EARLY-PREG study tracks thousands of proteins day by day in cervicovaginal fluid

Researchers at Chile’s MELISA Institute validated a proteomics workflow in the EARLY-PREG biobank that measured about 50% more proteins than a comparison method across seven consecutive days. The approach could help scientists study fertility, implantation and early biomarkers of disease in a longitudinal preconception cohort.

Why it matters: - The EARLY-PREG platform now has a validated way to track protein changes day by day in the female reproductive tract. - The workflow could support future studies of fertility, implantation and the earliest stages of pregnancy. - The same approach may help researchers test whether time-based protein changes can serve as biomarkers for clinical monitoring.

What happened: - Researchers at MELISA Institute analyzed cervicovaginal fluid from the EARLY-PREG biobank and compared two proteomics workflows. - The study, published in Scientific Reports, measured samples collected over seven consecutive days from the same women. - The validation used 42 samples from six women in cycles that did not result in conception. - Each participant contributed one sample per day from the urinary luteinizing hormone surge day, called d0, through d6. - The team compared a dia-PASEF workflow with dda-FracOffline using the same samples.

The details: - The dia-PASEF workflow quantified 4,229 proteins. - The dda-FracOffline workflow quantified 2,817 proteins. - dia-PASEF identified about 50% more proteins than the comparison workflow. - dia-PASEF produced more consistent measurements across repeated samples. - dia-PASEF also detected more proteins whose abundance changed from the reference day. - The analysis used a nanoElute liquid chromatography system and a timsTOF Pro mass spectrometer from Bruker Daltonics. - Under the study conditions, dia-PASEF took about one hour per sample for instrument acquisition. - dda-FracOffline took about 16 hours per sample for instrument acquisition. - EARLY-PREG is a longitudinal preconception cohort that links each specimen to menstrual-cycle timing. - The biobank uses the urinary LH surge as a reference point for ovulation. - Cervicovaginal fluid was collected with a minimally invasive procedure. - The fluid contains proteins involved in reproductive processes. - The study also tracked daily changes in CA-125 and HE4, proteins previously studied as biomarkers of ovarian and endometrial cancer. - The article cites the study as Hernandez M. et al., "A dia-PASEF workflow improves proteome coverage and quantitative performance in repeated-measures analysis of cervicovaginal fluid from a preconception cohort (EARLY-PREG)." - The paper DOI is 10.1038/s41598-026-75386-3. - EARLY-PREG is registered at ClinicalTrials.gov as NCT07358026. - The proteomics data are available in ProteomeXchange/PRIDE under PXD071350. - Funding came from Fundación de Investigación San Ramón, with additional support from grant REH042024-01.

Between the lines: - The main advance here is methodological, not clinical. - Better proteome coverage and shorter run times make repeated-measures studies more practical when each participant contributes multiple samples. - That matters because day-to-day variation within the same woman can be more informative than one-off measurements. - The study authors say the biological findings are exploratory and need confirmation in larger cohorts. - Any diagnostic use of CA-125 or HE4 over time would require separate studies of performance and clinical utility. - The preconception design gives researchers a rare in vivo view of the days around implantation, when mother-embryo communication is otherwise difficult to study.

What's next: - MELISA Institute plans to use the workflow in larger longitudinal studies comparing cycles with and without conception. - Future work may test whether day-to-day protein patterns reveal signals tied to implantation, fertility or early pregnancy. - Clinical populations could also be studied to see whether CA-125, HE4 or other proteins add value for diagnosis or treatment monitoring.

The bottom line: - EARLY-PREG now has a faster, more sensitive proteomics method for watching thousands of reproductive-tract proteins change across the menstrual cycle.