Proteomics

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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.  

TISSUE(S): Skeletal Muscle Fiber, Skeletal Muscle Tissue

SUBMITTER: Britta Eggers  

LAB HEAD: Katrin Marcus

PROVIDER: PXD025359 | Pride | 2021-06-07

REPOSITORIES: Pride

Dataset's files

Source:
Action DRS
QExHF04255.mzML Mzml
QExHF04255.raw Raw
QExHF04257.mzML Mzml
QExHF04257.raw Raw
QExHF04259.mzML Mzml
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