FragPipe-Analyst is an R Shiny web-based tool designed to facilitate downstream analysis and visualization of quantitative proteomics data generated by the FragPipe platform. It supports major quantification workflows including label-free quantification (LFQ), tandem mass tags (TMT), and data-independent acquisition (DIA). The tool provides a range of functionalities such as missing value imputation, data quality control, unsupervised clustering, differential expression analysis using Limma, and gene ontology and pathway enrichment analysis using Enrichr. Additionally, FragPipeAnalystR, an R package, extends these functionalities to support site-specific analysis of post-translational modifications (PTMs). Both FragPipe-Analyst and FragPipeAnalystR are open-source and freely available. The tool was tested on several datasets, including an LFQ affinity purification mass spectrometry (AP-MS) interactome dataset, clear cell renal cell carcinoma (ccRCC) TMT global proteome and phosphoproteomics datasets, a ccRCC DIA whole proteome dataset, and a limited proteolysis coupled to mass spectrometry (LiP-MS) DIA dataset. The results demonstrated the effectiveness of FragPipe-Analyst in analyzing these datasets, including the identification of differentially expressed proteins and enriched pathways. The tool also supports peptide-level analysis and site-specific PTM analysis, which are essential for understanding protein modifications and their biological implications. The tool provides visualizations such as PCA plots, heatmaps, and volcano plots, which help in interpreting the results. The tool is user-friendly and allows for easy integration with other bioinformatics tools and for publication purposes. The tool is also available as a web server and can be used by researchers without requiring programming proficiency. The tool is designed to support a wide range of proteomics data analysis workflows and is suitable for both basic and advanced users.FragPipe-Analyst is an R Shiny web-based tool designed to facilitate downstream analysis and visualization of quantitative proteomics data generated by the FragPipe platform. It supports major quantification workflows including label-free quantification (LFQ), tandem mass tags (TMT), and data-independent acquisition (DIA). The tool provides a range of functionalities such as missing value imputation, data quality control, unsupervised clustering, differential expression analysis using Limma, and gene ontology and pathway enrichment analysis using Enrichr. Additionally, FragPipeAnalystR, an R package, extends these functionalities to support site-specific analysis of post-translational modifications (PTMs). Both FragPipe-Analyst and FragPipeAnalystR are open-source and freely available. The tool was tested on several datasets, including an LFQ affinity purification mass spectrometry (AP-MS) interactome dataset, clear cell renal cell carcinoma (ccRCC) TMT global proteome and phosphoproteomics datasets, a ccRCC DIA whole proteome dataset, and a limited proteolysis coupled to mass spectrometry (LiP-MS) DIA dataset. The results demonstrated the effectiveness of FragPipe-Analyst in analyzing these datasets, including the identification of differentially expressed proteins and enriched pathways. The tool also supports peptide-level analysis and site-specific PTM analysis, which are essential for understanding protein modifications and their biological implications. The tool provides visualizations such as PCA plots, heatmaps, and volcano plots, which help in interpreting the results. The tool is user-friendly and allows for easy integration with other bioinformatics tools and for publication purposes. The tool is also available as a web server and can be used by researchers without requiring programming proficiency. The tool is designed to support a wide range of proteomics data analysis workflows and is suitable for both basic and advanced users.