Analysis and Visualization of Quantitative Proteomics Data Using FragPipe-Analyst

• DOI: 10.1021/acs.jproteome.4c00294
• Publication Date: 2024-09-10T12:13:30Z
• Authors: Yi Hsiao; Haijian Zhang; Ginny Xiaohe Li; Yamei Deng; Fengchao Yu; Hossein Valipour ...; Joel R. Steele; Ralf B. Schittenhelm; Alexey I. Nesvizh...

The FragPipe computational proteomics platform is gaining widespread popularity among the research community because of its fast processing speed and user-friendly graphical interface. Although produces well-formatted output tables that are ready for analysis, there still a need an easy-to-use downstream statistical analysis visualization tool. FragPipe-Analyst addresses this by providing R shiny web server to assist users in conducting analyses resulting quantitative data. It supports major quantification workflows, including label-free quantification, tandem mass tags, data-independent acquisition. offers range useful functionalities, such as various missing value imputation options, data quality control, unsupervised clustering, differential expression (DE) using Limma, gene ontology pathway enrichment Enrichr. To support advanced customized visualizations, we also developed FragPipeAnalystR, package encompassing all functionalities extended site-specific post-translational modifications (PTMs). FragPipeAnalystR both open-source freely available.