Many analytical tools have become available in the last decade to study multiple biomarkers from DNA, RNA, proteins, and their correlations. . Transcriptomics and confocal microscopy are established techniques at the single-cell level, but single-cell RNAseq is probably the best amongst these methods, producing unique and powerful biological insights from complex biological systems and revealing cell heterogeneity invisible to bulk analytical methods. Recently mass cytometry techniques (Fluidigm, Cy-TOF) as well as spectral flow cytometry (Cytek, Aurora) were introduced to measure up to 62 proteins from a single cell with good precision and high throughput . However, the cost to run these experiments can be prohibitive, especially given the limited number of proteins that can be measured and its strong dependence on the existence of specific antibodies. Currently, liquid chromatography tandem mass spectrometry (LC-MS/MS) is the most promising method that can allow quantification of more than a thousand protein abundances in a single cell at proteome wide level . There are many technical challenges to this workflow, which includes challenges in sample preparation, mass spectrometry (MS) acquisition strategies and data analysis, where each plays a vital role in the successful quantification of proteins in a single cell. An original technique developed by us and others, SCoPE MS, allowed quantification of large numbers of proteins, but required a substantial amount of MS time and had a lot of missing data over the analytical domain .