Advances in proteomics enable studying limited cell populations, typically requiring high mass accuracy instruments. Here, the authors present a workflow using a unit mass resolution linear ion trap to develop targeted assays from global measurements with free software.

Although the field of plant EVs (PEVs) is experiencing exponential growth, rigorous characterisation complying with MISEV guidelines has not been yet implemented due to the lack of bona fide referenc....

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.

PROTEOMICS, EarlyView.

Analytical ChemistryDOI: 10.1021/acs.analchem.5c02013

Neutrophils are vital innate immune cells shown to infiltrate glioblastomas, however we currently lack the molecular understanding of their functional states within the tumour niche. Neutrophils are k...

YouTube video by Brett Phinney

Cascadia is a mass spectrometry-based de novo sequencing model that uses a transformer architecture to handle data-independent acquisition data and achieves substantially improved performance across a...

All eukaryotic cell surfaces are coated with various types of glycans, which are essential molecules in biological events. In this review, we summariz…

This mass spectrometry-based proteomic study profiles the plasma proteome in 2,147 children and adolescents and reveals its association with age, sex, puberty, body mass index and genetics.