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

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 platforms. Spectronaut
reported 1250 upregulated proteins and 266 downregulated proteins
(tumor versus peritumor), while DIA-NN reported 1819 and 174 proteins,
respectively. A total of 1130 differentially expressed proteins (DEPs)
were common to both platforms. Of the top 50 DEPs, 34 were shared
between Spectronaut and DIA-NN. Two of these DEPsHSPA5 and
CAV1were also among the top 50 proteins showing the highest
degrees of protein–protein interaction. The DEPs enabled classification
of the LUAD patients into three subtypes; the clinical validity of
the current subtypes will need to be substantiated in the future with
additional LUAD samples and experimentation.