MELISA Institute: dia-PASEF quantified 4,229 proteins in cervicovaginal fluid versus 2,817 with dda-FracOffline

A team from the MELISA Institute (San Pedro de la Paz, Concepción, Chile) compared two mass spectrometry workflows for longitudinal analysis of cervicovaginal fluid (CVF). The work was published in Scientific Reports on 13 October 2026 and is available on nature.com. The samples came from the EARLY-PREG preconception cohort. With the data-independent acquisition workflow dia-PASEF, the authors quantified 4,229 proteins, versus 2,817 with dda-FracOffline nature.comnature.comnature.comOpen source ↗.

Study design and samples

EARLY-PREG is an open preconception cohort in which women enroll before pregnancy and each specimen is recorded relative to the menstrual cycle. According to the release, the team uses the urinary luteinizing hormone surge as a reference point for ovulation nature.comnature.comnature.comOpen source ↗. Serial CVF samples were collected across a seven-day window anchored to ovulation (d0-d6).

According to the institute, both methods were applied to the same 42 samples: six participants each provided one sample per day for seven consecutive days during a cycle without conception. Day 0, the day of ovulation, served as the reference for day-to-day comparisons nature.comnature.comnature.comOpen source ↗.

Coverage and reproducibility

The mean coefficient of variation was 5.27 ± 0.68% for dia-PASEF and 9.37 ± 1.75% for dda-FracOffline, meaning more consistent measurements with the first approach nature.comnature.comnature.comOpen source ↗. The release puts the gain in quantified proteins at about 50%.

In pairwise comparisons against day 0, dia-PASEF identified 952–1,116 differentially expressed proteins, versus 161–460 for dda-FracOffline nature.comnature.comnature.comOpen source ↗. Pathway analyses showed broader biological coverage with dia-PASEF.

The authors conclude that dia-PASEF is a sensitive and reproducible approach for repeated-measures proteomic analysis of CVF and say it can be adapted to other biofluids nature.comnature.comnature.comOpen source ↗. They note that large-scale discovery of CVF biomarkers has been limited by the sensitivity, reproducibility and data completeness of mass spectrometry workflows. The institute states that the method provides a basis for research on fertility, the earliest stages of pregnancy and potential biomarkers of gynecological disease. This is a methodological study; no clinical biomarkers are reported in it.