Nanowell-mediated two-dimensional liquid chromatography enables deep proteome profiling of <1000 mammalian cells

• Published in: Chemical science (Cambridge) Vol. 9; no. 34; pp. 6944 - 6951
• Main Authors: Dou, Maowei, Zhu, Ying, Liyu, Andrey, Liang, Yiran, Chen, Jing, Piehowski, Paul D, Xu, Kerui, Zhao, Rui, Moore, Ronald J, Atkinson, Mark A, Mathews, Clayton E, Qian, Wei-Jun, Kelly, Ryan T
• Format: Journal Article
• Language: English
• Published: England Royal Society of Chemistry 14.09.2018
• Subjects: BASIC BIOLOGICAL SCIENCES; Biological properties; Chromatography; Depth profiling; Fractionation; Liquid chromatography; Peptides; Proteins; Workflow
• ISSN: 2041-6520; 2041-6539
• DOI: 10.1039/c8sc02680g

Multidimensional peptide separations can greatly increase the depth of coverage in proteome profiling. However, a major challenge for multidimensional separations is the requirement of large biological samples, often containing milligram amounts of protein. We have developed nanowell-mediated two-dimensional (2D) reversed-phase nanoflow liquid chromatography (LC) separations for in-depth proteome profiling of low-nanogram samples. Peptides are first separated using high-pH LC and the effluent is concatenated into 4 or 12 nanowells. The contents of each nanowell are reconstituted in LC buffer and collected for subsequent separation and analysis by low-pH nanoLC-MS/MS. The nanowell platform minimizes peptide losses to surfaces in offline 2D LC fractionation, enabling >5800 proteins to be confidently identified from just 50 ng of HeLa digest. Furthermore, in combination with a recently developed nanowell-based sample preparation workflow, we demonstrated deep proteome profiling of >6000 protein groups from small populations of cells, including ∼650 HeLa cells and 10 single human pancreatic islet thin sections (∼1000 cells) from a pre-symptomatic type 1 diabetic donor.