InstaDeepAI/winnow-general-model

Winnow recalibrates confidence scores and provides FDR control for de novo peptide sequencing (DNS) workflows. This repository hosts a calibrator trained on the HeLa Single Shot dataset as referenced in our paper: De novo peptide sequencing rescoring and FDR estimation with Winnow.

# InstaNovo: De novo Peptide Sequencing Model ## Model Description

# InstaNovo: De novo Peptide Sequencing Model ## Model Description

InstaNovoPlus is a diffusion-based model for de novo peptide sequencing from mass spectrometry data. This model leverages multinomial diffusion for accurate, database-free peptide identification for large-scale proteomics experiments.

InstaNovo-P is a specialized transformer-based model for de novo peptide sequencing from phosphoproteomics mass spectrometry data. This model is specifically trained and optimized for identifying phosphorylated peptides and their modification sites.

This package wraps the functionality of the Thermo Fisher Scientic RawFileReader .NET 8.0 assembly. Within the R environment, spectra and chromatograms are represented by S3 objects. The package provides basic functions to download and install the required third-party libraries. The package is developed, tested, and used at the Functional Genomics Center Zurich, Switzerland.