An Improvement of Shotgun Proteomics Analysis by Adding Next-Generation Sequencing Transcriptome Data in Orange 英文参考文献.docVIP

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An Improvement of Shotgun Proteomics Analysis by Adding Next-Generation Sequencing Transcriptome Data in Orange 英文参考文献.doc

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An Improvement of Shotgun Proteomics Analysis by Adding Next-Generation Sequencing Transcriptome Data in Orange 英文参考文献

AnImprovementofShotgunProteomicsAnalysisby AddingNext-GenerationSequencingTranscriptome DatainOrange JiapingSong1.,RenjieSun1.,DazhiLi2,FengjiTan1,XinLi1,PingpingJiang1,XinjieHuang1,LiangLin1, ZiniuDeng2,YongZhang1* 1The Shenzhen Proteome Engineering Laboratory, BGI Shenzhen, Shenzhen, P. R. China, 2National Center for Citrus Improvement, Hunan Agricultural University, Changsha,Hunan,P.R.China Abstract Background: Shotgun proteomics data analysis usually relies on database search. Because commonly employed protein sequencedatabasesofmostspeciesdonotcontainsufficientproteininformation,theapplicationofshotgunproteomicsto theresearchofproteinsequenceprofileremainsabigchallenge,especiallytothespecieswhosegenomehasnotbeen sequencedyet. Methodology/Principal Findings: In this paper, we present a workflow with integrated database to partly address this problem. First, we downloaded the homologous species database. Next, we identified the transcriptome of the sample, created a protein sequence database based on the transcriptome data, and integtrated it with homologous species database.Lastly,wedevelopedaworkflowforidentifyingpeptidessimultaneouslyfromshotgunproteomicsdata. Conclusions/Significance:Weuseddatasetsfromorangeleavessamplestodemonstrateourworkflow.Theresultsshowed that the integrated database had great advantage on orange shotgun proteomics data analysis compared to the homologousspeciesdatabase,an18.5%increaseinnumberofproteinsidentification. Citation:SongJ,SunR,LiD,TanF,LiX,etal.(2012)AnImprovementofShotgunProteomicsAnalysisbyAddingNext-GenerationSequencingTranscriptome DatainOrange.PLoSONE7(6):e39494.doi:10.1371/journal.pone.0039494 Editor:FatahKashanchi,GeorgeMasonUniversity,UnitedStatesofAmerica ReceivedOctober27,2011;AcceptedMay22,2012;PublishedJune29,2012 Copyright: ? 2012 Song et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricteduse,distribution,andreproductioninanymedi