处理工作站（opentrons OT-2）上自动化常规蛋白质组学（proteomics）工作流的开源模板。该机器人辅助平台可为各类蛋白质谱分析应用提供一种多功能且经济实惠的可靠样本处理方案。