PXD004476

PXD004476 is an original dataset announced via ProteomeXchange.

Title	Human Bile LC-MS/MS
Description	The proteome analysis of bile fluid represents a promising strategy to identify biomarker candidates for various diseases of the hepatobiliary system. However, to obtain substantive results in biomarker discovery studies large patient cohorts necessarily need to be analyzed. Consequently, this would lead to an unmanageable number samples to be measured if sample preparation protocols with extensive fractionation methods are applied. Hence, the performance of simple workflows allowing for "one sample, one shot" experiments have been evaluated in this study. In detail, sixteen different protocols implying modifications at the stages of desalting, delipidation, deglycosylation and tryptic digestion have been tested. Each method has been individually evaluated regarding various performance criteria and comparative analyses have been conducted to uncover possible complementarities. Here, the best performance in terms of proteome coverage has been assessed for a combination of acetone precipitation with in-gel digestion. Finally, a mapping of all obtained protein identifications with putative biomarkers for hepatocellular carcinoma (HCC) and cholangiocellular carcinoma (CCC) revealed several proteins easily detectable in bile fluid. These results can build the basis for future studies with large and well-defined patient cohorts in a more disease-related context, instead of a technical one as reported here.
HostingRepository	PRIDE
AnnounceDate	2017-05-03
AnnouncementXML	Submission_2017-05-03_08:46:46.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD004476
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Dominik Andre Meger
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	Propionamide; residues isobaric at 128.058578 Da; Deamidated; Oxidation; Carbamidomethyl
Instrument	LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2016-06-30 07:53:34	ID requested
⏵ 1	2017-05-03 08:46:49	announced

Megger DA, Padden J, Rosowski K, Uszkoreit J, Bracht T, Eisenacher M, Gerges C, Neuhaus H, Schumacher B, Schlaak JF, Sitek B, One Sample, One Shot - Evaluation of sample preparation protocols for the mass spectrometric proteome analysis of human bile fluid without extensive fractionation. J Proteomics, 154():13-21(2017) [pubmed]

curator keyword: Biomedical

submitter keyword: Bile fluid, proteomics, method comparison, biomarkers, hepatocellular carcinoma, cholangiocellular carcinoma

Dominik Andre Megger
contact affiliation	Medizinisches Proteom-Center (MPC) Ruhr-Universität Bochum Clinical Proteomics - Infection Research Universitaetsstrasse 150, D-44801 Bochum
contact email	dominik.megger@rub.de
lab head
Dominik Andre Meger
contact affiliation	Medizinisches Proteom-Center (MPC), Ruhr-Universität Bochum, Germany
contact email	dominik.megger@rub.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/2017/05/PXD004476

PRIDE project URI

• PRIDE
  1. PXD004476
     1. Label: PRIDE project
     2. Name: Human Bile LC-MS/MS