PXD006401

PXD006401 is an original dataset announced via ProteomeXchange.

Title	Reproducible proteomics sample preparation for single FFPE tissue slices using acid-labile surfactant and direct trypsinization
Description	Four single consecutive murine kidney tissue specimens were prepared with the direct trypsinization with RapiGest (DTR) approach or with the filter aided sample preparation (FASP) protocol using both 10k and 30k filter devices and analyzed by label-free, quantitative liquid chromatography – tandem mass spectrometry (LC-MS/MS). Furthermore, we probed compatibility of the DTR protocol for the analysis of common histological stainings, namely hematoxylin & eosin (H&E), hematoxylin, and hemalaun. These were proteomically compared to an unstained control by analyzing four human tonsil FFPE tissues per condition.
HostingRepository	PRIDE
AnnounceDate	2018-08-15
AnnouncementXML	Submission_2018-08-15_07:57:30.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Melanie Christine Föll
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2017-04-28 00:35:46	ID requested
⏵ 1	2018-08-15 07:57:31	announced

F, ö, ll MC, Fahrner M, Oria VO, K, ü, hs M, Biniossek ML, Werner M, Bronsert P, Schilling O, Reproducible proteomics sample preparation for single FFPE tissue slices using acid-labile surfactant and direct trypsinization. Clin Proteomics, 15():11(2018) [pubmed]

curator keyword: Technical

submitter keyword: shotgun proteomics, label-free quantitation, FFPE, archival tissue, FASP, RapiGest, biomarker discovery

Oliver Schilling
contact affiliation	Insitute for Molecular Medicine and Cell Research, University of Freiburg, Germany
contact email	oliver.schilling@mol-med.uni-freiburg.de
lab head
Melanie Christine Föll
contact affiliation	Institute of Molecular Medicine and Cell Research Albert-Ludwigs University, Freiburg
contact email	melanie.foell@mol-med.uni-freiburg.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/2018/08/PXD006401

PRIDE project URI

• PRIDE
  1. PXD006401
     1. Label: PRIDE project
     2. Name: Reproducible proteomics sample preparation for single FFPE tissue slices using acid-labile surfactant and direct trypsinization