PXD007527

PXD007527 is an original dataset announced via ProteomeXchange.

Title	Mining the secretome of C2C12 muscle cells
Description	Secretome analysis faces several challenges, including detection of low abundant proteins and the discrimination of bona fide secreted proteins from false-positive identifications stemming from cell leakage or serum. Here, we developed a two-step secretomics approach and applied it for the analysis of secreted proteins of C2C12 skeletal muscle cells as the skeletal muscle has been identified as an important endocrine organ secreting myokines as active signaling molecules. First, we compared culture supernatants and corresponding cell lysates by high-resolution MS-based proteomics and label-free quantification. We found 672 protein groups as candidate secreted proteins, as they showed a higher abundance in the secretome. By Brefeldin A mediated blocking of classical secretory processes, we estimate a sensitivity of > 80% for the detection of classical secreted proteins by our experimental approach. In the second step, peptide level information was integrated with UniProt based protein information by the bioinformatics tool “lysate and secretome peptide feature plotter” (LSPFP) to detect proteolytic protein processing events which might occur during secretion e.g. As a proof on concept, we identified truncations of the cytoplasmic part of the protein Plexin-B2. Our workflow provides an efficient combination of experimental workflow and data analysis to identify putative secreted and proteolytic processed proteins.
HostingRepository	PRIDE
AnnounceDate	2018-01-24
AnnouncementXML	Submission_2018-01-24_03:12:50.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Gereon Poschmann
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2017-08-22 03:07:03	ID requested
⏵ 1	2018-01-24 03:12:51	announced

Grube L, Dellen R, Kruse F, Schwender H, St, ü, hler K, Poschmann G, Mining the Secretome of C2C12 Muscle Cells: Data Dependent Experimental Approach To Analyze Protein Secretion Using Label-Free Quantification and Peptide Based Analysis. J Proteome Res, 17(2):879-890(2018) [pubmed]

curator keyword: Biological

submitter keyword: Secretome, skeletal muscle cells, ESI-LC-MS/MS, LSPFP, proteolytic processing, Plexin-B2

Gereon Poschmann
contact affiliation	Molecular Proteomics Laboratory (MPL) Biologisch-Medizinisches Forschungszentrum (BMFZ) Heinrich-Heine-Universität Düsseldorf Universitätsstraße 1 40225 Düsseldorf Germany
contact email	gereon.poschmann@hhu.de
lab head
Gereon Poschmann
contact affiliation	Molecular Proteomics Laboratory
contact email	gereon.poschmann@hhu.de
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD007527
     1. Label: PRIDE project
     2. Name: Mining the secretome of C2C12 muscle cells