Abstract
Some exciting biological questions require quantifying thousands of proteins in single cells. To achieve this goal, we develop Single Cell ProtEomics by Mass Spectrometry (SCoPE-MS) and validate its ability to identify distinct human cancer cell types based on their proteomes. We use SCoPE-MS to quantify over a thousand proteins in differentiating mouse embryonic stem cells. The single-cell proteomes enable us to deconstruct cell populations and infer protein abundance relationships. Comparison between single-cell proteomes and transcriptomes indicates coordinated mRNA and protein covariation, yet many genes exhibit functionally concerted and distinct regulatory patterns at the mRNA and the protein level.
Highlights
IntroductionCellular systems, such as tissues, cancers, and cell cultures, consist of a variety of cells with distinct molecular and functional properties
Cellular systems, such as tissues, cancers, and cell cultures, consist of a variety of cells with distinct molecular and functional properties. Characterizing such cellular differences is key to understanding normal physiology, combating cancer recurrence, and enhancing targeted stem cell differentiation for regenerative therapies [1,2,3,4,5]; it demands quantifying the proteomes of single cells
We identified biological functions over-represented [40] within the distribution of principal components (PC) loadings and colorcoded each cell based on the average levels of proteins annotated to these functions
Summary
Cellular systems, such as tissues, cancers, and cell cultures, consist of a variety of cells with distinct molecular and functional properties. Multiple antibody-based methods for quantifying proteins in single cells have been recently developed, including CyTOF [7, 8], single-cell Western blots [9], and Proseek Multiplex, an immunoassay readout by PCR [10]. These methods can quantify up to a few dozen endogenous proteins recognized by highly specific cognate antibodies and have enabled exciting research avenues [5]. The throughput and accuracy of antibody-based methods are limited by cellular permeability, molecular crowding, epitope accessibility, and the availability of
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