Qualitative and Quantitative Analysis of Proteome and Peptidome of Human Follicular Fluid Using Multiple Samples from Single Donor with LC–MS and SWATH Methodology

Human
follicular fluid (hFF) is a natural environment of oocyte
maturation, and some components of hFF could be used to judge oocyte
capability for fertilization and further development. In our pilot
small-scale study three samples from four donors (12 samples in total)
were analyzed to determine which hFF proteins/peptides could be used
to differentiate individual oocytes and which are patient-specific.
Ultrafiltration was used to fractionate hFF to high-molecular-weight
(HMW) proteome (>10 kDa) and low-molecular-weight (LMW) peptidome
(<10 kDa) fractions. HMW and LMW compositions were analyzed using
LC–MS in SWATH data acquisition and processing methodology.
In total we were able to identify 158 proteins, from which 59 were
never reported before as hFF components. 55 (45 not reported before)
proteins were found by analyzing LMW fraction, 67 (14 not reported
before) were found by analyzing HMW fraction, and 36 were identified
in both fractions of hFF. We were able to perform quantitative analysis
for 72 proteins from HMW fraction of hFF. We found that concentrations
of 11 proteins varied substantially among hFF samples from single
donors, and those proteins are promising targets to identify biomarkers
useful in oocyte quality assessment.