Proteomics

Dataset Information

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

ABSTRACT: Here's a suggested Project Description for your PRIDE submission: Project Description This dataset contains mass spectrometry raw files used as training data for SpecFormer, a transformer-based ion intensity prediction model integrated within PatternLab for Proteomics (Spectral Cruncher module). The dataset includes bulk proteomics data from HeLa cells and Mus musculus (C57BL/6) kidney tissue, as well as single-cell proteomics data from WT83 human brain organoids acquired using the cellenOne platform. All samples were analyzed on an Orbitrap Astral mass spectrometer using data-dependent acquisition (DDA). These raw files were used to train instrument-specific models for accurate fragment ion intensity prediction in both bulk and single-cell proteomics workflows. The SpecFormer model and analysis tools described in this dataset are freely available within PatternLab 5.1 at http://patternlabforproteomics.org/51.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human) Mus Musculus (mouse)

SUBMITTER: Paulo Carvalho  

LAB HEAD: Paulo Costa Carvalho

PROVIDER: PXD069898 | Pride | 2026-02-16

REPOSITORIES: Pride

Json Xml

Dataset's files

Source:
Action DRS
20250604_HeLaPurified_Protein_DDA.sepr2 Other
BulkTrainHeLa200ngAstral.raw Raw
BulkTrainMusMusculusAstral1.raw Raw
BulkTrainMusMusculusAstral2.raw Raw
BulkTrainMusMusculusAstral3.raw Raw
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Publications

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

Martins Aline A M AAM   Tsu Blake L BL   Brum Hulyana H   Sales Lucas L   Mariano Dos Santos Marlon Dias MD   Fischer Juliana de Saldanha da Gama JSDG   Almeida Stephanie S   Vieira Coelho Luisa Bulcao LB   Moreira Natalia N   Muotri Alysson R AR   Carvalho Paulo Costa PC  

Journal of the American Society for Mass Spectrometry 20251229 2

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 i  ...[more]

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