Experimental workflow (a) & plots (b-d) of proteome coverage, PCA, and CD marker expression. Source: Üresin et al., 2024. “Unraveling the proteome landscape of mouse hematopoietic stem and progenitor compartment with high sensitivity low-input proteomics”, bioRxiv 2024.05.03.592307. Licensed under an Attribution-noderivatives 4.0 international license.

A new ultra-low-input proteomics workflow presented by Üresin et al allows for analyzing rare hematopoietic stem and progenitor cell (HSPC) populations from murine bone marrow.

The researchers developed a method requiring only 500 cells per sample, enabling comprehensive proteomic profiling of the entire hematopoietic hierarchy from a single mouse.

Using data-independent acquisition mass spectrometry (DIA-MS) on an Orbitrap Eclipse Tribrid MS instrument combined with the Evosep One and Aurora Series chromatography, they identified approximately 7,000 protein groups per cell type.

The study recapitulated known differentiation trajectories and uncovered novel insights into transcription factor dynamics and cell surface markers across various HSPC populations. The researchers successfully profiled long-term hematopoietic stem cells (LT-HSCs) and multipotent progenitor (MPP) populations, revealing potential new markers for LT-HSC isolation.

This approach significantly reduces the number of mice required for proteomic studies, addressing ethical concerns in animal research. The study’s importance lies in its potential to revolutionize proteomics research on rare cell populations, including those relevant to cancer and other diseases.

By enabling high-quality proteomic analysis with minimal sample input, this method opens new avenues for investigating clinically relevant rare cell types.

The Aurora Elite XT 15×75 C18 UHPLC column helped the researchers achieve high proteome coverage and sensitivity.

Publication
bioRxiv

Authors

Nil Üresin, Valdemaras Petrosius, Pedro Aragon-Fernandez, Benjamin Furtwängler, Erwin M. Schoof, Bo T. Porse

Title

Unraveling the proteome landscape of mouse hematopoietic stem and progenitor compartment with high sensitivity low-input proteomics