PXD006255

PXD006255 is an original dataset announced via ProteomeXchange.

Title	Rapid processing of archival tissue samples for proteomic analysis using pressure-cycling technology
Description	Advent of mass spectrometry based proteomics has revolutionized our ability to study proteins from biological specimenin a high-throughput manner. Unlike cell line based studies, biomedical research involving tissue specimen is often challenging due to limited sample availability. In addition, investigation of clinically relevant research questions often requires enormous amount of time for sample collection prospectively. Formalin fixed paraffin embedded (FFPE) archived tissue samples are a rich source of tissue specimen for biomedical research. However, there are several challenges associated with analysing FFPE samples. Protein cross-linking and degradation of proteins particularly affects proteomic analysis We demonstrate that barocycler that uses pressure-cycling technology enables efficient protein extraction and processing of small amounts of FFPE tissue samplesfor proteomic analysis. We identified 3,525 proteins from six 10µm esophageal squamous cell carcinoma (ESCC) tissue sections. Barocycler allows efficient protein extraction and proteolytic digestion of proteins from FFPE tissue sections where conventional methods have limited success
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:01:00.232.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Harsha Gowda
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2017-04-04 03:57:15	ID requested
1	2018-01-08 00:28:14	announced
⏵ 2	2024-10-22 04:01:00	announced	2024-10-22: Updated project metadata.

Dataset with its publication pending

curator keyword: Technical

submitter keyword: Pressure cycling technology, Mass spectrometry, Barocycler

Harsha Gowda
contact affiliation	Harsha Gowda, Institute of Bioinformatics, Discoverer, 7th floor, International tech park, whitefield road, Bengaluru. 560066
contact email	harsha@ibioinformatics.org
lab head
Harsha Gowda
contact affiliation	QIMR Berghofer Medical Research Institute
contact email	harsha@ibioinformatics.org
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/2018/01/PXD006255

PRIDE project URI

• PRIDE
  1. PXD006255
     1. Label: PRIDE project
     2. Name: Rapid processing of archival tissue samples for proteomic analysis using pressure-cycling technology