Nanowell-mediated two-dimensional liquid chromatography enables deep proteome profiling of <1000 mammalian cells.
Maowei DouYing ZhuAndrey LiyuYiran LiangJing ChenPaul D PiehowskiKerui XuRui ZhaoRonald J MooreMark A AtkinsonClayton E MathewsWei-Jun QianRyan T KellyPublished in: Chemical science (2018)
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.
Keyphrases
- liquid chromatography
- mass spectrometry
- simultaneous determination
- cell cycle arrest
- high resolution mass spectrometry
- tandem mass spectrometry
- induced apoptosis
- liquid chromatography tandem mass spectrometry
- single cell
- ultra high performance liquid chromatography
- solid phase extraction
- capillary electrophoresis
- cell death
- ms ms
- high performance liquid chromatography
- type diabetes
- endothelial cells
- pi k akt
- amino acid
- optical coherence tomography
- wastewater treatment
- oxidative stress
- endoplasmic reticulum stress
- high throughput
- protein protein
- healthcare
- binding protein
- pseudomonas aeruginosa
- psychometric properties
- staphylococcus aureus
- cell proliferation
- candida albicans