scplainer: using linear models to understand mass spectrometry-based single-cell proteomics data

作者：Christophe Vanderaa, Laurent Gatto · 发表于：Genome biology · 年份：2025 · DOI：10.1186/s13059-025-03713-4 · 被引用次数：8 · 研究领域：Single-cell and spatial transcriptomics、Advanced Proteomics Techniques and Applications、Bioinformatics and Genomic Networks

Analyzing mass spectrometry (MS)-based single-cell proteomics (SCP) data faces important challenges inherent to MS-based technologies and single-cell experiments. We present scplainer, a principled and standardized approach for extracting meaningful insights from SCP data using minimal data processing and linear modeling. scplainer performs variance analysis, differential abundance analysis, and component analysis while streamlining result visualization. scplainer effectively corrects for technical variability, enabling the integration of data sets from different SCP experiments. In conclusion, this work reshapes the analysis of SCP data by moving efforts from dealing with the technical aspects of data analysis to focusing on answering biologically relevant questions.