CLINICAL PROTEOMICS INITIATIVE LUXEMBOURG

SCHEME: PEARL

CALL: 2009

DOMAIN: BM - Life Sciences, Biology and Medicine

FIRST NAME: Gunnar

LAST NAME: Dittmar

INDUSTRY PARTNERSHIP / PPP: No

INDUSTRY / PPP PARTNER:

HOST INSTITUTION: LIH

KEYWORDS: Proteomics, Bioinfomatics

START: 2010-07-01

END: 2017-06-30

WEBSITE: https://www.lih.lu

Submitted Abstract

Proteomics deals with the analysis of all the proteins in cells, tissues or bodily fluids. Multipleproteins are generated from the same genome locus by alternative splicing or proteinprocessing. In addition, post-translational modifications (PTM) increase the complexity of theproteome to an unknown extent. Furthermore, the level of expression of each protein in aspecific proteome is very dynamic and subject to tight regulation.Several technology developments emerged over the past decade, and today LC-MS/MS is arobust and powerful protein discovery technique allowing the analysis of large fractions of aproteome with high confidence in the assignment of peptide sequences and the inferredproteins.However, the recurring analysis of the proteome in each study is not appropriate to interfaceproteomics with clinical applications for several reasons:Firstly, the complete analysis of an even moderately complex proteome remains anexpensive and slow process.Secondly, due to the stochastic nature of precursor ion selection in MS/MS differentsubsets of the proteome are identified and quantified in replicate experiments.Thirdly, in each shotgun experiment a majority of proteins identified and quantified arenot related to a specific question while other relevant ones are missed.Consequently, datasets are noisy, incomplete, and contain large amounts of irrelevantdata.Fourthly, no prior information on the system studied is used to design the experiment.Lastly, the complexity of samples to be analyzed is such that reliable quantification oflow abundant components requires additional specific sample preparation

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