Simple, Fast, and Reliable Analysis of Label‐Free Proteomics Data With the Proteomics Eye (ProtE)

In label-free mass spectrometry experiments, the data output is typically a proteome table that requires further processing, quality testing, and visualization to fully interpret the captured proteomic signals. Currently, post-quantification analysis of these tables often relies on complex programmatic pipelines, which can become challenging to use. Here, we introduce the Proteomics Eye (ProtE), a single-function R package designed to streamline the analysis of proteome tables generated by commonly used software tools (DIA-NN, ProteomeDiscoverer, and MaxQuant). ProtE provides a broad range of options for data processing, preparation, and statistical testing. It also performs gene set enrichment analysis and offers a comprehensive suite of visualization plots to assess data quality and facilitate biological interpretation. Given a categorical variable with two or more groups, ProtE enables group-wide and pairwise statistical comparisons across all group combinations, using both traditional statistical tests and linear models for differential expression analysis. By integrating all these features into a single, user-friendly R function, ProtE simplifies the analysis of large-scale label-free DDA and DIA datasets, making advanced proteomic analysis accessible to both experienced researchers and beginners.