Proteomic dataset of wolframin-deficient mouse heart and skeletal muscles

The data presented in this article are related to the research article entitled "Increased Mitochondrial Protein Levels and Bioenergetics in the musculus rectus femoris of Wfs1-Deficient mice" (Eimre et al., accepted for publication). This dataset reports the analysis of Wfs1-deficient mouse heart, musculus soleus, and white part of musculus rectus femoris by liquid chromatography/tandem mass spectrometry. Label-free quantitative analysis of the mass spectrometry data identified 4056 proteins, with 114, 212, and 1290 proteins differentially expressed (t-test; p < 0.05) in the heart, m. soleus, and m. rectus femoris, respectively, between the Wfs1-deficient and wild-type groups. Eight proteins were found to be differentially expressed in all mentioned muscles, with 1 protein differently expressed in oxidative (m. soleus and heart) and 88 in skeletal muscles. This dataset supports the cited study and can be used to extend additional analyses. Data are available via ProteomeXchange with identifier PXD011019.


a b s t r a c t
The data presented in this article are related to the research article entitled "Increased Mitochondrial Protein Levels and Bioenergetics in the musculus rectus femoris of Wfs1-Deficient mice" (Eimre et al., accepted for publication). This dataset reports the analysis of Wfs1-deficient mouse heart, musculus soleus, and white part of musculus rectus femoris by liquid chromatography/tandem mass spectrometry. Label-free quantitative analysis of the mass spectrometry data identified 4056 proteins, with 114, 212, and 1290 proteins differentially expressed (t-test; p o 0.05) in the heart, m. soleus, and m. rectus femoris, respectively, between the Wfs1deficient and wild-type groups. Eight proteins were found to be differentially expressed in all mentioned muscles, with 1 protein differently expressed in oxidative (m. soleus and heart) and 88 in skeletal muscles. This dataset supports the cited study and can be used to extend additional analyses.

Value of the data
This is the first proteomic dataset of Wfs1 deficient muscles. The data may be a valuable starting point for studying the direct and indirect mechanisms of Wfs1 deficiency on mouse muscles.
These data and further experiments based on these data may provide valuable information for understanding the mechanisms of Wolfram syndrome and type 1 diabetes.

Data
Proteins found to be differentially expressed in all studied Wfs1-deficient muscles are presented in Fig. 1 and at the beginning of Table S4. The level of Bcl2-associated agonist of the cell death protein was decreased in both oxidative muscles (Table S4). Protein expression in wolframin-deficient skeletal muscle was compared to that in wild-type, which showed that the expression of 35 proteins was decreased, while 61 proteins were increased ( Table 1). Data of differentially expressed proteins in the woframin-deficient heart are in Table S1, wolframin-deficient musculus soleus in Table S2, and woframin-deficient musculus rectus femoris in Table S3. Label-free quantitative (LFQ) intensities and other information for all proteins identified by liquid chromatography (LC)/tandem mass spectrometry (MS/MS) analysis of muscles are in Tables S4 and S5 (P3; P5; P6; P8; P17; P21; P23; P25: m. rectus femoris in wild-type mice; P1; P19; P22; P24; P26: m. rectus femoris in Wfs1-deficient mice; P4; P7; P18: m. soleus in wild-type mice; P2; P20: m. soleus of Wfs1-deficient mice; P9; P11; P12; P14: heart in wild-type mice; P10; P13; P15; P16: heart in Wfs1-deficient mice). All peptides identified and quantified are shown in Table S6.

Animals and proteomics sample preparation
The heart, m. soleus, and white glycolytic part of the m. rectus femoris from 9-12-month-old Wfs1

Proteomics data analysis
LC/MS/MS analysis was performed using an Ultimate 3000 RSLCnano system (Dionex, Sunnyvale, CA, USA) and Q Exactive Plus (Thermo Fisher Scientific, Waltham, MA, USA) tandem mass spectrometer.
Mass spectrometric raw data were processed using the MaxQuant 1.5.3.17 software package [2]. LFQ was conducted using the MaxQuant LFQ algorithm [3]. A search was performed against the UniProt (www.uniprot.org) Mus musculus reference proteome database (downloaded on November 11, 2015; 57,320 entries). The peptide-spectrum match and protein false discovery rate was kept below 1% using a target-decoy approach [1]. Statistical analysis of LFQ intensities of proteins was performed by Student's t-test. Data are given as the mean 7 standard error of the mean. A value of p o 0.05 was considered statistically significant.