NovoBoard: A Comprehensive Framework for Evaluating the False Discovery Rate and Accuracy of De Novo Peptide Sequencing.

ABSTRACT: De novo peptide sequencing is one of the most fundamental research areas in mass spectrometry-based proteomics. Many methods have often been evaluated using a couple of simple metrics that do not fully reflect their overall performance. Moreover, there has not been an established method to estimate the false discovery rate (FDR) of de novo peptide-spectrum matches. Here we propose NovoBoard, a comprehensive framework to evaluate the performance of de novo peptide-sequencing methods. The framework consists of diverse benchmark datasets (including tryptic, nontryptic, immunopeptidomics, and different species) and a standard set of accuracy metrics to evaluate the fragment ions, amino acids, and peptides of the de novo results. More importantly, a new approach is designed to evaluate de novo

SUBMITTER: Tran NH 

PROVIDER: S-EPMC11532909 | biostudies-literature | 2024 Nov

REPOSITORIES: biostudies-literature