Label-Free Quantitative Proteomics Reveals Differentially Regulated Proteins in Experimental Gingivitis

We investigated the sequential protein expression in
gingival crevicular
fluid samples during the induction (I) and resolution (R) of experimental
gingivitis. Periodontally and systemically healthy volunteers (n = 20) participated in a three-week experimental gingivitis
protocol, followed by debridement and two weeks of regular plaque
control. Gingival crevicular fluid (GCF) samples were collected at
baseline, Day 7, 14, and 21 (induction; I-phase), and at Day 21, 25,
30, and 35 (resolution; R-phase). Liquid chromatography–tandem
mass spectrometry (LC–MS/MS) for label-free quantitative proteomics
was applied. A total of 287 proteins were identified including 254
human, 14 bacterial, 12 fungal, and 7 yeast proteins. Ontology analysis
revealed proteins primarily involved in cytoskeletal rearrangements,
immune response, antimicrobial function, protein degradation, and
DNA binding. There was considerable variation in the number of proteins
identified, both among subjects and within subjects across time points.
After pooling of samples between subjects at each time point, the
levels of 59 proteins in the I-phase and 73 proteins in the R-phase
were quantified longitudinally. Our data demonstrate that LC–MS/MS
label-free quantitative proteomics is valuable in the assessment of
the protein content of the GCF and can facilitate a better understanding
of the molecular mechanisms involved in the induction and resolution
of plaque-induced gingival inflammation in humans.