Initial recommendations for performing, benchmarking, and reporting single-cell proteomics experiments

TL;DR

This paper proposes best practices, quality controls, and reporting standards to improve the reliability, reproducibility, and comparability of single-cell proteomics experiments using tandem mass spectrometry.

Contribution

It introduces community guidelines and standardized metrics to enhance rigor and data quality in single-cell proteomics research.

Findings

Proposes best practices for experimental design and data analysis.

Recommends quality control measures for reproducibility.

Suggests standardized reporting to facilitate data comparison.

Abstract

Analyzing proteins from single cells by tandem mass spectrometry (MS) has become technically feasible. While such analysis has the potential to accurately quantify thousands of proteins across thousands of single cells, the accuracy and reproducibility of the results may be undermined by numerous factors affecting experimental design, sample preparation, data acquisition, and data analysis. Broadly accepted community guidelines and standardized metrics will enhance rigor, data quality, and alignment between laboratories. Here we propose best practices, quality controls, and data reporting recommendations to assist in the broad adoption of reliable quantitative workflows for single-cell proteomics.