A new principled approach for single-cell proteomics data analysis
Laurent Gatto,Christophe Vanderaa
de Duve Institute, UCLouvain, Belgium
In a Nature Methods Technology Feature in August 2019 (doi:10.1038/s41592-019-0540-6), Vivien Marx dreamt of single-cell proteomics. Today, thanks to some pioneers' groundbreaking efforts, we can confidently claim that a new and exciting single cell modality is available: mass spectrometry-based, that is un-targeted, single-cell proteomics. Now that that dream has come true, what can we learn from the growing number of studies and datasets published since 2019? In this presentation, we will describe the opportunities and challenges from the standpoint of a computational biologist and proponent of open and reproducible research. We will highlight some specific technical challenges related to single-cell proteomics data processing and propose a principled approach that addresses some of these, leading to more interpretable results.