PXD047762 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | An automated and fast sample preparation workflow for laser microdissection guided ultrasensitive proteomics |
Description | Spatial tissue proteomics integrating whole-slide imaging, laser microdissection and ultrasensitive mass spectrometry is a powerful approach to link cellular phenotypes to functional proteome states in (patho)physiology. To be applicable to large patient cohorts and low sample input amounts, including single-cell applications, loss-minimized and streamlined end-to-end workflows are key. We here introduce an automated sample preparation protocol for laser microdissected samples utilizing the cellenONE® robotic system, which has the capacity to process 192 samples in three hours. Following laser microdissection collection directly into the proteoCHIP LF 48 or EVO 96 chip, our optimized protocol facilitates lysis, formalin de-crosslinking and tryptic digest of low-input archival tissue samples. The seamless integration with the Evosep ONE LC system by centrifugation allows ‘on-the-fly’ sample clean-up, particularly pertinent for laser microdissected workflows. We validate our method in human tonsil archival tissue, where we profile proteomes of spatially-defined B-cell, T-cell and epithelial microregions of 4,000 µm2 to a depth of ~2,000 proteins and with high cell type specificity. We finally provide detailed equipment templates and experimental guidelines for broad accessibility. |
HostingRepository | PRIDE |
AnnounceDate | 2024-03-22 |
AnnouncementXML | Submission_2024-03-22_07:27:20.070.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Fabian Coscia |
SpeciesList | scientific name: Mus musculus (Mouse); NCBI TaxID: 10090; scientific name: Homo sapiens (Human); NCBI TaxID: 9606; |
ModificationList | No PTMs are included in the dataset |
Instrument | timsTOF SCP |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2023-12-12 09:17:29 | ID requested | |
⏵ 1 | 2024-03-22 07:27:20 | announced | |
Publication List
Keyword List
submitter keyword: spatial proteomics, mass spectrometry, tissue proteomics, sample preparation, robotics |
Contact List
Dr. Fabian Coscia |
contact affiliation | Max Delbrueck Center Robert-Roessle-Strasse 10 13125 Berlin, Germany |
contact email | fabian.coscia@mdc-berlin.de |
lab head | |
Fabian Coscia |
contact affiliation | Max Delbrück Center |
contact email | fabian.coscia@mdc-berlin.de |
dataset submitter | |
Full Dataset Link List
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/2024/03/PXD047762 |
PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD047762
- Label: PRIDE project
- Name: An automated and fast sample preparation workflow for laser microdissection guided ultrasensitive proteomics