Evaluating Experimental Bias and Completeness in Comparative Phosphoproteomics Analysis 英文参考文献.docVIP

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Evaluating Experimental Bias and Completeness in Comparative Phosphoproteomics Analysis 英文参考文献.doc

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Evaluating Experimental Bias and Completeness in Comparative Phosphoproteomics Analysis 英文参考文献

EvaluatingExperimentalBiasandCompletenessin ComparativePhosphoproteomicsAnalysis JosBoekhorst1*¤,PaulJ.Boersema2,5,BastiaanB.J.Tops2,BasvanBreukelen2,AlbertJ.R.Heck2, BerendSnel1,3,4 1TheoreticalBiologyandBioinformatics,DepartmentofBiology,FacultyofScience,UtrechtUniversity,Utrecht,TheNetherlands,2BiomolecularMassSpectrometryand ProteomicsGroup,BijvoetCenterforBiomolecularResearchandUtrechtInstituteforPharmaceuticalSciences,UtrechtUniversity,Utrecht,TheNetherlands,3Netherlands ConsortiumforSystemsBiology(NCSB),Amsterdam,TheNetherlands,4CentreforBiosystemsGenomics,Wageningen,TheNetherlands,5DepartmentofProteomicsand SignalTransduction,MaxPlanckInstituteofBiochemistry,Martinsried,Germany Abstract Unraveling the functional dynamics of phosphorylation networks is a crucial step in understanding the way in which biological networks form a living cell. Recently there has been an enormous increase in the number of measured phosphorylation events. Nevertheless, comparative and integrative analysis of phosphoproteomes is confounded by incomplete coverage and biases introduced by different experimental workflows. As a result, we cannot differentiate whetherphosphositesindentifiedinonlyoneortwosamplesaretheresultofconditionorspeciesspecificphosphorylation, orreflectmissingdata.Here,weevaluatetheimpactofincompletephosphoproteomicsdatasetsoncomparativeanalysis, and we present bioinformatics strategies to quantify the impact of different experimental workflows on measured phosphoproteomes.Weshowthatplottingthesaturationinobservedphosphositesinreplicatesprovidesareproducible pictureoftheextentofaparticularphosphoproteome.Still,wearestillfarawayfromacompletepictureofthetotalhuman phosphoproteome.Theimpactofdifferentexperimentaltechniquesonthesimilaritybetweenphosphoproteomescanbe estimated by comparing datasets from different experimental pipelines to a common reference. Our results show that comparative analysis is most powerful when datasets have been generated using the same e