Evosep One Enables Robust Deep Proteome Coverage Using Tandem Mass Tags while Significantly Reducing Instrument Time

Area of Science:

• Proteomics
• Mass Spectrometry
• Cancer Research

Background:

• Optimizing proteome analysis time and depth is a key challenge in proteomics.
• Multidimensional fractionation enhances proteome coverage but increases analysis time.
• Recent advances include high-throughput liquid chromatography systems like Evosep One.

Purpose of the Study:

• To integrate Evosep One technology into a multiplexing workflow for analyzing tandem mass tag (TMT)-labeled nonsmall cell lung carcinoma (NSCLC) patient-derived xenografts (PDXs).
• To evaluate the efficiency and depth of proteome coverage using the Evosep One system compared to conventional methods.

Main Methods:

• Incorporation of the Evosep One liquid chromatography system into a multiplexing workflow.
• Analysis of TMT-labeled NSCLC patient-derived xenografts (PDXs).
• Comparison with a conventional concatenated EASY-nLC workflow.

Main Results:

• A 30 samples per day Evosep workflow identified >12,000 proteins in 48 hours of mass spectrometry time.
• This protein identification depth is comparable to 60 hours using the conventional EASY-nLC workflow.
• Shorter Evosep gradients reduced analysis time by 50% with only a 10% decrease in protein identifications.

Conclusions:

• The Evosep One workflow enables high-throughput quantitative proteomic analysis of multiplexed samples.
• This approach significantly reduces mass spectrometry time without sacrificing proteome coverage depth.
• This technology facilitates more efficient analysis of complex biological samples like PDXs for cancer research.