Spectral Cruncher: A Visualization Tool Integrating Manual Curation, Ion-Intensity Prediction, and De Novo Tag...

Here, we introduce Spectral Cruncher, an interactive extension to the PatternLab for Proteomics platform, designed to bridge the gap between manual curation and state-of-the-art computational analysis of proteomic tandem mass spectra. Spectral Cruncher integrates de novo sequence tag extraction, automated spectral annotation, targeted tag search, and a customized transformer-based fragment-ion intensity predictor (SpecFormer) within a unified graphical environment, designed for interactive and instrument-specific visualization. Central to this workflow is SpecFormer, a compact transformer architecture trained on multiple data sets, providing independent ion intensity models for Q-Exactive + bulk, Astral bulk, and Astral single-cell proteomics data, enabling accurate and instrument-specific intensity prediction even under conditions of sparse fragmentation and low signal-to-noise ratios. Evaluation of SpecFormer demonstrates high predictive performance, with average cosine similarities of approximately 0.98 for bulk Q-Exactive + data sets, 0.91 for bulk Astral, and 0.87 for Astral single-cell data. These tools enable researchers to interrogate ambiguous spectra, validate peptide identifications, and develop intuition for algorithmic limitations. The tools are freely available within PatternLab 5.1, lowering technical barriers and promoting broader adoption of interactive, expert-driven workflows as well as providing a learning environment. A video of our tool in action is available at https://youtu.be/tc2sPiqJkLA.