The current state of single-cell proteomics data analysis
Christophe Vanderaa,Laurent Gatto
Mass spectrometry-based single-cell proteomics is a fast growing field that enables quantitative proteomics at single-cell resolution. This is achieved thanks to technical improvements that dramatically increase the throughput, sensitivity and accuracy of the technology. However, little efforts have been invested in understanding single-cell proteomics data analysis. We have addressed this need with scp, an R/Bioconductor package that standardizes single-cell proteomics data analysis. We use our software to reproduce published analyses, leading to a comprehensive overview of the current state of single-cell proteomics data processing. Our work sheds light upon the limitations of current practices, proposes a principled approach to tackle these, and provides guidelines for future experiments.