Article

Protein Language Model Decoys for Target Decoy Competition in Proteomics: Quality Assessment and Benchmarks

2026-03-31

Abstract excerpt

Large-scale proteomics relies heavily on target–decoy competition for false discovery rate estimation in peptide identification, and the performance of this strategy depends strongly on the design of the decoy database. Classical generators such as reversal and shuffling remain widely used. Here, we introduce the first protein language model-based (PLM) decoy generation for peptide identification and benchmark it...

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Literature Corpus work: 929e5aaa-ba62-5371-bedc-76fb4e2588dd
DOI: 10.64898/2026.03.27.714819

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