Stable-protein Pair Analysis as A Novel Strategy to Identify Proteomic Signatures: Application To Seminal Plasma From Infertile Patients

The seminal plasma proteome from infertile patients differing in seminal parameters was determined using quantitative MS-based proteomics. Conventional analyses together with a new strategy based on the identification of stable-protein pairs were conducted. A stable-protein pair pattern was established for normozoospermic individuals but not for patients-groups with altered seminal parameters, reflecting multiple causes affecting seminal parameters. Moreover, the evaluation of stable-proteomic pattern in control population, adding an individual patient once a time, opens a window to personalized male infertility diagnosis. [Display omitted] Highlights •Differences in the analysis of quantitative proteomics data at protein or peptide level.•Stable-protein pairs as a new approach to analyze quantitative proteomic data.•Seminal plasma proteome in patients with altered seminal parameters is heterogeneous.•Stable-protein pairs may open a window to personalized male infertility diagnosis. Our aim was to define seminal plasma proteome signatures of infertile patients categorized according to their seminal parameters using TMT-LC-MS/MS. To that extent, quantitative proteomic data was analyzed following two complementary strategies: (1) the conventional approach based on standard statistical analyses of relative protein quantification values; and (2) a novel strategy focused on establishing stable-protein pairs. By conventional analyses, the abundance of some seminal plasma proteins was found to be positively correlated with sperm concentration. However, this correlation was not found for all the peptides within a specific protein, bringing to light the high heterogeneity existing in the seminal plasma proteome because of both the proteolytic fragments and/or the post-translational modifications. This issue was overcome by conducting the novel stable-protein pairs analysis proposed herein. A total of 182 correlations comprising 24 different proteins were identified in the normozoospermic-control population, whereas this proportion was drastically reduced in infertile patients with altered seminal parameters (18 in patients with reduced sperm motility, 0 in patients with low sperm concentration and 3 in patients with no sperm in the ejaculate). These results suggest the existence of multiple etiologies causing the same alteration in seminal parameters. Additionally, the repetition of the stable-protein pair analysis in the control group by adding the data from a sin