Automated 16-Plex Plasma Proteomics with Real-Time Search and Ion Mobility Mass Spectrometry Enables Large-Scale Profiling in Naked Mole-Rats and Mice,Journal of Proteome Research

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Automated 16-Plex Plasma Proteomics with Real-Time Search and Ion Mobility Mass Spectrometry Enables Large-Scale Profiling in Naked Mole-Rats and Mice
Journal of Proteome Research ( IF 3.8 ) Pub Date : 2021-01-26 , DOI: 10.1021/acs.jproteome.0c00681
Aleksandr Gaun ₁ , Kaitlyn N Lewis Hardell _{1,

2} , Niclas Olsson ₁ , Jonathon J O'Brien ₁ , Sudha Gollapudi ₁ , Megan Smith ₁ , Graeme McAlister ₃ , Romain Huguet ₃ , Robert Keyser ₁ , Rochelle Buffenstein ₁ , Fiona E McAllister ₁

Affiliation

Performing large-scale plasma proteome profiling is challenging due to limitations imposed by lengthy preparation and instrument time. We present a fully automated multiplexed proteome profiling platform (AutoMP3) using the Hamilton Vantage liquid handling robot capable of preparing hundreds to thousands of samples. To maximize protein depth in single-shot runs, we combined 16-plex Tandem Mass Tags (TMTpro) with high-field asymmetric waveform ion mobility spectrometry (FAIMS Pro) and real-time search (RTS). We quantified over 40 proteins/min/sample, doubling the previously published rates. We applied AutoMP3 to investigate the naked mole-rat plasma proteome both as a function of the circadian cycle and in response to ultraviolet (UV) treatment. In keeping with the lack of synchronized circadian rhythms in naked mole-rats, we find few circadian patterns in plasma proteins over the course of 48 h. Furthermore, we quantify many disparate changes between mice and naked mole-rats at both 48 h and one week after UV exposure. These species differences in plasma protein temporal responses could contribute to the pronounced cancer resistance observed in naked mole-rats. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE [1] partner repository with the dataset identifier PXD022891.

中文翻译：

带有实时搜索和离子淌度质谱的自动化16重血浆蛋白质组学，可对裸鼠和小鼠进行大规模分析

由于冗长的准备工作和仪器时间的限制，执行大规模血浆蛋白质组图谱分析具有挑战性。我们介绍了一种使用Hamilton Vantage液体处理机器人的全自动多重蛋白质组分析平台（AutoMP3），该机器人能够制备数百至数千个样品。为了在单次运行中最大化蛋白质深度，我们将16重串联质谱标签（TMTpro）与高场非对称波形离子迁移谱（FAIMS Pro）和实时搜索（RTS）相结合。我们定量了40种蛋白质/分钟/样品，是以前公布的速度的两倍。我们应用AutoMP3来研究裸鼠mole鼠血浆蛋白质组与昼夜周期的关系以及对紫外线（UV）处理的响应。为了避免裸mole鼠缺乏同步的昼夜节律，我们发现在48小时内血浆蛋白中几乎没有昼夜节律模式。此外，我们量化了小鼠和裸鼠之间在紫外线照射后48小时和1周之间许多不同的变化。血浆蛋白时间反应中的这些物种差异可能有助于在裸observed鼠中观察到明显的抗癌性。质谱蛋白质组学数据已通过PRIDE [1]伙伴资料库以数据集标识符PXD022891存放到ProteomeXchange联盟。

更新日期：2021-02-05

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