{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"omics_type":["Unknown"],"volume":["11(5)"],"submitter":["Yu Z"],"pubmed_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"],"journal":["ACS omega"],"pagination":["8080-8093"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC12903166"],"repository":["biostudies-literature"],"pubmed_title":["Spectronaut and DIA-NN: A Comparison of their Performance in the Analysis of Lung Adenocarcinoma Biopsies."],"pmcid":["PMC12903166"],"pubmed_authors":["Zhang W","Chu IK","Du A","Li Y","Siu KWM","Zhang Y","Ma X","Yu Z","Xu X"],"additional_accession":[]},"is_claimable":false,"name":"Spectronaut and DIA-NN: A Comparison of their Performance in the Analysis of Lung Adenocarcinoma Biopsies.","description":"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","dates":{"release":"2026-01-01T00:00:00Z","publication":"2026 Feb","modification":"2026-07-15T16:40:56.674Z","creation":"2026-07-07T03:08:22.861Z"},"accession":"S-EPMC12903166","cross_references":{"pubmed":["41696233"],"doi":["10.1021/acsomega.5c10421"]}}