AM-DMF-SCP-pro: An Ultrafast and Streamlined Nanolitre-Scale Lab-on-a-Chip Platform for Single-Cell Proteomics and Tumor Microenvironment Profiling

Jin, K.; Yang, Z.; Ding, A.; Wang, R.; Ma, Y.; Wang, Y.; Tang, M.; Wu, Y.; Liu, Q.; Ji, J.; Chang, C.; Hu, S.; Dong, W.; Ding, J.; Chen, Y.; Ma, H.; Zhou, H.

doi:10.64898/2026.04.29.721532

bioRxiv · 10.64898/2026.04.29.721532

AM-DMF-SCP-pro: An Ultrafast and Streamlined Nanolitre-Scale Lab-on-a-Chip Platform for Single-Cell Proteomics and Tumor Microenvironment Profiling

Jin, K.·Yang, Z.·Ding, A.·Wang, R.·Ma, Y.·Wang, Y.·Tang, M.·Wu, Y.·Liu, Q.·Ji, J.·Chang, C.·Hu, S.·Dong, W.·Ding, J.·Chen, Y.·Ma, H.·Zhou, H.

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Abstract

Single-cell proteomics (SCP) remains constrained by slow sample preparation and background interference in low-input, multistep workflows, limiting its broader practical use in complex biological samples. Here we report AM-DMF-SCP-pro, a streamlined active-matrix digital microfluidic workflow that enables rapid on-chip lysis and digestion in 6 nL droplets within a closed nanolitre-confined microenvironment. AM-DMF-SCP-pro reduces total sample-preparation time to as little as 30 min, including a 15 min digestion step, while maintaining quantitative reproducibility and digestion performance. Systematic optimization of mass spectrometry acquisition and nanolitre-scale digestion conditions enables deeper, more sensitive and lower-background proteome profiling from ultra-low peptide inputs. In murine tumor samples, AM-DMF-SCP-pro reliably resolves immune and tumor compartments, identifies treatment-associated tumor cell states and enables quantitative analysis of neutrophil-associated proteomic signatures. These results establish AM-DMF-SCP-pro as a practical workflow for rapid, low-background single-cell proteome profiling in complex biological samples.

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Jin, K., Yang, Z., Ding, A., Wang, R., Ma, Y., Wang, Y., Tang, M., Wu, Y., Liu, Q., Ji, J., Chang, C., Hu, S., Dong, W., Ding, J., Chen, Y., Ma, H., Zhou, H.. 2026-05-04. AM-DMF-SCP-pro: An Ultrafast and Streamlined Nanolitre-Scale Lab-on-a-Chip Platform for Single-Cell Proteomics and Tumor Microenvironment Profiling. https://doi.org/10.64898/2026.04.29.721532

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