posted on 2024-09-10, 10:44authored byYi Hsiao, Haijian Zhang, Ginny Xiaohe Li, Yamei Deng, Fengchao Yu, Hossein Valipour Kahrood, Joel R. Steele, Ralf B. Schittenhelm, Alexey I. Nesvizhskii
The FragPipe computational proteomics platform is gaining
widespread
popularity among the proteomics research community because of its
fast processing speed and user-friendly graphical interface. Although
FragPipe produces well-formatted output tables that are ready for
analysis, there is still a need for an easy-to-use and user-friendly
downstream statistical analysis and visualization tool. FragPipe-Analyst
addresses this need by providing an R shiny web server to assist FragPipe
users in conducting downstream analyses of the resulting quantitative
proteomics data. It supports major quantification workflows, including
label-free quantification, tandem mass tags, and data-independent
acquisition. FragPipe-Analyst offers a range of useful functionalities,
such as various missing value imputation options, data quality control,
unsupervised clustering, differential expression (DE) analysis using
Limma, and gene ontology and pathway enrichment analysis using Enrichr.
To support advanced analysis and customized visualizations, we also
developed FragPipeAnalystR, an R package encompassing all FragPipe-Analyst
functionalities that is extended to support site-specific analysis
of post-translational modifications (PTMs). FragPipe-Analyst and FragPipeAnalystR
are both open-source and freely available.