Comparative analysis of nasosorption and nasopharyngeal swabbing for airway proteomics

ABSTRACT: The human nasopharynx is the site of numerous host-pathogen interactions, yet its proteomic composition has been difficult to study due to limitations of current sampling methods. Nasopharyngeal (NP) swabs are widely used for diagnostic and research applications, but their collection can be uncomfortable, particularly in children, and their suitability for close-interval sequential sampling is limited. Synthetic absorptive matrices (SAMs) represent a minimally invasive alternative, but their performance in untargeted, deep proteomic applications has not been systematically evaluated. Here, we directly compared proteomes obtained from paired NP and SAM samples collected from healthy adults, each separately eluted in different buffer chemistries: Qiagen RLT and urea-triethylammonium bicarbonate. High-performance liquid chromatography tandem mass spectrometry identified thousands of proteins in each sampling condition, spanning a dynamic range of more than five orders of magnitude. SAM and NP yielded broadly comparable proteome depth, with similar distributions of high-, intermediate-, and low-abundance proteins. Immune-relevant proteins, including soluble mediators, complement components, antimicrobial peptides, immunoglobulin transporters, oxidative stress proteins, markers of epithelial integrity, and interferon-stimulated gene products, were consistently recovered by both methods. Buffer chemistry introduced modest shifts in overall abundance distributions but generally preserved the relative differences between donors. These results establish that SAM sampling, in combination with either RLT or urea extraction, provides an acceptable and well-tolerated alternative to NP swabs for airway proteomics. This approach enables minimally invasive profiling of the human nasopharyngeal proteome and supports its application in studies of airway immunity and infection.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

SUBMITTER: Prof. Charles J. Sande  

PROVIDER: MSV000099535 | MassIVE | Sun Oct 19 09:47:00 BST 2025

SECONDARY ACCESSION(S): PXD069634

REPOSITORIES: MassIVE