Proteolysis is a crucial step in both bottom-up and structural proteomics workflows, directly influencing peptide identification and sequence coverage in mass spectrometry-based analyses. While classi...

Abstract. Tremendous advances in mass spectrometric and bioinformatic approaches have expanded proteomics into the field of microbial ecology. The commonly

Autoregressive (AR) models, common in sequence generation, are limited in many biological tasks such as de novo peptide sequencing and protein modeling by their unidirectional nature, failing to captu...

AbstractSummary. PepMapViz is a versatile R package that provides flexible peptide mapping and visualization capabilities. PepMapViz can import peptide dat

Two-dimensional tandem mass spectrometry (2D MS/MS) provides in-depth biopolymer structural information previously not directly accessible with traditional one-dimensional MS/MS workflows, and in sign...

De novo peptide sequencing enables peptide identification from fragmentation spectra without relying on sequence databases. However, incomplete spectra create ambiguity, making unambiguous identificat...

Post-translational modifications (PTMs) play a central role in cellular regulation and are implicated in numerous diseases. Database searching remains the standard for identifying modified peptides fr...

npj Biofilms and Microbiomes - Peptide abundance correlations in metaproteomics enhance taxonomic and functional analysis of the human gut microbiome

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.

Mass spectrometry-based metaproteomics allows for the identification and quantification of thousands of proteins from clinical and environmental samples and is rapidly gaining importance in microbiome...

Background Individual meat consumption in Germany has fallen slightly in recent years, but still exceeds the recommended quantities. High meat consumption has negative impacts both on human health and...

The ability to sequence proteins without reliance on a genomic template defines a critical frontier in modern proteomics. This approach, known as de novo protein sequencing, is essential for applicati...