Dataset Information

Human Bile LC-MS/MS - One Sample, One Shot - Evaluation of sample preparation protocols for the mass spectrometric proteome analysis of human bile fluid without extensive fractionation

ABSTRACT: 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.

INSTRUMENT(S): LTQ Orbitrap Elite

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Bile

SUBMITTER: Dominik Andre Meger

LAB HEAD: Dominik Andre Megger

PROVIDER: PXD004476 | Pride | 2017-05-03

REPOSITORIES: Pride

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One Sample, One Shot - Evaluation of sample preparation protocols for the mass spectrometric proteome analysis of human bile fluid without extensive fractionation.

Megger Dominik A DA Padden Juliet J Rosowski Kristin K Uszkoreit Julian J Bracht Thilo T Eisenacher Martin M Gerges Christian C Neuhaus Horst H Schumacher Brigitte B Schlaak Jörg F JF Sitek Barbara B

Journal of proteomics 20161205

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 of samples to be analyzed if sample preparation protocols with extensive fractionation methods are applied. Hence, the performance of simple workflows allowing for "one ...[more]

PMID: 27932303

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			Action	DRS
	AAFV1 OEI15687.pride.mgf.gz	Mgf
	AAFV1OEI15687.mgf	Mgf
	AAFV2 OEI15707.pride.mgf.gz	Mgf
	AAFV2OEI15707.mgf	Mgf
	AAFV3 OEI15763.pride.mgf.gz	Mgf