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Advances in mass spectrometry and associated computational tools have resulted in the wide-spread adoption of Data-Independent Acquisition (DIA) for proteomics. Experiments using state-of-the-art inst...

What's Changed fix bugs and add plots for mzid by @yueqixuan in #295 Multiple fix in mzidentml by @ypriverol in #296 MaxQuant: Fix NaN intensity errors by @cbielow in #304 Fix bug in proteobench_u...

Oxidative damage plays a critical role in various diseases including cardiovascular and neurological disorders. Thiol redox reactions, acting as oxidative stress sensors, influence protein structure a...

𝐖𝐡𝐲 𝐃𝐈𝐀-𝐍𝐍 𝐢𝐬 𝐠𝐫𝐞𝐚𝐭 𝐟𝐨𝐫 𝐜𝐡𝐞𝐦𝐨𝐩𝐫𝐨𝐭𝐞𝐨𝐦𝐢𝐜𝐬? You can analyse almost anything with it, and with high data quality: Below is an excellent benchmark by Ana Martínez del Val and colleagues. Bottom panel (c):...

🚀 PX Submission Tool v2.10.4 📦 Downloads Versioned: px-submission-tool-v2.10.4.zip Latest: px-submission-tool-latest.zip (always points to current version) 🔗 Universal Links Latest Release: http...

Quantitative mass spectrometry (MS)-based proteomics has become a streamlined technology with a wide range of usage. Many emerging applications, such as single-cell proteomics, spatial proteomics of t...

Indole-2,3-dioxygenase (IDO1) depletes tryptophan to dampen anti‑tumor T cells, yet IDO1 inhibitors (IDO1i) have failed clinically. Using deep visual proteomics, we isolated IDO1 high, medium and low ...

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.