Spectronaut and DIA-NN: A Comparison of their Performance in the Analysis of Lung Adenocarcinoma Biopsies.

ABSTRACT: Direct data-independent acquisition (DIA) in liquid chromatography-tandem mass spectrometry (LC-MS/MS) has developed into a powerful methodology for proteomics. Herein, we directly compare the performance of two widely used DIA computational platformsSpectronaut and DIA-NNusing paired tumor and peritumor tissue biopsies from human lung carcinoma (LUAD) patients, samples that one would encounter in a clinical research lab in a hospital setting. The evaluations include the following: (1) protein identification depth, (2) quantitative consistency, and (3) differential expression on the same set of LC-MS/MS runs, using nominally identical computational parameters and settings. Both Spectronaut and DIA-NN identified ∼>7600 proteins in the LUAD samples, with 7180 proteins common to both platfo

SUBMITTER: Yu Z 

PROVIDER: S-EPMC12903166 | biostudies-literature | 2026 Feb

REPOSITORIES: biostudies-literature