简介：三位字节频率(TP)的阶段移动的概念从17个细菌的染色体在基因被用于寻找的潜在的DNA插入。为这些插入的察觉的一个数学算法被开发了。这条途径能与不是三个底的multiples的长度检测潜在的插入和删除，特别相对大的DNA碎片的插入(>100个底)。在三位字节矩阵之间的新类似措施被采用为检测TP阶段移动改进敏感。有每由超过1,200个底组成的17,220细菌的基因的序列被分析，并且TP阶段移动的存在在16%分析基因(2,809基因)被显示出，它是多于在我们的以前的工作检测了那的大约4次。我们建议TP阶段的移动可以显示与不是三个底的multiples的长度在DNA碎片的插入以后在基因读框架的移动。在TP的阶段移动和在基因的框架移动之间的一种关系被讨论。

简介：Shigellaflexneriisaninfectiouspathogenthatcausesdysenterytohuman,whichremainsaseriousthreattopublichealth,particularlyindevelopingcountries.Inthisstudy,theglobalproteinexpressionpatternsofS.flexneriduringtransitionfromexponentialgrowthtostationaryphaseinvitrowereanalyzedbyusing2-DPAGEcombinedwithMALDI-TOFMS.Inatime-courseexperimentwithfivetimepoints,therelativeabundanceof49proteinspotsvariedsignificantly.In-terestingly,aputativeoutermembraneproteinYciD(OmpW)wasalmostnotdetectedintheexponentialgrowthphasebutbecameoneofthemostabundantproteinsinthewholestationary-phaseproteome.SomeproteinsregulatedbytheglobalregulatorFNRwerealsosignificantlyinduced(suchasAnsB,AspA,FrdAB,andKatG)orrepressed(suchasAceEF,OmpX,SodA,andSucAB)duringthegrowthphasetransition.Theseproteinsmaybethekeyeffectorsofthebacterialcellcycleorplayimportantrolesinthecellularmaintenanceandstressresponses.Ourexpressionprofiledataprovidevaluableinformationforthestudyofbacterialphysiologyandformthebasisforfutureproteomicanalysesofthispathogen.

简介：Inthisstudywesystematicallyanalyzedtheelutionconditionoftrypticpeptidesandthecharacteristicsofidentifiedpeptidesinreversephaseliquidchromatographyandelectrospraytandemmassspectrometry(RPLC-MS/MS)analysis.Followingproteindigestionwithtrypsin,thepeptidemixturewasanalyzedbyon-lineRPLC-MS/MS.Bovineserumalbumin(BSA)wasusedtooptimizeacetonitrile(ACN)elutiongradientfortrypticpeptides,andCytochromeCwasusedtoretestthegradientandthesensitivityofLC-MS/MS.Thecharacteristicsofidentifiedpeptideswerealsoanalyzed.Inourexperiments,thesuitableACNgradientis5%to30%fortrypticpeptideelutionandthesensitivityofLC-MS/MSis50fmol.Analysisofthetrypticpeptidesdemonstratedthatlonger(morethan10aminoacids)andmulti-chargestate(+2,+3)peptidesarelikelytobeidentified,andthehydropathicityofthepeptidesmightnotberelatedtowhetheritismorelikelytobeidentifiedornot.Thenumberofidentifiedpeptidesforaproteinmightbeusedtoestimateitsloadingamountunderthesamesamplebackground.Moreover,inthisstudytheidentifiedpeptidespresentthreetypesofredundancy,namelyidentification,charge,andsequenceredundancy,whichmayrepresslowabundanceproteinidentification.