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1 SupplementalInformation: Content: FigureS1.AccessibilityoftheL.interrogansproteomebyLC MSanalysis. FigureS2.Functionalannotationoftheidentifiedproteins. FigureS3.DistributionofMS1 featureintensities. FigureS4.ComparisonoftheDDA anddirected(inl)lc MS/MSstrategyemployed. FigureS5.PerformanceofthedirectedMS workflowusingdifferentlc MS/MSplatforms. FigureS6.Reproducibilityoflabel freequantificationofthel.interrogansproteome. FigureS7.Correlationoftheestimatedproteinabundances(incopies/cell)witharecentlypublished study. FigureS8.Determinationofcellularproteinconcentrations. FigureS9.Significantproteinchangesincontrolsamplesafter24and48hourswithoutanytreatment. Figure S10. Impact of relative (in fold) and absolute (in copies/cell) protein level changes on the L. interrogansproteome. FigureS11.ProteinsofthebacterialchemotaxispathwaycoveredinclusterS 5asassignedbyDAVID usingthekeggdatabase. Figure S12. Proteins of the TCA cycle covered in cluster S 5 as assigned by DAVID using the KEGG database. Figure S13. Proteins of the oxidative phosphorylation pathway covered in cluster S 5 as assigned by DAVIDusingtheKEGGdatabase. TableSI.ProteinabundancelevelsdeterminedbystableisotopedilutionLC MS. TableSII.Identifiedfeaturesduringdiscoveryphase(seexls file). TableSIII.Identifiedproteotypicpeptides(PTPs)duringdiscoveryphase(seexls file). TableSIV.Identifiedproteinsduringdiscoveryphase(seexls file). TableSV.Monitoredproteinsduringscoringphase(alltreatments,seexls file). 1
2 FigureS1: Figure S1. Accessibility of the L. interrogans proteome by LC MS analysis. Number of proteins with their correspondingnumberofproteotypicpeptidesavailableforlc MS/MSanalysisaftertrypticcleavage. 2
3 FigureS2: FigureS2.Functionalannotationoftheidentifiedproteins.DistributionoftheproteinsidentifiedbytheLConly(red)andOGE/LC(green)MSanalysisincomparisontoallpredictedgenes(blue)accordingtotheir functionalcategoriesasassignedbydavid(huangetal,2007). 3
4 FigureS3: Figure S3. Distribution of MS1 feature intensities. Binned extracted precursor ion intensities (log 10 ) of all 13,113features(blue)identifiedandtheselected4953proteotypicpeptides(green)forproteinquantification. 4
5 FigureS4: FigureS4.ComparisonoftheDDA anddirected(inl)lc MS/MSstrategyemployed.(A)Analysisofthesame peptidesample(control)withthesamenumberoflc MS/MSrunsusingeitherthedata dependentacquisition (DDA,blue)orthedirected(INL,red)LC MS/MSapproach.Thenumbersofpeptidesandproteinsidentifiedby eitherapproachareindicated.(b)distributionoftheproteinsidentifiedbythedifferentapproachesaccording totheirabundanceasdeterminedbycodonbias. 5
6 FigureS5: FigureS5.PerformanceofthedirectedMS workflowusingdifferentlc MS/MSplatforms.(A)Numberof timesaproteinwasidentifiedin6differentcontrolsamplesusingdirectedmassspectrometryontheltq FT ICRLC MS/MSplatform.(B)AnalysisofthesamesamplesonadifferentLC(ProxeonEasy LC)andMS(Orbitrap Velos)systemusingthesamepeptidemasslistsgeneratedinthediscoveryphase.(C)Venndiagramshowing thenumberofoverlappingandspecificproteinfractionsidentified. 6
7 FigureS6: FigureS6.Reproducibilityoflabel freequantificationofthel.interrogansproteome.(a C)Scatterplotsof proteinms intensities(log 2 )betweenvariousuntreatedreplicatecontrolsamplesasdeterminedbythe Progenesissoftware,includingtherespectivesquaredPearsoncorrelationR 2.(D F)Distributionoftheprotein ratios(log 2 )determinedfromthesamesamplesasindicatedina Cversusthesignificancevaluecalculated fromtheanovaanalysis.thecoefficientofvarianceaswellasthesignificantthresholdssetforp value (ANOVA,<0.05)andratio(>1.5 fold)indicatedasredlinesareshown. 7
8 FigureS7: FigureS7.Correlationoftheestimatedproteinabundances(incopies/cell)witharecentlypublishedstudy. Comparisonoftheproteinabundancesdeterminedwitharecentlypublisheddatasetusingasimilarapproach (Malmströmetal,2009). 8
9 FigureS8: FigureS8.Determinationofcellularproteinconcentrations.(A)Averageextractedprecursorionintensitiesof thethreemostabundantpeptidesperprotein(log 10 )plottedagainsttheirproteinconcentrationincopies/cell (log 10 )determinedusingthespikedinheavylabeledreferencepeptides.(b)distributionoffold errorrates calculatedbybootstrappingaccordingto(malmströmetal,2009). 9
10 FigureS9: Figure S9. Significant protein changes detected in control samples. Volcano plots showing the significant proteinabundancechangesdetectedincontrolsamplesthatwerenotsubjectedtoanytreatmentafter(a)24 and (B) 48 hours. Protein regulations considered as significant ((ANOVA, <0.05) and ratio (>1.5 fold)) are indicatedwithintheredlinestogetherwiththenumberofup anddown regulatedproteins. 10
11 FigureS10: Figure S10. Impact of relative (in fold) and absolute (in copies/cell) protein level changes on the L. interrogansproteome.(a)averagerelativeabundanceratios(log 10 )ofallproteinsgroupedinto6clustersof different concentration levels in the cell (control state). (B) Like A, using absolute protein concentration changes (log 10 ) instead fold changes. The standard deviations calculated are indicated as error bars. (C) Hierarchical clustering of relative protein abundance changes (log 10 ) to the corresponding untreated control samplesincopiespercell(log 10 )forall24treatments.thecolumndendrogramrepresentingtheclusteringof thedifferentiallyperturbedsamplesisdisplayedandtheclusters(1 6)obtainedareindicated. 11
12 Fig.S11: FigureS11.ProteinsofthebacterialchemotaxispathwaycoveredinclusterS 5asassignedbyDAVID(Huang etal,2007)usingthekeggdatabase(kanehisaetal,2010).proteinspresentintheclusterareindicatedwith aredstar.green(white)labeledgenesarepresent(notpresent)inthel.interrogansgenome. 12
13 Fig.S12: FigureS12.ProteinsoftheTCAcyclecoveredinclusterS 5asassignedbyDAVID(Huangetal,2007)using thekeggdatabase(kanehisaetal,2010).proteinspresentintheclusterareindicatedwitharedstar.green (white)labeledgenesarepresent(notpresent)inthel.interrogansgenome. 13
14 Fig.S13: FigureS13.ProteinsoftheoxidativephosphorylationpathwaycoveredinclusterS 5asassignedbyDAVID (Huangetal,2007)usingtheKEGGdatabase(Kanehisaetal,2010).Proteinspresentintheclusterare indicatedwitharedstar.green(white)labeledgenesarepresent(notpresent)inthel.interrogansgenome. 14
15 Table SI. Protein abundance levels determined by stable isotope dilution LC MS Protein Protein Name Peptide Sequence Peptide Copies/Cell 1 Protein Copies/Cell 2 gi ref YP_ fatty acid synthase subunit beta TEVITHANLVR gi ref YP_ DNA directed RNA polymerase beta subunit ITNLDYLPNLIQIQK gi ref YP_ DNA directed RNA polymerase beta subunit TFDLGEVGR 1219 gi ref YP_ DNA directed RNA polymerase beta' subunit FATSDLNDLYR gi ref YP_ flagellar hook protein ENIGGVNPQQVGLGSLIAAIDK gi ref YP_ flagellar hook protein VATAVFNNPAGLDK 437 gi ref YP_ ATP synthase subunit A ILEVPVGPELLGR 14,633 12,691 gi ref YP_ ATP synthase subunit A TSIALDTILNQK 10,749 gi ref YP_ ATP synthase subunit B FSQAGSEVSALLGR 10,042 10,042 gi ref YP_ MreB GIVLTGGGCLLR gi ref YP_ MreB TGGDEFDEAIIK 2921 gi ref YP_ GroEL AVTAAVESIQK 10,572 13,649 gi ref YP_ GroEL VEDALSATR 16,726 gi ref YP_ GroES ESDILAVVK 13,686 11,704 gi ref YP_ GroES VGDTVLYGK 9723 gi ref YP_ flagellar M ring protein GFTPDGPAGTEPNIAPGYK gi ref YP_ flagellar M ring protein IISDFEEDLEK 60 gi ref YP_ ATP dependent protease ATP binding subunit LLEEVSFEGPDLPESQR gi ref YP_ recombinase A IVEIYGPESSGK gi ref YP_ ATP dependent CLP protease like, proteolytic subunit IAEVFEELTGSK gi ref YP_ ATP dependent CLP protease like, proteolytic subunit IFLWGPVTDESSK 1401 gi ref YP_ ATP dependent CLP protease like, proteolytic subunit LNQILADACGHPISK 4015 gi ref YP_ ATP dependent protease AVDLIDEASSK gi ref YP_ ATP dependent protease IADIQLEGLR 437 gi ref YP_ S ribosomal protein S6 EFLINQNILR gi ref YP_ Hsp15 like protein ILELPTEVDSEK gi ref YP_ Hsp15 DVQVQLEK gi ref YP_ S ribosomal protein S5 FSFNALSVVGDQR gi ref YP_ fatty acid synthase subunit beta EFFDTSFK ) Endogenous peptide abundances determined by stable isotope dilution 2) If multiple peptides per protein were identified and quantified, the average abundance level is shown 15
f(x) = x R² = RPKM (M8.MXB) f(x) = x E-014 R² = 1 RPKM (M31.
14 12 f(x) = 1.633186874x - 21.46732234 R² =.995616541 RPKM (M8.MXA) 1 8 6 4 2 2 4 6 8 1 12 14 RPKM (M8.MXB) 14 12 f(x) =.821767782x - 4.192595677497E-14 R² = 1 RPKM (M31.XA) 1 8 6 4 2 2 4 6 8 1 12 14
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