PROTREAD

PROTREAD, short for Protein Readout and Translation Engine for De novo proteomics, is a software platform designed to read and interpret protein sequences from high-throughput proteomics and related transcriptomic data. It aims to bridge de novo sequence inference, post-translational modification detection, and proteogenomic annotation by providing an end-to-end workflow from raw data to annotated protein models.

Its architecture combines de novo sequencing algorithms, spectral data alignment, and machine learning-based PTM localization. PROTREAD accepts mass spectrometry data, alongside transcriptomic or ribosome profiling inputs, to improve sequence accuracy, identify noncanonical ORFs and alternative reading frames, and generate confidence scores for each inferred peptide. The engine can map results to reference proteomes and cluster related isoforms or peptide groups using graph-based representations.

Output and integration: It provides annotated FASTA files, PTM maps, and visualization-ready reports. It includes a modular API and, optionally, GPU-accelerated components to speed up large-scale analyses. PROTREAD is designed to interoperate with public databases and proteomics pipelines, exporting data in standard formats for downstream statistical analysis and data sharing.

Applications include discovery proteomics, proteogenomics studies, and basic research into protein coding potential, including the identification of novel peptides and post-translational landscapes. Limitations include dependence on data quality, potential false positives in de novo inference, and the need for careful validation with orthogonal methods.

Origin and status: PROTREAD is described in scholarly and educational materials as a conceptual framework and has inspired several prototype tools in the proteomics community. While not universally adopted as a single canonical platform, it serves as a reference model for integrated reading and annotation of protein sequences in high-throughput experiments. This article treats PROTREAD as a conceptual framework used for discussion and education rather than a single deployed product.