PXD043011

PXD043011 is an original dataset announced via ProteomeXchange.

Title	Direct 3D sampling of the embryonic mouse head: Layer-wise nanosecond infrared laser (NIRL) ablation from scalp to cortex for spatially resolved proteomics
Description	Common workflows in bottom-up proteomics require homogenization of tissue samples giving to get access to the biomole-cules within the cells. The homogenized tissue samples often contain many different cell types, thereby representing an average of the natural proteome composition and rare cell types are not sufficiently represented. To overcome this problem, small vol-ume sampling and spatial resolution is needed to maintain a better representation of the sample composition and their proteo-me signatures. Using nanosecond infrared laser ablation, the region of interest can be targeted in a three dimensional (3D) fash-ion whereby the spatial information is maintained during the simultaneous process of sampling and homogenization. In this study, we ablated 40 µm thick consecutive layers directly from the scalp through the cortex of the embryonic mouse heads and analyzed them by subsequent bottom-up proteomics. Extra- and intracranial ablated layers showed distinct proteome profiles comprising expected cell specific proteins. Additionally, known cortex markers like SOX2, KI67, NESTIN and MAP2 showed a layer specific spatial protein abundance distribution. We propose potential new marker proteins for cortex layers such as MTA1 and NMRAL1. The obtained data confirm that the new 3D -tissue sampling and homogenization method is well suited for investigating the spatial proteome signature of tissue samples in a layer-wise manner. Characterization of the proteome composition of embryonic skin and bone structures, meninges, and cortex lamination in situ, enables to a better understanding of molecular mechanisms of development during embryogenesis and disease pathogenesis.
HostingRepository	PRIDE
AnnounceDate	2024-01-26
AnnouncementXML	Submission_2024-01-26_10:34:20.209.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Manuela Moritz
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	acetylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2023-06-15 04:26:24	ID requested
⏵ 1	2024-01-26 10:34:21	announced

Navoli, ć J, Moritz M, Vo, ß H, Schlumbohm S, Schumann Y, Schl, ü, ter H, Neumann JE, Hahn J, Direct 3D Sampling of the Embryonic Mouse Head: Layer-wise Nanosecond Infrared Laser (NIRL) Ablation from Scalp to Cortex for Spatially Resolved Proteomics. Anal Chem, 95(47):17220-17227(2023) [pubmed]

10.1021/acs.analchem.3c02637;

submitter keyword: NIRL ablation,Spatial proteomics, Tissue sampling, Bottom-up proteomics

Hartmut Schlueter
contact affiliation	Section / Core Facility Mass Spectrometryic and Proteomics, Center of Diagnostics, University Medical Center Hamburg–Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
contact email	hschluet@uke.de
lab head
Manuela Moritz
contact affiliation	Institute of Clinical Chemistry and Laboratory Medicine Section / Core Facility Mass Spectrometry and Proteomics
contact email	ma.moritz@uke.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/2024/01/PXD043011

PRIDE project URI

• PRIDE
  1. PXD043011
     1. Label: PRIDE project
     2. Name: Direct 3D sampling of the embryonic mouse head: Layer-wise nanosecond infrared laser (NIRL) ablation from scalp to cortex for spatially resolved proteomics