PSManalyst: A Dashboard for Visual Quality Control of FragPipe Results

FragPipe
is recognized as one of the fastest computational platforms
in proteomics, making it a practical solution for the rapid quality
control of high-throughput sample analyses. Starting with version
23.0, FragPipe introduced the “Generate Summary Report”
feature, offering .pdf reports with essential quality control metrics
to address the challenge of intuitively assessing large-scale proteomics
data. While traditional spreadsheet formats (e.g., tsv files) are
accessible, the complexity of the data often limits user-friendly
interpretation. To further enhance accessibility, PSManalyst, a Shiny-based
R application, was developed to process FragPipe output files (psm.tsv,
protein.tsv, and combined_protein.tsv) and provide interactive, code-free
data visualization. Users can filter peptide-spectrum matches (PSMs)
by quality scores, visualize protease cleavage fingerprints as heatmaps
and SeqLogos, and access a range of quality control metrics and representations
such as peptide length distributions, ion densities, mass errors,
and wordclouds for overrepresented peptides. The tool facilitates
seamless switching between PSM and protein data visualization, offering
insights into protein abundance discrepancies, samplewise similarity
metrics, protein coverage, and contaminants evaluation. PSManalyst
leverages several R libraries (lsa, vegan, ggfortify, ggseqlogo, wordcloud2,
tidyverse, ggpointdensity, and plotly) and runs on Windows, MacOS,
and Linux, requiring only a local R setup and an IDE. The app is available
at (https://github.com/41ison/PSManalyst.