PXD017755

PXD017755 is an original dataset announced via ProteomeXchange.

Title	High-throughput Proteomics fiber typing (ProFiT) for comprehensive characterization of single skeletal muscle fibers
Description	Skeletal muscles are composed of a heterogeneous collection of fiber types with different physiological adaption in response to a stimulus and disease-related conditions. Each fiber has a specific molecular expression of myosin heavy chain molecules (MyHC). So far MyHCs are currently the best marker proteins for characterization of individual fiber types and several proteome profiling studies have helped to dissect the molecular signature of whole muscles and individual fibers. Herein, we describe a mass spectrometric workflow to measure skeletal muscle fiber type-specific proteomes. To bypass the limited quantities of protein in single fibers, we developed a Proteomics high-throughput Fiber Typing (ProFiT) approach enabling profiling of MyHC in single fibers. Aliquots of protein extracts from separated muscle fibers were subjected to capillary LC-MS gradients to profile MyHC isoforms in a 96-well format. Muscle fibers with the same MyHC protein expression were pooled and subjected to proteomic, pulsed-SILAC and phosphoproteomic analysis. Our fiber type-specific quantitative proteome analysis confirmed the distribution of fiber types in the soleus muscle, substantiates metabolic adaptions in oxidative and glycolytic fibers, and highlighted significant differences between the proteomes of type IIb fibers from different muscle groups, including a differential expression of desmin and actinin-3. A detailed map of the Lys-6 incorporation rates in muscle fibers showed an increased turnover of slow fibers compared to fast fibers. In addition, labeling of mitochondrial respiratory chain complexes revealed a broad range of Lys-6 incorporation rates, depending on the localization of the subunits within distinct complexes.
HostingRepository	PRIDE
AnnounceDate	2020-05-04
AnnouncementXML	Submission_2020-05-04_10:40:53.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Sebastian Kallabis
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	phosphorylated residue; acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive HF-X; LTQ Orbitrap; Q Exactive Plus

Revision	Datetime	Status	ChangeLog Entry
0	2020-02-26 23:15:29	ID requested
⏵ 1	2020-05-04 10:40:54	announced

Dataset with its publication pending

submitter keyword: Muscle fiber proteomics, MyHC profiling, protein turnover, phosphoproteomics

Marcus Krüger
contact affiliation	CECAD Research Center, Institute for Genetics, University of Cologne, 50931 Cologne, Germany
contact email	marcus.krueger@uni-koeln.de
lab head
Sebastian Kallabis
contact affiliation	CECAD Research Center University of Cologne
contact email	skallab5@uni-koeln.de
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/05/PXD017755

PRIDE project URI

• PRIDE
  1. PXD017755
     1. Label: PRIDE project
     2. Name: High-throughput Proteomics fiber typing (ProFiT) for comprehensive characterization of single skeletal muscle fibers