PSManalyst: A Dashboard for Visual Quality Control of FragPipe Results
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| Název: | PSManalyst: A Dashboard for Visual Quality Control of FragPipe Results |
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| Autoři: | Alison Felipe Alencar Chaves |
| Rok vydání: | 2025 |
| Témata: | Biochemistry, Biotechnology, Developmental Biology, Inorganic Chemistry, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Information Systems not elsewhere classified, traditional spreadsheet formats, throughput sample analyses, samplewise similarity metrics, local r setup, intuitively assessing large, https :// github, free data visualization, fastest computational platforms, based r application, visual quality control, rapid quality control, quality control metrics, peptide length distributions, fragpipe results fragpipe, protein data visualization, protein abundance discrepancies, scale proteomics data, quality scores, fragpipe introduced, filter peptide, protein coverage, version 23, spectrum matches |
| Popis: | 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. |
| Druh dokumentu: | article in journal/newspaper |
| Jazyk: | unknown |
| Relation: | https://figshare.com/articles/journal_contribution/PSManalyst_A_Dashboard_for_Visual_Quality_Control_of_FragPipe_Results/29922914 |
| DOI: | 10.1021/acs.jproteome.5c00557.s002 |
| Dostupnost: | https://doi.org/10.1021/acs.jproteome.5c00557.s002 https://figshare.com/articles/journal_contribution/PSManalyst_A_Dashboard_for_Visual_Quality_Control_of_FragPipe_Results/29922914 |
| Rights: | CC BY-NC 4.0 |
| Přístupové číslo: | edsbas.B0251268 |
| Databáze: | BASE |
Nájsť tento článok vo Web of Science | Abstrakt: | 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. |
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| DOI: | 10.1021/acs.jproteome.5c00557.s002 |