Human follicular fluid proteomic and peptidomic composition quantitative studies by SWATH-MS methodology. Applicability of high pH RP-HPLC fractionation

ABSTRACT: Analysis of proteomic composition of human follicular fluid (hFF) has been proposed as a potential tool of oocyte quality evaluation. In order to develop an efficient method to investigate the hFF proteome and peptidome components, we applied a prefractionation scheme of hFF material consisting of ultrafiltration, optional immunodepletion, and high pH RP-HPLC separation. Resulting from ultrafiltration Low Molecular-Weight Fraction peptides (LMWF, <10 kDa) and High Molecular-Weight Fraction proteins (HMWF, >10 kDa) were processed, measured, and analyzed separately. We identified 302 proteins in HMWF and 161 proteins in LMWF in all qualitative experiments. Combining data from single fractionation experiments we obtained and compared 18 spectral libraries (10 for HMWF, 8 for LMWF). We conducted quantitative SWATH-MS measurements of pool hFF samples for 108 HMWF proteins and 250 LMWF peptides. HMWF proteomic libraries were of similar quality with a few exceptions, even when comparing most basic and complex libraries. All LMWF peptidomic libraries turned out to be of poor quantification quality, however they enabled measurement of higher numbers of peptides with increasing input of experiment data, in contrast to proteomic libraries.

INSTRUMENT(S): TripleTOF 5600

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Follicular Fluid

SUBMITTER: Aleksandra Bogucka  

LAB HEAD: Stanislaw Oldziej

PROVIDER: PXD008073 | Pride | 2018-03-19

REPOSITORIES: Pride