Ultra-sensitive LC-MS workflow for in-depth label-free analysis of single mammalian cells with nanodroplet sample processing

In the last decade, single-cell RNA sequencing has advanced our understanding of transcript heterogeneity. Currently, there are strong efforts to enable single-cell proteomic analysis using mass spectrometry (MS)-based workflows. While the analysis of single-cell-sized aliquots from bulk-prepared tryptic digests has been demonstrated, only recently have label-free strategies been reported for profiling hundreds of proteins from single mammalian cells. Further development in sample processing, separations, MS and data analysis seems necessary to realize single-cell proteomics with greater depth of coverage and quantitative accuracy. Here we introduce an improved LC separation coupled to the new Thermo ScientificTM Orbitrap EclipseTM TribridTM mass spectrometers with a Thermo ScientificTM FAIMS ProTM interface to increase proteome coverage for single mammalian cells.