A comparison of peptide- and spectrum-centric search engines beyond bar charts
Date and Time: Tuesday, August 27, 2024 | 15:30 – 16:30
Presenter: Michelle T. Berger
Data-independent acquisition (DIA) is known for its reproducibility, quantitative precision, and proteome coverage, at the expense of producing more complex spectra. In recent years, various algorithms were developed for peptide identification from DIA datasets. While peptide-centric search engines rely on correlating fragment ion elution curves, spectrum-centric methods analyze spectra one at a time. To minimize the number of reported false identifications (IDs), all tools provide self-calculated q-values controlling the false discovery rate (FDR) using a target-decoy approach and a diverse set of scores. Here, we compare DIA-NN 1.8.1, Spectronaut 18 and a Chimerys 4 pre-release version on both high- and low-abundant Orbitrap (Astral) datasets and scrutinize their tailor-made statistics and scores.
