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Streamlined Single-cell Proteomics by an Integrated Microfluidic Chip and Data-independent Acquisition Mass Spectrometry

Nature Communications 2022, 13, 37.
S. T. Gebreyesusⴕ, A. A. Siyalⴕ, R. B. Kitata, E. S.-W. Chen, B. Enkhbayar, T. Angata, K.-I Lin, Y.-J. Chen* and H.-L. Tu*

Streamlined single-cell proteomics by an integrated microfluidic chip and data-independent acquisition mass spectrometry


Single-cell proteomics (SCP) can reveal cellular phenotypic heterogeneity and cell-specific functional networks underlying biological processes. Yet its development is relatively limited until recent years. To improve the sensitivity and proteome depth of SCP, a team led by Dr. Hsiung-Lin Tu and Dr. Yu-Ju Chen at Institute of Chemistry recently reported a highly streamlined workflow, which combines microfluidic chips for all-in-one proteomic sample preparation and data-independent acquisition (DIA) mass spectrometry (MS) for proteomic analysis down to the single-cell level. The proteomics chips enable multiplexed and automated cell isolation/counting/imaging and sample processing in a single device. Combining with DIA-MS using project-specific mass spectral libraries, this strategy profiles on average ~1,500 protein groups across 20 single mammalian cells. Applying the chip-DIA workflow to profile the proteomes of adherent and non-adherent malignant cells, the method demonstrates a dynamic range of 5 orders of magnitude with good reproducibility and < 16% missing values between runs. Taken together, the chip-DIA workflow offers all-in-one cell characterization, analytical sensitivity and robustness, and the option to add additional functionalities in the future, thus providing a basis for advanced single-cell proteomics applications.

This study is supported by Academia Sinica and Ministry of Science and Technology in Taiwan. Two Ph.D. students in the TIGP program, Mr. Sofani T. Gebreyesus and Mr. Asad A. Siyal, share the co-first authorship in this study. The corresponding authors include Dr. Hsiung-Lin Tu and Dr. Yu-Ju Chen. Additional collaborators include Dr. Kuo-I Lin and Dr. Takashi Angata from the Genomics Research Center and Institute of Biological Chemistry in Academia Sinica. The full article entitled “Streamlined single-cell proteomics by an integrated microfluidic chip and data-independent acquisition mass spectrometry” is available at the Nature Communications website:



此研究由本院以及科技部支持。共同第一作者為涂熊林實驗室博士生宋方寧(Sofani Gebreyesus)與陳玉如實驗室博士生史昂德(Asad Siyal);通訊作者為涂熊林助研究員以及陳玉如特聘研究員。研究團隊還包括本院基因體中心林國儀研究員與生物化學研究所安形高志副研究員。期刊論文標題為 “Streamlined single-cell proteomics by an integrated microfluidic chip and data-independent acquisition mass spectrometry”,可於以下連結閱讀: