PXD025842

PXD025842 is an original dataset announced via ProteomeXchange.

Title	Comparison of extracellular matrix enrichment protocols for the improved characterization of the skin matrisome by mass spectrometry
Description	Four protocols were adapted and compared to enrich extracellular matrix proteins from mouse skin: 1. compartmental enrichment; 2. chemical decellularization; 3. enzymatic decellularization using phospholipase A2; 4. quantitative detergent solubility profiling (QDSP). All four protocols were started the same day, each using 35 mg of frozen back skin taken from the same initial back skin piece. The experiment was repeated three times starting from three different mice. Compartmental enrichment: skin samples were processed using the CNMCS commercial kit. Briefly, the skin tissue was homogenized in buffer C and successively incubated under agitation in buffers W, N, M and CS supplemented with the protease inhibitors from the kit. Extraction buffer C and insoluble pellet were kept aside, flash-frozen in liquid nitrogen immediately. Chemical decellularization: skin samples were cut into small pieces and successively incubated in buffers containing NaCl, SDS/sodium deoxycholate, Triton X-100 and GuHCl. Extractions buffers as well as the final insoluble pellet were kept aside, flash-frozen in liquid nitrogen immediately. Enzymatic decellularization: skin samples were cut into small pieces and successively incubated in buffers containing NaCl, phosopholipase A2/sodium deoxycholate. Extraction buffers as well as the insoluble pellet were kept aside, flash-frozen in liquid nitrogen immediately. QDSP: skin samples were homogenized in sterile PBS and successively incubated in 3 buffers containing increasing concentrations in detergents (including SDS, sodium deoxycholate, NP-40) as previously described. Extraction buffers as well as the insoluble pellet were kept aside, flash-frozen in liquid nitrogen immediately. For comparison with the four protocols described above, total skin lysates were also prepared for two of the mice. In this case, 20 mg of mouse skin were homogenized and incubated in a lysis buffer containing SDS, β-mercaptoethanol. Samples were centrifuged and the supernatant was kept aside, flash-frozen in liquid nitrogen immediately.
HostingRepository	PRIDE
AnnounceDate	2021-11-02
AnnouncementXML	Submission_2021-11-02_07:14:04.220.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD025842
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Frederic DELOLME
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2021-05-06 08:38:37	ID requested
⏵ 1	2021-11-02 07:14:04	announced

Dataset with its publication pending

submitter keyword: Mouse skin matrisome, ECM enrichment protocols comparison

Catherine Moali
contact affiliation	University of Lyon, CNRS, Tissue Biology and Therapeutic Engineering Laboratory, LBTI, UMR5305, F-69367 Lyon, France
contact email	catherine.moali@ibcp.fr
lab head
Frederic DELOLME
contact affiliation	CNRS UMS3444 Protein Science Facility
contact email	frederic.delolme@ibcp.fr
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD025842
     1. Label: PRIDE project
     2. Name: Comparison of extracellular matrix enrichment protocols for the improved characterization of the skin matrisome by mass spectrometry