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.

简介：Identificationofproteinsbymassspectrometry(MS)isanessentialstepinpro-teomicstudiesandistypicallyaccomplishedbyeitherpeptidemassfingerprinting(PMF)oraminoacidsequencingofthepeptide.AlthoughsequenceinformationfromMS/MSanalysiscanbeusedtovalidatePMF-basedproteinidentification,itmaynotbepracticalwhenanalyzingalargenumberofproteinsandwhenhigh-throughputMS/MSinstrumentationisnotreadilyavailable.Atpresent,avastmajorityofproteomicstudiesemployPMF.However,therearehugedisparitiesincriteriausedtoidentifyproteinsusingPMF.Therefore,toreduceincorrectproteinidentificationusingPMF,andalsotoincreaseconfidenceinPMF-basedproteinidentificationwithoutaccompanyingMS/MSanalysis,definitiveguidingprinciplesareessential.Tothisend,weproposeavalue-basedscoringsystemthatprovidesguidanceonevaluatingwhenPMF-basedproteinidentificationcanbedeemedsufficientwithoutaccompanyingaminoacidsequencedatafromMS/MSanalysis.

简介：Inthisstudy,wepresentapreprocessingmethodforquadrupoletime-of-flight(Q-TOF)tandemmassspectratoincreasetheaccuracyofdatabasesearchingforpeptide(protein)identification.Basedonthenaturalisotopicinformationinherentintandemmassspectra,weconstructadecisiontreeafterfeatureselectiontoclassifythenoiseandionpeaksintandemspectra.Furthermore,werecognizeoverlappingpeakstofindthemonoisotopicmassesofionsforthefollowingidentificationprocess.Theexperimentalresultsshowthatthispreprocessingmethodincreasesthesearchspeedandthereliabilityofpeptideidentification.