Dataset on the mass spectrometry-based proteomic profiling of the kidney from wild type and the dystrophic mdx-4cv mouse model of X-linked muscular dystrophy

The proteomic data presented in this article provide supporting information to the related research article “Proteomic and cell biological profiling of the renal phenotype of the mdx-4cv mouse model of Duchenne muscular dystrophy” (Dowling et al., 2019) [1]. This article supplies additional datasets on protein species with increased versus decreased concentration in the kidney from the dystrophic mdx-4cv mouse, as well as tables with mass spectrometrically identified kidney marker proteins that exhibit characteristic tissue distributions, subcellular localizations and physiological functions. Information is provided on the underlying multi-consensus protein listings from the proteomic screening of both wild type and mdx-4cv mouse kidneys. The data article provides comprehensive information on the systematic and mass spectrometric identification of the mouse kidney proteome.

provides comprehensive information on the systematic and mass spectrometric identification of the mouse kidney proteome. © 2019 The Author(s). Published by Elsevier Inc. This is an open access article under the CC BY license (http://creativecommons. org/licenses/by/4.0/).

Data
This data paper presents the findings from the mass spectrometric profiling of mouse kidney extracts, and relates to the comparative survey of the renal proteome from wild type versus the dystrophic mdx-4cv mouse model of Duchenne muscular dystrophy [1]. With the help of an Orbitrap Fusion Tribrid mass spectrometer, 5878 protein species were identified in renal tissue extracts. The multi-consensus file of mouse kidney that contains data from the analysis of 28 separate mass spectrometric sample runs, as well as the raw data underlying the cataloguing of the kidney, has been deposited to the Open Science Framework under the project title 'Proteomic profiling of mouse kidney'; Link: https://osf.io/bz3kv/(Date created: 2018-10-04; Date made public: 2019-12-02). The analyses were carried out with 2 technical repeats of 7 biological repeats of 12-month old wild type kidney extracts, as well as 2 technical repeats of 7 biological repeats of 12-month old mdx-4cv kidney extracts. In relation to the report by Dowling et al. [1], additional datasets on proteins with an increased versus decreased concentration in the kidney from the dystrophic mdx-4cv mouse are presented in Tables 1 and 2. Table 1 lists the mass spectrometric identification of kidney proteins with a less than 1.
Specifications Table   Subject Biochemistry Specific subject area Biomedicine Type of data Tables How data were acquired LC-MS/MS analysis, using an Orbitrap Fusion Tribrid Mass Spectrometer (Thermo Scientific) Data format Raw data and analysed data Parameters for data collection Renal protein was extracted from whole kidneys from wild type and dystrophic mdx-4cv mice. Description of data collection Comparative mass spectrometry-based proteomic profiling of kidney extracts Data source location Maynooth, Co. Kildare, Ireland Data accessibility The data on kidney marker proteins are available with this article. The multi-consensus file and raw data files of all identified kidney proteins is available through a public repository. Value of the Data Mass spectrometric data presented in this article provide a detailed listing of the protein isoforms of the assessable mouse kidney proteome. Proteomic data provide a summary of changed renal proteins in the dystrophic mdx-4cv mouse model of X-linked muscular dystrophy. The proteomic data give an overview of the identification of tissue-specific kidney marker proteins. The mass spectrometric data are valuable to serve as a comprehensive repository of the mouse proteome for comparative biochemical studies.   5-fold increase in the mdx-4cv mouse. Kidney proteins with a less than 1.5-fold increased concentration in the mdx-4cv mouse are presented in Table 2. The most abundant high-molecular-mass kidney proteins are presented in Table 3. Information on typical tissue-specific kidney marker proteins [2e6] is provided in Table 4. In Table 5 are listed mass spectrometrically identified kidney marker proteins with characteristic physiological functions in ion homeostasis, including specific isoforms of the sodium/ calcium exchanger, sodium/glucose cotransporter, the plasma membrane calcium-transporting ATPase, the sodium/potassium-transporting ATPase, the endoplasmic reticulum calcium ATPase, calcium-binding proteins, voltage-dependent calcium channels and chloride channels [2]. In relation to  Table 4 List of mass spectrometrically identified mouse kidney marker proteins with a characteristic cellular localization.  the comparative survey of fatty acid binding proteins in the kidney from wild type versus the dystrophic mdx-4cv mouse model of dystrophinopathy [1], Table 6 lists the fatty acid binding proteins that were identified by mass spectrometry. This includes fatty acid-binding protein isoforms FABP1, FABP3, FABP4, FABP5 and FABP7 [7]. Kidney dystrophin and its associated proteins were identified in renal extracts, including dystrophin (Dp140), dystroglycan, alpha-1-syntrophin, beta-2-syntrophin, epsilon-sarcoglycan, alpha-dystrobrevin and beta-dystrobrevin [8], as listed in Table 7.

Biological samples and materials
The systematic cataloguing of the assessable kidney proteome was carried out with 12-month old wild type C57/BL6 mice and age-matched dystrophic mdx-4cv mice [9]. Animals were obtained from the Bioresource Unit of the University of Bonn [10] and kept under standard conditions and all procedures adhered to German legislation on the use of animals in experimental research.
For kidney protein extraction, protein digestion and the mass spectrometric analysis of the renal proteome, general materials and analytical grade reagents were purchased from Bio-Rad Laboratories (Hemel-Hempstead, Hertfordshire, UK), GE Healthcare (Little Chalfont, Buckinghamshire, UK) and Sigma Chemical Company (Dorset, UK). For the filter-aided sample preparation procedure, filter units Vivacon 500 (product number: VN0H22) were purchased from Sartorius (G€ ottingen, Germany). Protein digestion was carried out with sequencing grade modified trypsin from Promega (Madison, WI, USA). Pierce C18 spin columns and Acclaim PepMap 100 columns were from Thermo Fisher Scientific (Dublin, Ireland).

Kidney protein extraction and mass spectrometric analysis
Crude protein extracts were prepared as described in detail in the accompanying research paper [1]. The filter-aided sample preparation method was used as described by Wi sniewski et al. [11]. For the mass spectrometric establishment of the assessable mouse kidney proteome, peptide characterization was carried out by reverse-phased capillary high pressure liquid chromatography using an UltiMate Table 6 List of mass spectrometrically identified fatty acid binding proteins from mouse kidney.  Table 7 List of mass spectrometrically identified mouse kidney dystrophin and associated proteins. 3000 nano system from Thermo Scientific [12]. The liquid chromatographic separation of peptides was coupled directly in-line with a Orbitrap Fusion Tribrid Mass Spectrometer from Thermo Scientific. Data analysis was carried out as previously described in detail [13].