PT  - JOURNAL ARTICLE
AU  - Erwin M. Schoof
AU  - Nicolas Rapin
AU  - Simonas Savickas
AU  - Coline Gentil
AU  - Eric Lechman
AU  - James Seymour Haile
AU  - Ulrich auf dem Keller
AU  - John E. Dick
AU  - Bo T. Porse
TI  - A Quantitative Single-Cell Proteomics Approach to Characterize an Acute Myeloid Leukemia Hierarchy
AID  - 10.1101/745679
DP  - 2019 Jan 01
TA  - bioRxiv
PG  - 745679
4099  - http://biorxiv.org/content/early/2019/08/24/745679.short
4100  - http://biorxiv.org/content/early/2019/08/24/745679.full
AB  - In recent years, cellular life science research has experienced a significant shift, moving away from conducting bulk cell interrogation towards single-cell analysis. It is only through single cell analysis that a complete understanding of cellular heterogeneity, and the interplay between various cell types that are fundamental to specific biological phenotypes, can be achieved. Single-cell assays at the protein level have been predominantly limited to targeted, antibody-based methods. However, here we present an experimental and computational pipeline, which establishes a comprehensive single-cell mass spectrometry-based proteomics workflow.By exploiting a leukemia culture system, containing functionally-defined leukemic stem cells, progenitors and terminally differentiated blasts, we demonstrate that our workflow is able to explore the cellular heterogeneity within this aberrant developmental hierarchy. We show our approach is capable to quantifying hundreds of proteins across hundreds of single cells using limited instrument time. Furthermore, we developed a computational pipeline (SCeptre), that effectively clusters the data and permits the extraction of cell-specific proteins and functional pathways. This proof-of-concept work lays the foundation for future global single-cell proteomics studies.