Fully integrated on-line strategy for highly sensitive proteome profiling of 10–500 mammalian cells

Abstract

Recent development in proteomic sample preparation using nanofluidic devices has made single-cell proteome profiling possible. However, these nanofluidic devices require special expertise and costly nanopipetting instruments. They are also specially designed for single cells, are not well-suited for profiling rare samples consisting of a few hundred mammalian cells, arguably a more common need that remains a great challenge. Herein, we developed an easy-to-use and scalable device for processing low-input samples, which combined the merits of previously reported rare cell proteomic reactor (RCPR) and mixed-mode simple and integrated spintip-based proteomics technology, as an alternative to nanofluidic devices. All steps of proteomics sample preparation, including protein preconcentration, impurity removal, reduction, alkylation, digestion, and desalting, were fully integrated in our workflow, and the device can be directly connected to online nanoLC-MS system after processing the rare samples. Using the developed 3-frit mixed-mode RCPR, we identified on average 946 ± 158, 2 998 ± 106, and 3 934 ± 85 protein groups in data-dependent acquisition (DDA) mode from 10, 100, and 500 fluorescence-activated cell sorting (FACS)-sorted 293T cells, respectively. As an illustrative application of this technology, we performed a label-free proteome comparison of 500 FACS-sorted mouse cochlear hair cells of two different ages. On average, 2 595 ± 230 and 2 042 ± 120 protein groups were quantified in the juvenile and the adult samples in DDA mode, respectively, achieving dynamic ranges of over 6 orders of magnitude for both.