Tear fluid proteomics: a comparative study of DIA and DDA mass spectrometry

Mass spectrometry is a powerful technique for tear fluid proteomics, offering critical insights into its complex molecular composition. Traditional data-dependent acquisition (DDA) often favors high-abundance proteins because it selects only the most intense precursor ions within a given window during each scan cycle. A newer approach, data-independent acquisition (DIA), addresses this by fragmenting all precursor ions within defined mass windows, offering broader coverage and improved quantification. This study presents a systematic comparison of DDA and DIA workflows to assess their relative performance in detecting tear fluid proteins.

Tear fluid samples were collected from healthy individuals using Schirmer strips, processed using in-strip protein digestion, and analyzed via liquid chromatography-tandem mass spectrometry (LC-MS/MS). DDA and DIA workflows were compared for proteomic depth, reproducibility, and data completeness. Quantification accuracy was assessed using serial dilutions of tear fluid in a complex biological matrix.

DIA identified 701 unique proteins and 2,444 peptides, outperforming DDA, which identified 396 unique proteins and 1,447 peptides. Across eight replicates, DIA exhibited greater data completeness (78.7% for proteins and 78.5% for peptides) compared with DDA (42% for proteins and 48% for peptides). Reproducibility was markedly improved with DIA, with a median coefficient of variation (CV) of 9.8% for proteins and 10.6% for peptides, compared to 17.3% and 22.3%, respectively, for DDA. Quantification accuracy was also enhanced, with superior consistency across the dilution series.

Overall, DIA provides deeper, more reproducible, and more accurate proteome profiling of tear fluid than DDA, making it well suited for biomarker discovery.