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Valberg"],"software":["Mascot 2.6.0","X! Tandem CYCLONE (2010.12.01.1)","Scaffold Scaffold_4.8.7"],"tissue":["Skeletal Muscle Fiber","Skeletal Muscle"],"sample_protocol":["Muscle samples from nine horses were analyzed using a 10-plex tandem mas tag protein quantitation assay. Five MFM WB (2 castrated males, 1 male and 2 females) with the mean age of 14.4 ± 3yrs, four non-MFM WB (2 castrated males and 2 females) with the mean age of 13.8 ± 4.6yrs, and one technical replicate were included in the assay. Proteins was extracted from snap frozen gluteal muscle biopsies with radioimmunoprecipitation lysis buffer and quantified. Five hundred µg from each sample were digested in trypsin, labeled with TMT10 reagents, fractionated, and eluted from RSLC columns. The eluted peptides were sprayed into a ThermoScientific Q-Exactive HF-X mass spectrometer. Survey scans were taken in the Orbi trap (120,000 resolution, determined at m/z 200) and the top twenty ions in each survey scan subjected to automatic higher energy collision induced dissociation with fragment spectra acquired at 45,000 resolution."],"repository":["Pride"],"labhead":["Stephanie Valberg"],"instrument_platform":["Q Exactive HF"],"submission_type":["COMPLETE"],"labhead_affiliation":["Mary Anne McPhail Dressage Chair in Equine Sports Medicine Department Large Animal Clinical Sciences College of Veterinary Medicine Michigan State University"],"publication":["34112090 Williams ZJ, Velez-Irizarry D, Gardner K, Valberg SJ. Integrated proteomic and transcriptomic profiling identifies aberrant gene and protein expression in the sarcomere, mitochondrial complex I, and the extracellular matrix in Warmblood horses with myofibrillar myopathy. BMC Genomics. 2021 22(1):438 10.1186/s12864-021-07758-0"],"submitter_affiliation":["Michigan State University"],"labhead_mail":["valbergs@msu.edu"],"technology_type":["Mass Spectrometry","Shotgun proteomics"],"disease":["Myofibrillar Myopathy"],"submitter_keywords":["Lc-msms","Gluteal muscle","Horse"],"full_dataset_link":["http://www.ebi.ac.uk/pride/archive/projects/PXD019187"],"quantification_method":["TMT"],"modification":["Carbamidomethyl","Dehydrated","Ammonia-loss","iodoacetamide derivatized residue","methionine oxidation with neutral loss of 64 Da","Acetyl","Oxidation","TMT6plex-126 reporter+balance reagent acylated residue","mono N-acetylated residue","TMT6plex"],"data_protocol":["The resulting MS/MS spectra were converted to peak lists using Proteome Discoverer, v2.2 and searched against the UniprotKB Equus caballus reference proteome (UP000002281) appended with common laboratory contaminants using the Sequest HT search algorithm. The search output was then analyzed using Scaffold, v4.8.4 to probabilistically validate protein identifications (FDR < 0.01) . Spectra data were log-transformed, pruned of those matched to multiple proteins (retaining proteins with at least two identified peptides), and weighted by an adaptive intensity weighting algorithm. Of 108665 spectra in the experiment at the given thresholds, 79921 (74%) were included in quantitation. Differentially expressed proteins were determined by applying Permutation Test and corrected by Benjamini-Hochberg (FDR ≤ 0.05, P ≤ 0.003)."],"omics_type":["Proteomics"],"species":["Equus Caballus (horse)"],"submitter_mail":["valbergs@msu.edu"],"submitter_country":["United States"],"doi":["10.6019/PXD019187"],"pubmed_abstract":["