Dataset Information

Advanced fiber type-specific protein profiles derived from adult murine skeletal muscle

ABSTRACT: Skeletal muscle is a heterogeneous tissue consisting of blood vessels, connective tissue, and muscle fibers. The last are highly adaptive and can change their molecular composition depending on external and internal factors, such as exercise, age, and disease. Thus, examination of the skeletal muscles at the fiber type level is essential to detect potential alterations. Therefore, we established a protocol in which myosin heavy chain isoform immunolabeled muscle fibers were laser microdissected and separately investigated by mass spectrometry to develop advanced proteomic profiles of all murine skeletal muscle fiber types. Our in-depth mass spectrometric analysis revealed unique fiber type protein profiles, confirming fiber type-specific metabolic properties and revealing a more versatile function of type IIx fibers. Furthermore, we found that multiple myopathy-associated proteins were enriched in type I and IIa fibers. To further optimize the assignment of fiber types based on the protein profile, we developed a hypothesis-free machine-learning approach (available at: https://github.com/mpc-bioinformatics/FiPSPi), identified a discriminative peptide panel, and confirmed our panel using a public data set.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Ensifer adhaerens Aerococcus urinae NBRC 15544 = CCUG 36881 Escherichia coli Olavius algarvensis Panicum virgatum Clostridioides difficile 630 Lithobius forficatus Rhodopseudomonas palustris Synechocystis sp. PCC 6803 Archaea Cercopithecidae Olavius algarvensis sulfate-reducing endosymbiont Sus scrofa domesticus Globicatella sanguinis Taeniopygia guttata Ophrys sphegodes Naja sagittifera Cupriavidus metallidurans Schizosaccharomyces pombe 927 Danio rerio Zea mays Apis mellifera ligustica Macaca mulatta Vitis riparia Ophrys x arachnitiformis subsp. archipelagi Klebsiella pneumoniae Caenorhabditis elegans Vitis Streptomyces coelicolor A3(2) Helicobacter pylori 26695 Dentex dentex Oncorhynchus mykiss Ophrys garganica Halobacterium salinarum Streptococcus pneumoniae R6 Bradyrhizobium japonicum Ceratopteris richardii Ovis aries Craterostigmus tasmanianus Trypanosoma brucei Populus yunnanensis Hordeum vulgare Allexis Rhodococcus jostii RHA1 Physcomitrium patens Geobacter sulfurreducens albimanus section Bartonella quintana Homo sapiens Bacteria Gallus gallus Pseudomonas putida KT2440 Callinectes sapidus Canis lupus x Canis lupus familiaris Paucilactobacillus suebicus Escherichia coli O157:H7 str. TW14359 Alteromonadales Oryza sativa Mycobacterium tuberculosis Burkholderia cenocepacia Medicago truncatula Viruses Scolopendra morsitans Scutigera coleoptrata Bradyrhizobium diazoefficiens USDA 110 Entamoeba histolytica HM-1:IMSS-A Plasmodium falciparum 3D7 Canis lupus familiaris Beta vulgaris subsp. vulgaris Solanum lycopersicum Vitis vinifera Streptococcus agalactiae FSL S3-026 Pseudomonas fluorescens SBW25 Olavius algarvensis Delta 4 endosymbiont Populus tremula x Populus alba Pseudomonas pseudoalcaligenes CECT 5344 Avena strigosa Rattus norvegicus Mus musculus Pyrococcus furiosus Xenopus laevis Deinococcus radiodurans R1 Botrytis cinerea Sorghum bicolor Dasypogon diadema Sedum plumbizincicola Saccharopolyspora erythraea Acidithiobacillus ferrooxidans ATCC 53993 Emiliania huxleyi Tetrahymena thermophila Arabidopsis thaliana Onchocerca volvulus Pseudomonas aeruginosa PAO1 Candida albicans SC5314 Mycolicibacterium smegmatis Heloderma suspectum suspectum Nephila clavipes Bovine leukemia virus Listeria monocytogenes Rattus rattus Vibrio anguillarum Brugia malayi Brassica oleracea var. italica Enterococcus faecalis Schizosaccharomyces pombe Thermoplasma acidophilum DSM 1728 Rhizobium sp. Leaf68 Streptococcus pneumoniae D39 Sus scrofa Ctenopharyngodon idella Homo sapiens subsp. 'Denisova' Entamoeba histolytica Equus caballus Acinetobacter baumannii Cervus nippon nippon Oryza sativa Indica Group Daktulosphaira vitifoliae Pseudomonas putida BIRD-1 Bos taurus Olavius algarvensis spirochete endosymbiont Parasynechococcus marenigrum WH 8102 Lotus japonicus Pseudomonas syringae Chlorocebus sabaeus Strigamia maritima Olavius algarvensis Gamma 1 endosymbiont Camelus dromedarius Saccharomyces cerevisiae Dirofilaria immitis Staphylococcus aureus Crithidia fasciculata Lingula anatina Triticum aestivum Bacillus subtilis subsp. subtilis NCIB 3610 = ATCC 6051 = DSM 10 Pseudomonas aeruginosa Macaca fascicularis Histomonas meleagridis Drosophila melanogaster Bombyx mori Flavobacterium columnare Citrobacter rodentium Trypanosoma cruzi Olavius algarvensis Delta 1 endosymbiont Pectobacterium carotovorum Bursaphelenchus xylophilus Brassica napus Human immunodeficiency virus 1 Salmo salar Candida albicans Ictalurid herpesvirus 1 Staphylococcus sp. 1 Chlamydomonas reinhardtii Escherichia coli O157:NM Glycine max Eukaryota Cavia porcellus Sinorhizobium meliloti BL225C Trypanosoma brucei brucei Drosophila Schizosaccharomyces pombe 972h- Ostreococcus tauri Sphingomonas sp. Leaf257 Naja naja Streptococcus dysgalactiae subsp. equisimilis SK1249 Bartonella quintana JK 31 Cervus elaphus elaphus Pyricularia oryzae Apostichopus japonicus Bacillus subtilis subsp. subtilis str. 168 Helianthus annuus Cyanophora paradoxa Mytilus edulis Salmo sp.