Data on endogenous bovine ovarian follicular cells peptides and small proteins obtained through Top-down High Resolution Mass Spectrometry

The endogenous peptides and small proteins extracted from bovine ovarian follicular cells (oocytes, cumulus and granulosa cells) were identified by Top-down High Resolution Mass Spectrometry (TD-HR-MS/MS) in order to annotate peptido- and proteoforms detected using qualitative and quantitative profiling method based on ICM-MS (Intact Cell Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry). The description and analysis of these Top-down MS data in the context of oocyte quality biomarkers research are available in the original research article of Labas et al. (2017) http://dx.doi.org/10.1016/j.jprot.2017.03.027[1]. Raw data derived from this peptidomic/proteomic analysis have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository (dataset identifier PXD004892). Here, we described the inventory of all identified peptido- and proteoforms including their biochemical and structural features, and functional annotation of correspondent proteins. This peptide/protein inventory revealed that TD-HR-MS/MS was appropriate method for both global and targeted proteomic analysis of ovarian tissues, and it can be further employed as a reference for other studies on follicular cells including single oocytes.

. Raw data derived from this peptidomic/ proteomic analysis have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository (dataset identifier PXD004892). Here, we described the inventory of all identified peptido-and proteoforms including their biochemical and structural features, and functional annotation of correspondent proteins. This peptide/protein inventory revealed that TD-HR-MS/MS

Value of the data
The data presents the first inventory of endogenous peptides and small proteins identified in bovine ovarian follicular cells (oocytes, cumulus and granulosa cells) to annotate biomolecules detected by ICM-MS on whole follicular cells including single oocytes. The data could be used by others researchers in reproduction sciences for biomarker research.
The data obtained using analysis based on three Top-Down HR-MS/MS approaches (direct infusion, mLC-HR-MS/MS with or without pre-fractionations) allows other researchers to choice a strategy adapted to their biologic models.
The identifications of the proteoforms and peptidoforms from granulosa cells protein extract by combining mLC-HR-MS/MS and four different pre-fractionation strategies (3 separation methods based on reverse phase chromatography and one on gel filtration chromatography) could be compared to others separation and MS identification methods.

Data
This dataset represents a list of peptidoforms and proteoforms extracted from bovine ovarian follicular cells and identified by TD HR-MS/MS. They correspond to molecular species previously characterized by ICM-MS on whole follicular cells [1]. Depend upon the available quantity of biological materials biomolecules were analyzed by HR-MS/MS using three approaches: 1) Direct infusion of the proteins prepared from oocyte-cumulus complexes (OCCs); 15 biomolecules were identified (Supplementary data Table DB1 (Fig. 1A).
Comparison between the four separation methods is shown (Fig. 1B).
In total, 386 different intact proteins or fragments corresponding to 194 genes were identified (Supplementary data Table DB1-D). The distribution of molecular weight and isoelectric point of the identified masses is represented in Fig. 2A and B, respectively. Functional annotation of identified proteins was performed using Panther Functional Classification System (http://www.pantherdb.org/), GeneAnalytics and Database for Annotation, Visualization and Integrated Discovery (https://david. ncifcrf.gov/) ( Fig. 3 and Supplementary data Table DB2).

Experimental design, materials and methods
This dataset was produced with the objective to identify, using TD HR-MS/MS, the peptides and small proteins which have been previously characterized by ICM-MS on whole bovine ovarian follicular cells and especially on intact single oocytes. Due to partial similarity of protein ICM-MS profiles between the oocytes, cumulus cells (CC) and granulosa cells (GC) (39.5% oocyte peaks are common with CC and 45.5% with GC), it seemed pertinent to develop TD HR-MS/MS approach using these three cellular types as source. Depending on the amount of available biological material (abundant or not), we have therefore performed three different TD HR-MS/MS approaches a) direct infusion, b) injection on mLC-HR-MS/MS system of total protein extracts, c) combine mLC-HR-MS/MS with four offline pre-fractionations of protein extract from GC. Thus, in order to reduce sample heterogeneity and increase the number of identified proteins, we have combined reverse phase (RP) or gel filtration liquid chromatography separation methods with mLC-HR-MS/MS. Top-Down High Resolution Mass Spectrometry detailed protocols and identification parameters for each approach are provided in supplementary data DB3.