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PXD047762

PXD047762 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleAn automated and fast sample preparation workflow for laser microdissection guided ultrasensitive proteomics
DescriptionSpatial 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.
HostingRepositoryPRIDE
AnnounceDate2024-03-22
AnnouncementXMLSubmission_2024-03-22_07:27:20.070.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterFabian Coscia
SpeciesList scientific name: Mus musculus (Mouse); NCBI TaxID: 10090; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListNo PTMs are included in the dataset
InstrumenttimsTOF SCP
Dataset History
RevisionDatetimeStatusChangeLog Entry
02023-12-12 09:17:29ID requested
12024-03-22 07:27:20announced
Publication List
10.1016/J.MCPRO.2024.100750;
Keyword List
submitter keyword: spatial proteomics, mass spectrometry, tissue proteomics, sample preparation, robotics
Contact List
Dr. Fabian Coscia
contact affiliationMax Delbrueck Center Robert-Roessle-Strasse 10 13125 Berlin, Germany
contact emailfabian.coscia@mdc-berlin.de
lab head
Fabian Coscia
contact affiliationMax Delbrück Center
contact emailfabian.coscia@mdc-berlin.de
dataset submitter
Full Dataset Link List
Dataset FTP location
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PRIDE project URI
Repository Record List
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