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Bravo"],"technology_type":["Mass Spectrometry","SWATH MS"],"software":["Not available"],"submitter_keywords":["Metabolism.","Serelaxin","Mitochondrial respiration","Proteome","Phosphoproteome","Skeletal muscle","Myogenesis","Relaxin-2"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD078619"],"tissue":["Skeletal Muscle"],"sample_protocol":["Protein extraction and digestion  Freeze tissue (100 mg) from the different samples were homogenized in RIPA buffer [200 mmol/L Tris/HCl (pH 7.4), 130 mmol/L NaCl, 10% (v/v) glycerol, 0.1% (v/v) SDS, 1% (v/v) Triton X-100, 10 mmol/L MgCl2] with antiproteases and antiphosphatases (Sigma-Aldrich, St. Louis, MO, USA) in a TissueLyser II (Qiagen, Tokyo, Japan). The homogenate was centrifuged at 14,000g at 4 °C for 20 min. Protein concentration was measure sample using a RC-DC kit (Biorad Lab., Hercules, CA, USA) according to the manufacture protocol. Protein aliquots of 100 μg were concentrated in a SDS-PAGE single band(Bonzon-Kulichenko et al., 2011; Perez-Hernandez et al., 2013) and submitted to a manual digestion as describe elsewhere (Shevchenko et al., 1996). Finally, the peptides were dissolved in 0.1% formic acid for further analysis.  Phosphoproteome analysis  For fosfoproteome analysis, phosphopeptides were enriched using the High-Select™ TiO₂ Phosphopeptide Enrichment Kit (Thermo Fisher Scientific) according to the manufacturer’s instructions. Enriched fractions were then analyzed by LC–MS/MS using SWATH method (Aragón-Herrera et al., 2024; Vázquez-Abuín et al., 2025)."],"repository":["Pride"],"quantification_method":["Not available"],"modification":[""],"data_protocol":["Data analysis (DDA acquisition)  DDA data files were processed using ProteinPilotTM 5.0.1 (Sciex), which uses the algorithm ParagonTM for database search and ProgroupTM for data grouping. Data was searched using a rattus specific Uniprot database specifying iodoacetamide at cysteine alkylation as variable modification and methionine oxidation as fixed modification. False discovery rate was performed using a non-lineal fitting method, displaying only those results that reported a 1% Global false discovery rate or better.   Relative quantification: Spectral count  Scaffold (version Scaffold-5.2.2 or Scaffold DDA 6.8.0 Proteome Software Inc., Portland, OR) was used to validate MS/MS based peptide and protein identifications and to perform a semiquantitative analysis by spectral counting.Peptide identifications were accepted if they could be established at greater than 97.0% probability to achieve a false discovery rate (FDR) <1.0% by the Scaffold Local FDR algorithm. Protein identifications were accepted if they could be established at greater than 99.0% probability to achieve a FDR <1.0% and contained at least 2 identified peptides. Protein probabilities were assigned by the Protein Prophet algorithm. The Fisher’s exact test was used for quantification and fold change determination. Proteins were considered differentially expressed when P<0.05. Proteins with a FC=0 or FC=Infinity were considered present only in one sample type.  Functional and pathway analysis (DDA acquisition)  We conducted pathway analysis using String ( https://string-db.org/ ), applying a minimum required interaction score of PPI= 0.7 (protein protein interaction) and an FDR < 0.05. Venn diagram and biological processes pathway analysis were generated using FunRich software ( http://www.funrich.org/ ) for data-independent acquisition analysis. Statistical analyses were performed using Scaffold software.  Data analysis (SWATH acquisition) The targeted data extraction of the fragment ion chromatogram traces from the SWATH runs was performed by PeakView (version 2.2) using the SWATH Acquisition MicroApp(version 2.0). This application processed the data using the spectral library created from the shotgun data. Up to ten peptides per protein and seven fragments per peptide were selected, based on signal intensity; any shared and modified peptides were excluded from the processing. Five minute windows and30 ppm widths were used to extract the ion chromatograms; SWATH quantitation was attempted for all proteins in the ion library that were identified by ProteinPilot with an FDR below 1%. The retention times from the peptides that were selected for each protein were realigned in each run according to the iRT peptides spiked in each sample and eluted along the whole time axis. PeakView computed an FDR and a score for each assigned peptide according to the chromatographic and spectra components; only peptides with an FDR below 5% were used for protein quantitation. Protein quantitation was calculated by adding the peak areas of the corresponding peptides.  The integrated peak areas (processed. mrkvw files from PeakView) were directly exported to the MarkerView software (Sciex) for relative quantitative analysis. The export will generate three files containing quantitative information about individual ions, the summed intensity of different ions for a particular peptide and the summed intensity of different peptides for a particular protein. MarkerView has been used for analysis of SWATH-MS data reported in other proteomics studies (Luo et al., 2017; Meyer & Schilling, 2017; Ortea et al., 2018; Tan & Chung, 2018) because of its data-independent method of quantitation. MarkerView uses processing algorithms that accurately find chromatographic and spectral peaks direct from the raw SWATH data. Data alignment by MarkerView compensated for minor variations in both mass and retention time values, ensuring that identical compounds in different samples are accurately compared to one another. Unsupervised multivariate statistical analysis using principal component analysis (PCA) was performed to compare the data from the different samples. A most-like ratio (MLR) normalization was performed after statistical analysis to control for possible uneven sample loss across the different samples during the sample preparation process. The average MS peak area for each protein was derived from each sample  Functional and pathway analysis (SWATH acquisition) We performed pathway analysis using String ( https://string-db.org/ ), applying a minimum required interaction score of PPI= 0.7 (protein protein interaction) and an FDR < 0.05. The most functional enriched pathways were represented employing String diagrams. Volcano plots were generated using GraphPad Prism 9 (GraphPad Software Inc., USA)."],"omics_type":["Proteomics"],"labhead":["Susana B Bravo"],"instrument_platform":[""],"submission_type":["PARTIAL"],"labhead_affiliation":["Instituto de Invesstigaciones Sanitarias de Santiago de Compostela"],"species":["Rattus Norvegicus (rat)"],"publication":["42742485 Vázquez-Abuín X, Gómez-Cibeira L, García-Seara J, de la Fuente-López P, Minguito-Carazo C, Bravo SB, Otero-Santiago M, Gualillo O, González-Juanatey JR, Lago F, Feijóo-Bandín S, Aragón-Herrera A. Relaxin-2: Shaping the Proteomic Landscape of Skeletal Muscle Physiology, Glucose Trafficking, and Mitochondrial Function in Rat. FASEB J. 2026 40(18):e72291 10.1096/fj.202602643r"],"submitter_mail":["sbbravo@gmail.com"],"submitter_affiliation":["FIDIS"],"submitter_country":["Spain"],"pubmed_abstract":["Relaxin-2 is a hormone with robust beneficial effects on the heart and blood vessels and potential as a therapy for cardiovascular (CV) disease. Considering the interorgan communication between skeletal muscle and heart, and the relation between muscle quality/composition and CV events, we hypothesize that relaxin-2 may regulate skeletal muscle physiology and metabolism. We aim to evaluate the impact of relaxin-2 on the proteome of skeletal muscle from healthy Sprague-Dawley rats. Animals were treated with 0.4 mg/kg/day of serelaxin (recombinant form of human relaxin-2) or vehicle (PBS) for 2 weeks employing subcutaneous osmotic minipumps. Skeletal muscle protein identification and quantification were performed by LC-MS/MS using a Data-Independent Acquisition (DIA)-Sequential Window Acquisition of All Theoretical Fragment Ion Spectra (SWATH) method. SWATH/MS quantitative analysis identified that relaxin-2 significantly decreased 95 proteins and significantly increased 32 proteins in rat skeletal muscle when compared to control rats. From these, 34 proteins were associated with muscle function, myogenesis, muscle differentiation and/or regeneration, 20 are mitochondrial proteins (six from the complexes of the electron transport chain), and 10 proteins participate in glucose metabolism. Qualitative data-dependent workflow analysis identified 35 proteins exclusive to the skeletal muscle of the relaxin-2-treated group: eight proteins related to processes of skeletal muscle function (size, ion homeostasis or organization of caveolae structures and cytoskeleton) and myogenesis, and two proteins involved in muscle differentiation. Our work highlighted for the first time the role of relaxin-2 in crucial processes of muscle physiology and energetic metabolism, which could influence several processes involved in myopathy and CV."],"pubmed_title":["Relaxin-2: Shaping the Proteomic Landscape of Skeletal Muscle Physiology, Glucose Trafficking, and Mitochondrial Function in Rat."],"pubmed_authors":["Vázquez-Abuín Xocas X, Gómez-Cibeira Lucía L, García-Seara Javier J, de la Fuente-López Pablo P, Minguito-Carazo Carlos C, Bravo Susana B SB, Otero-Santiago Manuel M, Gualillo Oreste O, González-Juanatey José Ramón JR, Lago Francisca F, Feijóo-Bandín Sandra S, Aragón-Herrera Alana A"],"additional_accession":[]},"is_claimable":false,"name":"Relaxin-2: shaping the proteomic landscape of skeletal muscle physiology, glucose trafficking, and mitochondrial function in rat.","description":"Relaxin-2 is a hormone with robust beneficial effects on the heart and blood vessels and with a potential therapeutic efficacy in cardiovascular (CV) disease. Considering the interorgan communication between skeletal muscle and heart, and the relation between muscle quality/composition and CV events, we hypothesise that relaxin-2 may regulate skeletal muscle physiology and metabolism. We aim to evaluate the impact of serelaxin on the proteome of skeletal muscle from healthy Sprague-Dawley rats. Animals were treated with 0.4 mg/kg/day of serelaxin (recombinant form of human relaxin-2) or vehicle (PBS) for 14 days employing subcutaneous osmotic minipumps. Skeletal muscle proteomic profiles were analysed using SWATH/MS quantification and qualitative data-dependent workflow analysis (DDA) carried out in a TripleTOF 6600 System. Quantitative analysis identified that serelaxin significantly decreased 89 proteins and significantly increased 31 proteins in rat skeletal muscle when compared to control rats. From these, 34 proteins are associated with muscle function, myogenesis, muscle differentiation and/or regeneration, 15 are mitochondrial proteins (6 of them subunits of the complexes of the electron transport chain), and 10 proteins participate in glucose metabolism. Qualitative analysis identified 35 proteins exclusive to the skeletal muscle of the serelaxin-treated group: 8 proteins related to processes of muscle function (regulation of skeletal muscle size, ion homeostasis or organisation of caveolae structures and cytoskeleton) and myogenesis, and 2 proteins involved in muscle differentiation. We highlight the role of serelaxin shaping the skeletal muscle proteome, which could influence several processes involved in myopathy and CV, such as mitochondrial dysfunction and bioenergetic abnormalities.","dates":{"publication":"2026-09-21","submission":"2026-05-20"},"accession":"PXD078619","cross_references":{"TAXONOMY":["NEWT:68239","NEWT:108018","NEWT:377960","NEWT:1131","NEWT:190486","NEWT:2042546","NEWT:148942","NEWT:295546","NEWT:258594","NEWT:1126","NEWT:1129","NEWT:89187","NEWT:309807","NEWT:89184","NEWT:309800","NEWT:57577","NEWT:1323429","NEWT:876138","NEWT:44271","NEWT:193516","NEWT:2315688","NEWT:592321","NEWT:1073882","NEWT:6819","NEWT:77173","NEWT:428386","NEWT:1117","NEWT:498257","NEWT:10036","NEWT:32264","NEWT:10034","NEWT:661410","NEWT:488003","NEWT:224326","NEWT:376619","NEWT:3765","NEWT:3767","NEWT:433727","NEWT:135622","NEWT:672127","NEWT:656061","NEWT:37965","NEWT:656064","NEWT:3760","NEWT:36630","NEWT:381198","NEWT:418106","NEWT:10029","NEWT:913645","NEWT:2492962","NEWT:641809","NEWT:44250","NEWT:317447","NEWT:5537","NEWT:5530","NEWT:868565","NEWT:135674","NEWT:1562698","NEWT:12637","NEWT:2164133","NEWT:2767846","NEWT:1343074","NEWT:314344","NEWT:108061","NEWT:224308","NEWT:49928","NEWT:160621","NEWT:110368","NEWT:1916073","NEWT:1310161","NEWT:1230383","NEWT:77133","NEWT:1310165","NEWT:114727","NEWT:5516","NEWT:498211","NEWT:347256","NEWT:5518","NEWT:398007","NEWT:1527468","NEWT:498217","NEWT:498216","NEWT:11320","NEWT:33554","NEWT:1310173","NEWT:37919","NEWT:161934","NEWT:156587","NEWT:1148","NEWT:5508","NEWT:419481","NEWT:5507","NEWT:1140","NCBITaxon:2157","NEWT:2066563","NEWT:1143","NEWT:1462472","NEWT:1336795","NEWT:644042","NEWT:709964","NEWT:3712","NEWT:3711","NEWT:3714","NEWT:65121","NEWT:3715","NEWT:2065263","NEWT:1549675","NEWT:177437","NEWT:9014","NEWT:10891","NEWT:34869","NEWT:226126","NEWT:1616117","NEWT:34865","NEWT:28174","NEWT:550537","NEWT:284812","NEWT:980415","NEWT:3701","NEWT:3702","NEWT:66440","NEWT:1245466","NEWT:3704","NEWT:1246791","NEWT:34875","NEWT:9005","NEWT:34871","NEWT:9006","NEWT:33548","NEWT:1883426","NEWT:657321","NEWT:34878","NEWT:10886","NEWT:3708","NEWT:536231","NEWT:219813","NEWT:215451","NEWT:460519","NEWT:272843","NEWT:272844","NEWT:1348799","NEWT:55784","NEWT:485","NEWT:2709072","NEWT:2499525","NEWT:142786","NEWT:2853422","NEWT:487","NEWT:1679718","NEWT:480","NEWT:67767","NEWT:46835","NEWT:216778","NEWT:376686","NEWT:237610","EFO:0001352","NEWT:1385720","NEWT:219809","NEWT:219808","NEWT:119562","NEWT:1883446","NEWT:1233435","NEWT:118223","NEWT:141469","NEWT:272831","NEWT:987059","NEWT:491","NEWT:460523","NEWT:2423","NEWT:133894","NEWT:85694","NEWT:85692","NEWT:911045","NEWT:3750","NEWT:291146","NEWT:29466","NEWT:233271","NEWT:3745","NEWT:1715989","NCBITaxon:4751","NEWT:3747","NEWT:278161","NEWT:415978","NEWT:410289","NEWT:191701","NEWT:9054","NEWT:472","NEWT:29459","NEWT:1380096","NEWT:28128","NEWT:470","NEWT:41122","NEWT:1328300","NEWT:748693","NCBITaxon:50557","NEWT:3735","NEWT:29491","NEWT:911022","NEWT:446","NEWT:153481","NEWT:445","NEWT:2003758","NEWT:63366","NEWT:63367","NEWT:29488","NEWT:215402","NEWT:3726","NEWT:30455","NEWT:28141","NEWT:9030","NEWT:9031","NEWT:3728","NEWT:108931","NEWT:219799","NEWT:1325292","NEWT:219798","NEWT:548","NEWT:150475","NEWT:256737","NEWT:51350","NEWT:8694","NEWT:8692","NEWT:542","NEWT:394503","NEWT:13076","NEWT:219785","NEWT:451515","NEWT:8673","NEWT:550","NEWT:10804","NEWT:554","NEWT:451516","NEWT:552","NEWT:1325291","NEWT:42410","NEWT:1225786","NEWT:771870","NEWT:8665","NEWT:51338","NEWT:9995","NEWT:28112","NEWT:49012","NEWT:28110","NEWT:10832","NEWT:311339","NEWT:507601","NEWT:520","NEWT:64657","NEWT:186441","NEWT:2585209","NEWT:643680","NEWT:214092","NEWT:40697","NEWT:13095","NEWT:162425","NEWT:242124","NEWT:9986","NEWT:8654","NEWT:8658","NEWT:1268063","NEWT:8657","NEWT:9983","NEWT:8655","NEWT:595495","NEWT:80833","NEWT:479096","NEWT:28108","NEWT:28104","NEWT:1114957","NEWT:568703","NEWT:568708","NEWT:52641","NEWT:353152","NEWT:353153","NEWT:227377","NEWT:1774284","NEWT:27689","NEWT:207769","NEWT:40674","NEWT:51329","NCBITaxon:1763","NEWT:443906","NEWT:13037","NEWT:519","NEWT:941638","NEWT:7394","NEWT:6063","NEWT:404330","NEWT:1328388","NEWT:13064","NEWT:7375","NEWT:300641","NEWT:39655","NEWT:38323","NEWT:206411","NEWT:80869","NEWT:214053","NEWT:80863","NEWT:665890","NEWT:52639","NEWT:52638","NEWT:367774","NEWT:8697","NEWT:861109","NEWT:8695","NEWT:1196866","NEWT:6039","NEWT:510516","NEWT:1045775","NEWT:1123869","NCBITaxon:1335626","NEWT:7370","NEWT:280406","NEWT:83906","NEWT:99488","NEWT:1134506","NEWT:255470","NEWT:762903","NEWT:27697","NEWT:86185","NEWT:9935","NEWT:266940","NEWT:287889","NEWT:1028307","NEWT:52603","NEWT:92867","NEWT:92866","NEWT:1344414","NEWT:202950","NEWT:741158","NEWT:1293091","NEWT:202956","NEWT:315750","NEWT:99490","NEWT:632957","NEWT:9925","NCBITaxon:9606","NEWT:1436183","NEWT:1479235","NEWT:4232","NEWT:9922","NEWT:416348","NEWT:105812","NEWT:11298","NEWT:4233","NEWT:4236","NEWT:398031","NEWT:196627","NEWT:523840","NEWT:1076878","NEWT:200308","NEWT:200302","NEWT:9917","NEWT:95912","NEWT:9913","NEWT:9915","NEWT:105841","NEWT:1170227","NEWT:2666255","NEWT:999810","NEW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