Abstract
This data article presents a differentially mitochondrial proteomic dataset in human ovarian cancer tissues relative to control tissues. The mitochondrial samples were prepared from human ovarian cancer and control ovary tissues, and were digested with trypsin. The tryptic peptides from ovarian cancer and control mitochondrial samples were labeled by isobaric tags for relative and absolute quantification (iTRAQ) reagents, followed by strong-cation exchange (SCX) chromatography, liquid chromatography (LC)-tandem mass spectrometry (MS/MS), and bioinformatic analysis. This data article is related to a published article (Li et al., 2018) [1].
Specifications Table
| Subject area | Biological medicine |
| More specific subject area | Mitochondrial proteomics |
| Type of data | Table |
| How data was acquired | Isobaric tags for relative and absolute quantification (iTRAQ)-labeled samples were mixed and fractionated with strong-cation exchange (SCX) chromatography, followed by a 60-min liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis on a Q Exactive mass spectrometer (Thermo Scientific) that was coupled to Easy nLC (Proxeon Biosystems, now Thermo Fisher Scientific) for each fraction. |
| Data format | PDF file (Raw) |
| Experimental factors | Mitochondria were separated and purified from human ovarian cancer tissues and control ovary tissues. |
| Experimental features |
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| Data source location | Xiangya Hospital, Central South University, Hunan 410008 PR China |
| Data accessibility | Data is within this article, provided as supplementary file. |
| Related research article | N. Li, X.H. Zhan, X. Zhan. The lncRNA SNHG3 regulates energy metabolism of ovarian cancer by an analysis of mitochondrial proteomes. Gynecologic Oncology, 2018, 150 (2): 343–354. 10.1016/j.ygyno.2018.06.013[1] |
Value of the data
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Mitochondria were separated and purified from ovarian cancer tissues and control ovary tissues, with high purity.
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Dataset includes 1198 differentially expressed proteins identified from ovarian cancer and control mitochondrial samples.
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Relative abundance (ratio of cancer to control), statistically significant p-value, peptide spectrum matches (PSMs), and database accession number might be useful for other researchers to select the method of choice according to the target of interests.
1. Data
Differentially expressed proteins (DEPs) identified between ovarian cancer and control mitochondrial samples are reported, with the corresponding PSMs, relative abundance (ratio of cancer to control), statistically significant p-value, and database accession number. Data are provided as supplementary file (Supplementary Table 1).
2. Experimental design, materials and methods
2.1. Sample preparation
Ovarian tissue samples, which include seven ovarian cancers and eleven control ovaries with benign gynecologic diseases, were collected from Department of Gynecology, Xiangya Hospital, which was approved by the Xiangya Hospital Medical Ethics Committee of Central South University, China. Mitochondria were prepared, their proteins were extracted, according to the protocols [1], [2], [3].
2.2. iTRAQ labeling and SCX-LC-MS/MS analysis
iTRAQ-labeling technology integrated with SCX-LC-MS/MS analysis [4], [5] were performed to identify DEPs in extracted mitochondrial protein samples from ovarian cancers and controls. In brief, mitochondrial proteins were digested with trypsin, and the tryptic peptides were labeled with the iTRAQ reagents according to the manufacturer׳s instructions (Applied Biosystems). The iTRAQ-labeled peptides were equally pooled and fractionated by SCX. Each collected fractionation was subjected to a 60-min LC-MS/MS analysis with a Q Exactive mass spectrometer (Thermo Scientific) equipped with Easy nLC (Proxeon Biosystems, now Thermo Fisher Scientific). MS/MS data were used to identify proteins with MASCOT engine (Matrix Science, London, UK; version 2.2) embedded into Proteome Discoverer 1.4. Mitochondrial DEPs were determined with the intensity difference of iTRAQ reporter ions [1].
2.3. Bioinformatic analysis
DAVID Bioinformatics Resources 6.7 (https://david.abcc.ncifcrf.gov/home.jsp) was used to analyze the mitochondrial DEPs, including biological process, cellular compartment, molecular function, and KEGG pathway enrichments [6].
Acknowledgements
This work was supported by the Xiangya Hospital Funds for Talent Introduction, China (to XZ); and the grants from China “863” Plan Project (Grant no. 2014AA020610-1 to XZ), the National Natural Science Foundation of China (Grant nos. 81272798 and 81572278 to XZ), and the Hunan Provincial Natural Science Foundation of China (Grant no. 14JJ7008 to X)
Footnotes
Transparency document associated with this article can be found in the online version at https://doi.org/10.1016/j.dib.2018.08.028.
Supplementary data associated with this article can be found in the online version at https://doi.org/10.1016/j.dib.2018.08.028.
Transparency document. Supplementary material
Transparency document
Appendix A. Supplementary material
Supplementary material
References
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Associated Data
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Supplementary Materials
Transparency document
Supplementary material