PXD033584

PXD033584 is an original dataset announced via ProteomeXchange.

Title	Tissue sampling and homogenization with NIRL enables spatially resolved cell layer specific proteomic analysis of the murine intestine
Description	For investigating the molecular physiology and pathophysiology in organs the most exact data will be obtained, if not organ specific cell lines are analysed or the whole organ is homogenized, followed by the analysis of its biomolecules, but if the morphological organisation of the organ can be addressed and in the best case the composition of molecules in single cells of the target organ can be analysed. Laser capture microdissection (LCM) is a technique, which is enabling the selection of specific cells of a tissue for further analysis of their molecules. However, LCM is a time-consuming 2-dimensional technique and optimal results are only obtained, if the tissue is fixed e.g. by formalin. Especially for proteome analysis formalin fixation is reducing the number of identifiable proteins, which is an additional drawback. Recently, it was demonstrated that sampling of fresh-frozen (non-fixed) tissue with an infrared-laser is giving higher yields with respect to the absolute protein amount and number of identifiable proteins than conventional mechanical homogenization of tissues. In this study the applicability of the infrared laser tissue sampling for proteome analysis of different cell layers of murine intestine was investigated, using LC-MS/MS-based differential quantitative bottom-up proteomics. By laser ablation eight consecutive layers of the colon tissue were obtained and analyzed. Beside a clear distinguishability of protein profiles between ascending, descending and transversal colon, we identified in the different intestinal cell layers proteins, which are cell-specific as confirmed with data from the human protein atlas. Thus, for the first time the sampling directly from intact fresh-frozen tissue with 3-dimensional resolution is giving access to the different proteomes of the different cell layers of colon tissue.
HostingRepository	PRIDE
AnnounceDate	2022-06-22
AnnouncementXML	Submission_2022-06-22_02:11:09.886.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Hannah Voß
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	iodoacetamide derivatized residue
Instrument	Q Exactive; Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2022-05-04 09:13:21	ID requested
⏵ 1	2022-06-22 02:11:11	announced

Johnson G, Bond RF, Stack LB, Class CA, Hardebeck JR, Efficacy of military antishock trousers in compensatory and decompensatory hemorrhagic hypotension. Circ Shock, 21(3):233-45(1987) [pubmed]

submitter keyword: Mouse, Laser-ablstion, LC-MS/MS, Colon, 3D

Prof. Dr. Hartmut Schlüter
contact affiliation	Section of Mass Spectrometric Proteomics, University Medical Center Hamburg Eppendorf
contact email	hschleut@uke.de
lab head
Hannah Voß
contact affiliation	University Medical Center Hamburg Eppendorf, Institute of Clinical Chemistry and Laboratory Medicine, Group of Mass Spectrometric Proteomics
contact email	ha.voss@uke.de
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD033584
     1. Label: PRIDE project
     2. Name: Tissue sampling and homogenization with NIRL enables spatially resolved cell layer specific proteomic analysis of the murine intestine