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

ABSTRACT: 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 faci

SUBMITTER: Margelos T 

PROVIDER: S-EPMC12743176 | biostudies-literature | 2026 Jan

REPOSITORIES: biostudies-literature