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{"sheet":"Statistics","index":3,"n_rows":218,"n_cols":26,"rows_kept":218,"cut":false,"hidden":false,"merged":[]}
["Title: Solver"]
[]
["Weight","SD for Y","SD for X's","Observations","Parameters","Adjustable Intercept Term","Constants","SD for Constants","Variance-Covariance Matrix for Constants","Full Variance-Covariance Matrix","New Observations"]
["Unitary","N","N",30,4,1,0,"N","N","N",0]
[]
["ANOVA"]
["Source","Sum Sq.","Degr. Fred.","Mean Sq.","F calc.","Crit. F(.05)","Passed Prob.","Check"]
["Model",11725435641195.395,3,3908478547065.1313,7871.1607965128233,2.9751539639733933,1.4413863032323772E-38,"Ok"]
["Residual",12910477228.303421,26,496556816.47320849]
["Total",11738346118423.697,29]
[]
["R","Low. CI(.95)","Up. CI(.95)","R^2","R^2 adj"]
[0.9994499212681075,0.99879335529020818,0.99974927786473278,0.99890014512282621,0.99877323879084456]
[]
["Linssen's Modification of Beale's Measure of NonLinearity"]
["Total Nonlinearity","LB Crit.(.95)","Check(.95)"]
[2027690235.9791055,0.5187118951897538,"No"]
[]
["Parameters Statistics"]
["Par.","Value","Std. Err.","t calc.","Crit. t(.05)","Low. CI(.95)","Up. CI(.95)","Passed Prob.","Check","CV%"]
["p1",0.16348827103443578,0.32054043721684056,0.51003945852809374,2.0555294386428731,-0.49539203394023762,0.82236857600910918,0.61432655755818577,"No",196.06326202405347]
["C1",7621.4999403413849,18476.869206081978,0.41248870982063551,2.0555294386428731,-30358.248646714092,45601.248527396863,0.68336281184924053,"No",242.43087778931815]
["p2",0.87596860075987515,6.9327639484252157E-4,1263.5200149268783,2.0555294386428731,0.87454355072116019,0.87739365079859011,8.7843189722680283E-64,"Ok",7.9143977791113304E-2]
["C2",3169738.9455771609,17868.892227952765,177.38866546067456,2.0555294386428731,3133008.9115666673,3206468.9795876546,1.2834028163985904E-41,"Ok",0.56373387634605709]
[]
["F Joint Confidence Parameters Statistics"]
["Par.","Value","Low. CI(.95)","Up. CI(.95)","Passed Prob.","Check"]
["p1",0.16348827103443578,-0.89819162168406874,1.2251681637529404,0.99174932712190622,"No"]
["C1",7621.4999403413849,-53576.770976150467,68819.770856833231,0.99634819500369409,"No"]
["p2",0.87596860075987515,0.87367236127479964,0.87826484024495066,7.9350154164248365E-62,"Ok"]
["C2",3169738.9455771609,3110554.3891814328,3228923.5019728891,1.1580116240817801E-39,"Ok"]
[]
["Variance-Covariance Table for Parameters"]
[null,"p1","C1","p2","C2"]
["p1",0.10274617189116329,628.06255273380384,4.0385571243707811E-8,-0.31980448234411268]
["C1",628.06255273380384,341394695.65866041,6.6784326702480157E-4,-5164.818386540539]
["p2",4.0385571243707804E-8,6.6784326702480157E-4,4.8063215964584386E-7,-1.5778337904017576]
["C2",-0.31980448234411279,-5164.8183865405417,-1.5778337904017581,319297309.45419079]
[]
["Hessian Variance-Covariance Table for Parameters"]
[null,"p1","C1","p2","C2"]
["p1",0.69775292079624163,4260.923126333777,2.8588914611409364E-7,-2.3773664805492318]
["C1",4260.9192742297637,363629202.94397503,2.2540174662128163E-3,-31558.794440904454]
["p2",2.8499745635776936E-7,2.1779222097534781E-3,4.9948086229458363E-7,-1.63967201168018]
["C2",-2.2035625798947311,-16726.302183348613,-1.6396719263561401,319500195.75425285]
[]
["Correlation Table for Parameters"]
[null,"p1","C1","p2","C2"]
["p1",1,0.1060453648225165,1.8173433744089233E-4,-5.5834687785936813E-5]
["C1",0.1060453648225165,1,5.2136245629894839E-5,-1.5643324013166296E-5]
["p2",1.817343374408923E-4,5.2136245629894839E-5,1,-0.12736708510495059]
["C2",-5.5834687785936834E-5,-1.5643324013166303E-5,-0.12736708510495062,1]
[]
["Ratio Objects/Parameters","Check"]
[7.5,"Critical"]
[]
["Observation Statistics (CI based on t Statistic)",null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,"DFBETAS","DFBETAS","DFBETAS","DFBETAS"]
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[690800.5,660137.45958100818,637530.54964401876,682744.36951799761,30663.040418991819,30663.040418991819,6825.4365981909377,646107.5737218362,674167.34544018016,23305.437160223635,612232.44741772697,708042.47174428939,9.3819243257609861E-2,1.3760389953055128,33837.664495571204,1.4455174000069699,1.4780842380184154,5.4083370139704649E-2,0.47559549357085851,0.9233753317848522,6.4580577963234233E-5,1.8623228897461577E-5,0.40156725488414724,0.20160128211759351,981.9649658203125,1.0241061837416219]
[330288.21875,307722.20321076107,296203.76252543501,319240.64389608713,22566.015539238928,22566.015539238928,3477.6263906408822,300573.83978819737,314870.56663332478,22553.285831250629,261363.26024649819,354081.14617502393,2.435549147986462E-2,1.0126757466435183,23129.342032035031,1.0252377919836535,1.0262874517314056,6.5598591618018778E-3,0.1621517595100174,1.0166070041548041,2.317947815922232E-5,6.6794687226161555E-6,0.14180653271439803,5.9937102446213725E-2,982.3004150390625,0.89291848644439464]
[138177.234375,125703.89717973158,120794.14922728784,130613.64513217531,12473.337195268425,12473.337195268425,1482.3420562963204,122656.89944487608,128750.89491458707,22332.804446487979,79798.160192521085,171609.63416694207,4.4251491450089872E-3,0.55975526718000457,12528.778910552463,0.5609978930788817,0.55346360913313775,3.4971677468301622E-4,3.6899125062092114E-2,1.1191888061798767,5.4358335227819147E-6,1.5657289106249396E-6,3.292991850096285E-2,1.2318522793640308E-2,982.6358642578125,0.6680021322695735]
[48974.14453125,47641.912120047433,45838.030438139191,49445.793801955675,1332.2324112025672,1332.2324112025672,544.62463400880108,46522.420151832244,48761.404088262621,22290.209340990445,1823.7306261292185,93460.093613965641,5.9734552447781046E-4,5.9785452570097611E-2,1333.0286899244941,5.9803316860122212E-2,5.8646010527528609E-2,5.34411343420888E-7,1.4337750931669429E-3,1.169913854821456,2.155107175569738E-7,6.2057082781009817E-8,1.2967709166861676E-3,4.4148675203885512E-4,982.9713134765625,-0.20866374575115462]
["Cut Point",null,null,null,null,null,null,null,null,null,null,null,">.2667",null,null,null,">|2.1051|",">.1429",">|.7428|","<.7333",">|1|"]
[]
["Non-Weighted Residuals Statistics"]
["Mean ","Standard Deviation"]
[7549.0285993608677,19652.886288405029]
[]
["Collinearity Tests for the Jacobian Matrix"]
["Jacobian Correlation Matrix"]
[null,"C1","p2","C2"]
["C1",1.0000000000000002,1.116280948027087E-3,-0.35073853835490576]
["p2",1.116280948027087E-3,0.99999999999999989,0.14817158167500649]
["C2",-0.35073853835490576,0.14817158167500649,1]
[]
["Condition Number for the Correlation Matrix"]
["Value","Check"]
[1.4934945445087255,"Ok"]
[]
["Variable","Tolerance","VIF","Check"]
["p1",0.87410111958217129,1.1440323980799951,"Ok"]
["C1",0.97483177902654006,1.0258180144666527,"Ok"]
["p2",0.85491145421450165,1.169711781343258,"Ok"]
[]
["Durbin Watson Statistic for Autocorrelation of Residuals"]
["Note: DW tests do not apply directly to residuals from regression through the origin. See J. Durbin and G.S. Watson. Biometrika, 38 (1951)159-178."]
[]
["Durbin Watson Bounds Test"]
["DW","DWcritInf(.05)","DWcritSup(.05)","4-DWcritSup(.05)","4-DWcritInf(.05)","Result(.05)"]
[0.8046500744548154,1.21,1.66,2.34,2.79,"Positive Correlation"]
[]
["Approximate Durbin-Watson Statistic (t Distribution)"]
["Probability for No Positive Serial Correlation","Probability for No Negative Serial Correlation"]
[2.6210455986563469E-3,0.99737895440134361]
[]
["Beta Approximation for Durbin Watson Statistic"]
["DW","DWcritical Pos.Corr(.05)","Check(.05)","Passed Prob.","DWcritical Neg.Corr(.05)","Check(.05)","Passed Prob."]
[0.8046500744548154,1.6599944196192409,"No",2.6983380615067844E-6,2.3400055803807591,"Ok",0.99934535288944393]
[]
["a + bDu Approximation for Durbin Watson Statistic"]
["DW","DWcritical Pos.Corr(.05)","Check(.05)","Passed Prob.","DWcritical Neg.Corr(.05)","Check(.05)","Passed Prob."]
[0.8046500744548154,1.668044012152865,"No",1.1322561199902368E-5,2.329290446322255,"Ok",0.99836248780562842]
[]
["Box Pierce Ljung Q' Test for Autocorrelation Of High Order"]
["Autoregressive Order","Q'","ChiSqcrit(.05)","Check(.05)","Passed Prob."]
[1,11.793046714258132,5.9914645471079817,"No",5.9452357377947176E-4]
[2,12.924040156854446,5.9914645471079817,"No",1.561637890931922E-3]
[3,15.527121711715258,5.9914645471079817,"No",1.4173528499756174E-3]
[4,19.290415306197605,5.9914645471079817,"No",6.8911813167187356E-4]
[5,19.592480097367464,5.9914645471079817,"No",1.4899687170218197E-3]
[6,20.588856978603339,5.9914645471079817,"No",2.1740838070566136E-3]
[]
["Residuals Runs Test"]
["Res. +","Res. -","Runs","Low Crit. Runs (.05)","Up. Crit. Runs (.05)","Check(.05)","Passed Prob."]
[25,5,5,5,11,"No",1.031535514294135E-2]
[]
["Shapiro Wilk Statistic for Normality of Residual"]
["W","Wcrit(.05)","Check(.05)","Passed Prob."]
[0.88824879149009262,0.92700000000000005,"No",9.8694310165565839E-3]
[]
["Shapiro Wilk Statistic for Normality of Residual AS R84"]
["Z","Zcrit(.05)","Check(.05)","Passed Prob.","W Shapiro Statistic"]
[2.6013840495607492,1.6448536269514715,"No",4.6424223118420871E-3,0.88929584409533735]
[]
["Anderson Darling Statistic for Normality of Residual"]
["A2","A2crit(.05)","Check(.05)","Passed Prob."]
[1.6587283183769084,0.75176040863612714,"No",2.2886754116467712E-4]
[]
["Lilliefors Statistic for Normality of Residual"]
["Lf","Lfcrit(.05)","Check(.05)","Passed Prob."]
[0.19388456016177327,0.15918430382729118,"No",5.4957626920643559E-3]
[]
["Jarque-Bera Statistic for Normality of Residual"]
["JB","ChiSqcrit(.05)","Check(.05)","Passed Prob."]
[0.49625485842752132,5.9914645471079817,"Ok",0.78026050895956511]
[]
["D'Agostino Omnibus Statistics"]
["Test","Value","Critical Value(.05)","Check(.05)","Passed Prob.","Kurt./Skew."]
["D'A.Kurtosis",1.0786655123054958,1.9599639845400536,"Ok",0.28073686515047935,3.4764035730558924]
["D'A.Skewness",0.62470507856134017,1.9599639845400536,"Ok",0.53216463934497926,0.24037525005646349]
["D'A.Omnibus",1.5537757226176079,5.9914645471079817,"Ok",0.45983485661842932]
[]
["Modified Levene Test for Constant Variance"]
["F","Crit. F(.05)","Check","Passed Prob."]
[20.018219190325709,4.195971818557763,"No",1.1657100736208716E-4]
[]
["Multiple Levene Test for Constant Variance"]
["F","Crit. F(.05)","Check","Passed Prob."]
[6.4669556493522125,3.3541308285291991,"No",5.073362043658285E-3]
[]
["Breush-Pagan Test for Homoscedasticity of Residuals"]
["Breush-Pagan MSS/2","ChiSqcrit(.05)","Check(.05)","Passed Prob."]
[11.575344128697864,3.8414588206941236,"No",6.6832066444274336E-4]
["Koenkar-Evans NR2","ChiSqcrit(.05)","Check(.05)","Passed Prob."]
[6.6859546929750913,3.8414588206941236,"No",9.7175466472367474E-3]
[]
["Error Sum of Squares (RSS or SSE)","dF","Error Mean Squared (MSSE)","Error Mean Squared (RMSSE)"]
[12910477228.303421,26,496556816.47320849,22283.554843722948]
[]
["R","R^2","R^2 adj"]
[0.9994499212681075,0.99890014512282621,0.99877323879084456]
[]
["PRESS",19630187785.378845,"AIC",604.40322875738195]
["MEP",654339592.84596145,"AICc",606.00322875738198]
["R^2 prediction",0.99832768708748765,"HQC",606.19624908299431]
["SDEC",20744.860591082488,"HQCc",608.15485314811679]
["SDEP",25580.062408953607,"SBC (BIC)",610.00801828403053]
[null,null,"SBCc (BICc)",612.72897618936031]
[]
["Models Comparison using Information Criterion (Replace IC)"]
[null,null,"IC","IC"]
["Min IC",{"$f":"MIN(C198:D198)","v":606.00322875738198},606.00322875738198,606.00322875738198]
["Weight Sum",{"$f":"SUM(C199:D199)","v":2},{"$f":"EXP(-0.5*(C198-$B198))","v":1},{"$f":"EXP(-0.5*(D198-$B198))","v":1}]
[null,"Probability",{"$f":"(C199/$B199)","v":0.5},{"$f":"(D199/$B199)","v":0.5}]
[null,"Evidence Ratio",{"$f":"1/C199","v":1},{"$f":"1/D199","v":1}]
[]
["Log-Likelihood Section"]
["Log-Likelihood Function",-342.91628302944127]
[]
["Log-Likelihood Tests for Nested Models (Replace RSS and NPar values)"]
[null,"RSS","NPar",null,null,"Test Value","dF","Crit. Chi^2 (.05)","Passed Probability"]
["Restricted Model",12910477228.303421,4,null,"Lagrange Multiplier Test",{"$f":"30*(1-1/B210)","v":0},{"$f":"C209-C208","v":0},{"$f":"CHIINV(0.05,G208)","v":{"$error":"#NUM!"}},{"$f":"CHIDIST(F208,G208)","v":{"$error":"#NUM!"}}]
["Unrestricted Model",12910477228.303421,4,null,"Likelihood Ratio Test",{"$f":"30*LN(B210)","v":0},{"$f":"G208","v":0},{"$f":"H208","v":{"$error":"#NUM!"}},{"$f":"CHIDIST(F209,G209)","v":{"$error":"#NUM!"}}]
["Ratio",{"$f":"B208/B209","v":1},null,null,"Wald Statistic",{"$f":"30*(B210-1)","v":0},{"$f":"G209","v":0},{"$f":"H209","v":{"$error":"#NUM!"}},{"$f":"CHIDIST(F210,G210)","v":{"$error":"#NUM!"}}]
[]
["F Test for Models Comparison (Replace Residual Mean Square and dF)"]
["Residual Sum of Squares #1","dF #1","Residual Sum of Squares #2","dF #2","F calc. (>1)","Crit. F (.05)","Passed Prob."]
[12910477228.303421,26,12910477228.303421,26,{"$f":"(A214/B214)/(C214/D214)","v":1},{"$f":"FINV(0.05/2,B214,D214)","v":2.194306014529734},{"$f":"2*FDIST(E214,B214,D214)","v":0.99999999999999933}]
[]
["Extra Sum F Test for Significance of Extra Parameters in Nested Models (Replace Residual Mean Square and dF)"]
["Reduced Model Residual Sum Of Squares ","Reduced Model dF","Full Model Residual Sum Of Squares","Full Model dF","F calc. (>1)","Crit. F (.05)","Passed Prob."]
[12910477228.303421,26,12910477228.303421,26,{"$f":"((A218-C218)/(B218-D218))/(C218/D218)","v":{"$error":"#DIV/0!"}},{"$f":"FINV(0.05,B218-D218,D218)","v":{"$error":"#NUM!"}},{"$f":"FDIST(E218,B218-D218,D218)","v":{"$error":"#DIV/0!"}}]

{"sheet":"Solver","index":4,"n_rows":36,"n_cols":21,"rows_kept":36,"cut":false,"hidden":false,"merged":[]}
[null,null,null,null,null,null,null,"MC Search N",0]
[null,null,null,null,null,null,null,"Start Value"]
[null,null,null,null,null,null,null,"End Value"]
[null,null,null,null,null,null,"Title","ResidualSS","p1","C1","p2","C2"]
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[null,null,null,"W","X","Y","Ycalc","r^2","i"]
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{"sheet":"Bimodal Help","index":5,"n_rows":10,"n_cols":2,"rows_kept":10,"cut":false,"hidden":true,"merged":[]}
["Bimodal Deconvolution","The bimodal (and trimodal) fitting functionality is for applying multiple binomial functions to fit mass envelopes containing distinct species. This should only be used if no reasonable fits can be achieved with a single binomial and possible spectral overlap has been taken into account. This proceedure utilizes the Solver add-in within excel for fitting (for more information see release notes). "]
["Proceedure","To fit multiple binomials first process the data as you would normally but keep the peak height threshold low (5% or less) to try to get as much of the envelope recognized as possible. Alternatively it is possible (but not recommended) to use the raw spectral fitting for this, in which case run the preliminary analysis without the \"use isotopic peak detection\" option. Next, apply the binomial fitting to all the data. You may have to adjust the number of amides or check the 'optimize fits' box to achieve good fits. This should be gauged from a spectra that reflects a single species; the fully deuterated standard works best. After binomial fitting some spectra may be flagged as \"bimoda\" with red font. These are cases where the distribution was too wide to be fit with a single binomial function and may indicate the presence of a bimodal spectra."]
["Proceedure cont.","Next, go to the spectra that contains the bimodals and use the \"Bimodal deconvolution\" function to apply a 'double binomial' fit. Triple binomial fiting is also available but should be avoided unless there are clearly more than two species present. In some cases a good answer is not found (based on visual inspection). When this happens the initial fitting parametes (p(1), p(2), and weights) can be adjusted and the the fitting can be run again by calling the \"solver\" function in excel (found in the \"Data\" tab). The UN and TD samples should be left as a single binomial; if these do not fit well to a single function then check the data for overlap and make sure the correct number of amides are being used for the fitting. The keyboard shortcuts [Ctrl+Shift+\"D\"] and [Ctrl+Shift+\"T\"] can be used for applying a bimodal and trimodal fitting within the active sheet. The 'apply multimodal fit to all spectra' option allows you to fit all of the time points as bimodal, excluding the undeuterated and fully deuterated spectra. "]
["Proceedure cont.","In some cases, better fits fits can be achieved if using a different number of amides for the two binomial components. These can be adjusted manually on within each worksheet (Cells \"I3\" \"I22\" and \"I23\") followed by re-running Solver."]
["Summary Visualization","Once all the speactra have been fitted properly the Summarize Bimodals button will import all of the new fits into the summary sheet and plot both sets of fits. The third plot on the right shows both the deuterium uptake (left y-axis) and fraction of the total population (right y-axis) and is useful for visualizing both the exchange profile and the relative population of each species. If there are multiple conditions (protein states) within the workbook, only data from the first series will be shown in the double y-axis plot. "]
["Statistical Analyses","A new feature in HX Express v3 is the \"perform bimodal statistic analyes\". This option uses a statistical approach for calculating the level of confidence with the deconvolution of a bimodal mass spectra. This option should only be selected when using the \"Double binomial\" feature, it is not intended to be used for any other fitting routine. This feature was designed to use for spectra that appear bimodal, but the two components are sufficiently resolved to accurately deconvolute the two populations. When selected this option will perform additional analyses after the bimodal fitting to assess the certainty of the fits. This will result in three additional bar graphs presented on the right side that correspond to the level of certainty using three different metrics: Regression Metric, Delta Chi Metric, and Separation Metric. The green, orange, and red bars indicate a 99, 95 and 80% confidence interval. For a trustworthy doube binomial fit all of the metrics should be at least above the orange threshold. The resulting worksheet will also contain a direct error estimate for the relative intensity of the two populations which are as a percentage of the relative intensity value and shown in cells I32 and I33."]
["Restrained Fitting","It is possible to apply a double binomial or triple binomial fit where you restrain (fix) the population (p value) for each component. For this you fill out the fields for probability (values from 0-1) p1-p3 and the number of amides for each population (N1-N3). Leaving a zero or the cell empty for any of the p values will float (vary and find the best value) those values during minimization. When specifying the p value for different populations please keep in mind that p1 should be the least deuterated species and p2 (not p3) should be the most deuterated species. For any entry N1-N3 left blank or zero will automatically use the maximum (largest) number of amides used in the binomial fitting. "]
["Restrained Fitting cont. ","Restrained fitting can also utilize the 'apply multimodal fit to all spectra' option to apply the restrained double or triple fitting algorithm to all but the undeuterated and fully deuterated spectra. The data will then need to summarized using either the 'summarize double' or 'summarize triple' functions. Alternative, it is possible to shuffle between your worksheets and use the keyboard shortcuts: [Ctrl+Shift+\"R\"] for a restrained double, [Ctrl+Shift+\"Y\"] for a restrained triple fit. "]
["Tetramodal Fitting","This version of HX Express has an experimental routine for performing tetramodal fitting (quadruple binomial). SInce there are so many variables with tetramodal fitting, this should only be used when there is solid evidence of more than three components in the data. For this, as much of the various p values (p1-p4) and number of amides (N1-N4) should be restrained. Just as with the double/triple restrained fitting, the p1 should be the least deuterated species and the p2 should be the most deuterated species. After applying the quadruple fit it will be necessary to run the 'summarize quadruple' to summarize the data onto the summary worksheet. It is possible to shuffle between your worksheets and use the keyboard shortcuts: [Ctrl+Shift+\"Q\"] to apply a restrained quadruple fit. "]
["Exponential Fitting","When there is evidence of EX1 transition, or for pulse-labeling HDX-MS there is a 'Exponential (EX1)' fitting function that will fit either a single or double exponential function to the shift in the population fraction over time. This function only works on the summary worksheet after the bimodal summarization has been performed. A new plot will pop on the right side showing the transition of population fraction over time (data points) and the bets fit (dashed line). You can select which population you want to use for the exponential fitting (1, 2, or 3rd). The best-fit rate(s) are shown in cell U5 and U11 on the summary worksheet in bold. The units correspond to the same units used for the plots (sec, min, or hours). "]

{"sheet":"HX-Express","index":6,"n_rows":0,"n_cols":0,"rows_kept":0,"cut":false,"hidden":true,"merged":[]}

{"sheet":"Analyze Spectra Help","index":7,"n_rows":7,"n_cols":2,"rows_kept":7,"cut":false,"hidden":true,"merged":[]}
["Charge state","The charge state (z) of a peptide can be determined by taking the reciprocal of the m/z spacing of the isotopic peaks in the spectrum.  If z is set incorrectly, HX-Express will return an error message unless z is incorrectly set +1 for a spectrum of z > +1.  In this case HX-Express will simply detect peaks with a spacing of 1 Da."]
["Distribution width","The width of the isotopic distribution is measured at a fraction of the intensity of the most intense peak (the base peak).  This quantity is expressed a a percentage of base peak intensity (% BPI).  It can be set between 10 and 90% BPI.  Both the centroid and the isotopic distribution width will be measured over the portion of the spectrum defined by this quantity."]
["Use isotopic peak detection","For spectra with well-resolved isotopic peaks, this feature should be left ON.  The width of the isotopic distribution will obtained from a measurement of an empirical peak-to-peak envelope.  This feature can be turned off for spectra that lack isotopic peaks or where peak detection is problematic.  HX-Express will bypass peak detection where necessary, but it may not be consistent across a spectrum series."]
["Peak tolerances","The intensity tolerance is used to discriminate against noise in the spectrum during peak identification.  It is expressed as a percentage of the maximum peak in the spectrum (% BPI).  The m/z tolerance specifies how close an istopic peak needs to its predicted m/z value.  This quantity is expressed in terms of number of data points since the m/z data is discrete.  The actual m/z tolernace will depend on the spacing of the m/z data."]
["Deuterium uptake plot","Deuterium uptake can be expressed in terms of absolute mass in (Da), relative deuterium uptake (Da), or percent deuteration.  For relative deuterium uptake, the mass of the undeuterated control is subtracted from all other masses:  m-m0%.  Percent deuteration is computed according to the formula (m - m0%)/(m - m100%) x 100% where the subscripts 0% and 100% indicate the masses of an undeuterated and a fully deuterated control, respectively.  HX-Express checks for the presence of these controls before determining deuterium uptake."]
["Time units","The output plots can be displayed in time units of seconds, minutes, or hours.  The units do not need to match the input units."]
["Plot width of isotopic distribution","By default, HX-Express generates a plot of the width of the isotopic distribution as a function of time.  This feature can be disabled.  In which case, width values will not be reported on the Summary page."]

{"sheet":"Time Label Help","index":8,"n_rows":1,"n_cols":2,"rows_kept":1,"cut":false,"hidden":true,"merged":[]}
["Add exchange time labels","This feature automates the exchange time annotation of the spectra by adding labels in row 1 of the active worksheet.  If row 1 contains data, the data will automatically be shifted down to row 2.\n\nEnter the numerical value of the exchange time in the box.  Use the option buttons to set the time units.  Click the enter button or press Enter on the keyboard to put the label into the highlighted cell.  Use Previous/Next to navigate to different cells.  When all spectra are labelled, click Finish.  Cancel clears all annotations."]

{"sheet":"HX-Express Help","index":9,"n_rows":15,"n_cols":2,"rows_kept":15,"cut":false,"hidden":true,"merged":[]}
["Using HX-Express","All HX-Express features can be accessed from the HX-Expresss menu item."]
["Worksheets vs. workbooks","Each Excel file is a workbook.  A workbook usually contains one or more worksheets.  Different worksheets within a workbook may be accessed by clicking on the appropriate tab on the tabpane at the bottom of the Excel window."]
["Naming a worksheet","You can rename a worksheet by\n\n1.  Double clicking on the worksheet tab.\n\n2.  Right click on the tab and choose Rename.\n\n3.  Select the worksheet and use Format | Sheet | Rename."]
["Import data / Data format","It is important that spectra are well-smoothed before analysis.  If the peak tops are noisy, HX-Express will encounter difficulty with peak identification.  \n\nAll spectra of a particular peptide, protein charge state envelope, or mass domain spectrum for a given state of the protein (wild type vs. mutant, bound vs. unbound, etc.) are grouped together on a single worksheet.  The tab at the bottom is used to name that series.  Each workbook can only contain data on a single peptide or protein.  The data columns must contain only numeric data with no empty cells.  The Sample Data worksheet in the HX-Express workbook gives an example of how the spectra should be formatted on the worksheet.\n\nSpectra are entered into the worksheet in two column (m/z, intensity) format.  Do not leave empty columns between the data.  Row 1 is used to note the exchange time.  The exchange time label is placed over the first column (m/z) of each spectrum.  Any mixture of time units (sec, min, hr) is acceptable and the spectra can be placed in any order.  The \"Add Exchange Time Labels\" feature makes it easy to label the spectra.  \n\nHX-Express does extensive data validation before the analysis is started."]
["Analyze spectra","Basic instructions:\n\n1.  Open the HX-Express workbook.  This workbook must be opened every time you want to use HX-Express.  You will not be able to modify this workbook and it is advisable to save it as a read-only file and to keep a backup.\n\n2.  Create a new workbook.\n\n3.  Create one named tab worksheet for each series of spectra for the same peptide or protein charge state (i.e., bound vs. unbound, etc.)\n\n4.  Paste in mass spectra in x, y column format into consecutive columns starting at row 1.  Spectra should be of a single peptide or protein charge state at different exchange times.  Use a narrow m/z range centered on the peptide/protein.\n\n5.  Repeat steps 3 and 4 for each series of spectra for a given peptide/protein.\n\n6.  Label the exchange times using the Add Exchange Times feature from the HX-Express pull down menu or you can type them directly into the worksheet.\n\n7.  If you wish, you can save the workbook containing the raw spectral data.  (HX-Express will generate a new workbook for the analyzed spectra.)\n\n8.  Choose Analyze Spectra from the HX-Express menu.  Set parameters and click OK.\n\n9.  HX-Express creates a new workbook with each spectrum on its own tabed worksheet page.  A summary page containing the deuterium uptake plot and (if enabled) an isotopic distribution witdth plot.  The resulting workbook can be reanalyzed, however, the HX-Express workbook needs to be open."]
["Analyze single spectrum","Performs an analysis of a single spectrum in x, y format in columns A and B.  No summary report will be generated.  This is a good way to evaluate how changes in the parameters affect the analysis.  This feature will not overwrite other data on the worksheet."]
["Reanalyzing data","Data in the output workbook can be re-analyzed using the \"Analyze Spectra\" menu item.\n\nIf necessary, the spectra in the individual worksheets can be edited/replaced using standard Excel operations.  To protect a worksheet from \"damage\", HX-Express turns on Excel's worksheet protection feature when it creates the output workbook.  To allow editing turn off the protection on the worksheet using Tools | Protection | Unprotect sheet.  After editing a spectrum, make sure that the data starts in row 1, that it is in ascending m/z order, and that there are no blank cells in the data."]
["Get spectra from MassLynx","Spectra can be acquired directly from the Spectrum window of MassLynx.  They are acquired in order from the top spectrum (\"last\" according to MassLynx convention) to the bottom spectrum (\"first\" according to MassLynx convention).  Choose a narrow m/z region encompassing the peptide of interest.  This feature probably won't work if the Spectra window within MassLynx is minimized.  This feature will automate the creation of new worksheets or workbooks for the spectra and it can be accessed from any Excel window."]
["Get spectra from MassLynx (cont)","The timing labels can be automatically read from an existing workbook titled \"timing.xls\" or \"timing.xlsx\". If the import timing box is checked HX-express will attempt to import the time labels from this sheet. "]
["Get spectra from MassLynx (cont)","With windows 7 (and beyond) the get spectra function requires a delay to allow data to be transferred to the clipboard. This will vary by computer but generally requires a 350msec delay. If there are errors or spuriuos data imported from MassLynx try extending the delay time. For Windows XP this can be left at \"0\"."]
["Save charge state","Use this optional feature to store a charge state in a workbook containing unprocessed spectra.  This can be useful if you are importing a large amount of data for subsequent analysis.  When HX-Express analyzes a workbook with a stored charge state, it uses this charge state as the default value."]
["Macro security","The first time HX-Express is opened, you may get an error message that the macros are disabled because the security level is set to High or Very High.  You will need to reset it to Medium (recommended) or Low (not recommended) in order to use HX-Express.\n\nUnder Tools | Macro | Security, set the Security Level to Medium or Low and Click OK.  Close this workbook and reopen it.  \n\nAt the Medium security level, you will be prompted to Enable macros every time any workbook containing macros is opened.  At the Low security level, macros will always be enabled without a prompt.\n\nIf you can read this help item in a Help window, it means that the macros are running and your security settings are correct."]
["Running macros (advanced)","Do not attempt to directly access macros from Tools |  Macro | Macros... unless you have read the source code and you know which macros to access.  Many of the macros in the VBA source code are not designed for direct access.  The HX-Express workbook could be corrupted by running some macros."]
["New features in version 2","Updates to HX-Express as of version 2.0\n- Delay function for importing data directly from MassLynx in Win 7 (32 or 64 bit)\n- Option of importing time labels from an existing workbook when pulling data from MassLynx\n- Binomial fitting of exchange data (uses Solver and Analysis ToolPak add-ins within Excel)\n- Bimodal deconvolution with a double or triple binomial fitting scheme\n- Bubble plots to visualize bimodal exchange data"]
["License Agreement","This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.\n\nThis program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  The GNU General Public License can be viewed by clicking the \"View License\" button on the startup screen.  The startup screen may be accessed by choosing the \"About HX-Express\" item on the \"HX-Express\" menu.\n\nYou should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA."]

{"sheet":"GNU GPL","index":10,"n_rows":4,"n_cols":2,"rows_kept":4,"cut":false,"hidden":true,"merged":[]}
["Title","GNU GENERAL PUBLIC LICENSE\nVersion 2, June 1991\n\nCopyright (C) 1989, 1991 Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed.\n"]
["Preamble","Preamble\n\nThe licenses for most software are designed to take away your freedom to share and change it.  By contrast, the GNU General Public License is intended to guarantee your freedom to share and change free software--to make sure the software is free for all its users.  This General Public License applies to most of the Free Software Foundation's software and to any other program whose authors commit to using it.  (Some other Free Software Foundation software is covered by the GNU Lesser General Public License instead.)  You can apply it to your programs, too.\n\nWhen we speak of free software, we are referring to freedom, not price.  Our General Public Licenses are designed to make sure that you have the freedom to distribute copies of free software (and charge for this service if you wish), that you receive source code or can get it if you want it, that you can change the software or use pieces of it in new free programs; and that you know you can do these things.\n\nTo protect your rights, we need to make restrictions that forbid anyone to deny you these rights or to ask you to surrender the rights. These restrictions translate to certain responsibilities for you if you distribute copies of the software, or if you modify it.\n\nFor example, if you distribute copies of such a program, whether gratis or for a fee, you must give the recipients all the rights that you have.  You must make sure that they, too, receive or can get the source code.  And you must show them these terms so they know their rights.\n\nWe protect your rights with two steps: (1) copyright the software, and (2) offer you this license which gives you legal permission to copy, distribute and/or modify the software.\n\nAlso, for each author's protection and ours, we want to make certain that everyone understands that there is no warranty for this free software.  If the software is modified by someone else and passed on, we want its recipients to know that what they have is not the original, so that any problems introduced by others will not reflect on the original authors' reputations.\n\nFinally, any free program is threatened constantly by software patents.  We wish to avoid the danger that redistributors of a free program will individually obtain patent licenses, in effect making the program proprietary.  To prevent this, we have made it clear that any patent must be licensed for everyone's free use or not licensed at all. \n\nThe precise terms and conditions for copying, distribution and modification follow.\n"]
["GNU General Public License","GNU GENERAL PUBLIC LICENSE\n\nTERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION\n\n0. This License applies to any program or other work which contains a notice placed by the copyright holder saying it may be distributed under the terms of this General Public License.  The \"Program\", below, refers to any such program or work, and a \"work based on the Program\" means either the Program or any derivative work under copyright law: that is to say, a work containing the Program or a portion of it, either verbatim or with modifications and/or translated into another language.  (Hereinafter, translation is included without limitation in the term \"modification\".)  Each licensee is addressed as \"you\". Activities other than copying, distribution and modification are not covered by this License; they are outside its scope.  The act of running the Program is not restricted, and the output from the Program is covered only if its contents constitute a work based on the Program (independent of having been made by running the Program).  Whether that is true depends on what the Program does.\n\n1. You may copy and distribute verbatim copies of the Program's source code as you receive it, in any medium, provided that you conspicuously and appropriately publish on each copy an appropriate copyright notice and disclaimer of warranty; keep intact all the notices that refer to this License and to the absence of any warranty; and give any other recipients of the Program a copy of this License along with the Program.\n\nYou may charge a fee for the physical act of transferring a copy, and you may at your option offer warranty protection in exchange for a fee.\n\n2. You may modify your copy or copies of the Program or any portion of it, thus forming a work based on the Program, and copy and distribute such modifications or work under the terms of Section 1 above, provided that you also meet all of these conditions: \n\na) You must cause the modified files to carry prominent notices stating that you changed the files and the date of any change.\n\nb) You must cause any work that you distribute or publish, that in whole or in part contains or is derived from the Program or any part thereof, to be licensed as a whole at no charge to all third parties under the terms of this License.\n\nc) If the modified program normally reads commands interactively when run, you must cause it, when started running for such interactive use in the most ordinary way, to print or display an announcement including an appropriate copyright notice and a notice that there is no warranty (or else, saying that you provide a warranty) and that users may redistribute the program under these conditions, and telling the user how to view a copy of this License.  (Exception: if the Program itself is interactive but does not normally print such an announcement, your work based on the Program is not required to print an announcement.)\n\nThese requirements apply to the modified work as a whole.  If identifiable sections of that work are not derived from the Program, and can be reasonably considered independent and separate works in themselves, then this License, and its terms, do not apply to those sections when you distribute them as separate works.  But when you distribute the same sections as part of a whole which is a work based on the Program, the distribution of the whole must be on the terms of this License, whose permissions for other licensees extend to the entire whole, and thus to each and every part regardless of who wrote it.\n\nThus, it is not the intent of this section to claim rights or contest your rights to work written entirely by you; rather, the intent is to exercise the right to control the distribution of derivative or collective works based on the Program.\n\nIn addition, mere aggregation of another work not based on the Program with the Program (or with a work based on the Program) on a volume of a storage or distribution medium does not bring the other work under the scope of this License.\n\n3. You may copy and distribute the Program (or a work based on it, under Section 2) in object code or executable form under the terms of Sections 1 and 2 above provided that you also do one of the following:\na) Accompany it with the complete corresponding machine-readable source code, which must be distributed under the terms of Sections 1 and 2 above on a medium customarily used for software interchange; or,\n\nb) Accompany it with a written offer, valid for at least three years, to give any third party, for a charge no more than your cost of physically performing source distribution, a complete machine-readable copy of the corresponding source code, to be distributed under the terms of Sections 1 and 2 above on a medium customarily used for software interchange; or,\n\nc) Accompany it with the information you received as to the offer to distribute corresponding source code.  (This alternative is allowed only for noncommercial distribution and only if you received the program in object code or executable form with such an offer, in accord with Subsection b above.)\n\nThe source code for a work means the preferred form of the work for making modifications to it.  For an executable work, complete source code means all the source code for all modules it contains, plus any associated interface definition files, plus the scripts used to control compilation and installation of the executable.  However, as a special exception, the source code distributed need not include anything that is normally distributed (in either source or binary form) with the major components (compiler, kernel, and so on) of the operating system on which the executable runs, unless that component itself accompanies the executable.\n\nIf distribution of executable or object code is made by offering access to copy from a designated place, then offering equivalent access to copy the source code from the same place counts as distribution of the source code, even though third parties are not compelled to copy the source along with the object code.\n\n4. You may not copy, modify, sublicense, or distribute the Program except as expressly provided under this License.  Any attempt otherwise to copy, modify, sublicense or distribute the Program is void, and will automatically terminate your rights under this License.  However, parties who have received copies, or rights, from you under this License will not have their licenses terminated so long as such parties remain in full compliance.\n\n5. You are not required to accept this License, since you have not signed it.  However, nothing else grants you permission to modify or distribute the Program or its derivative works.  These actions are prohibited by law if you do not accept this License.  Therefore, by modifying or distributing the Program (or any work based on the Program), you indicate your acceptance of this License to do so, and all its terms and conditions for copying, distributing or modifying the Program or works based on it.\n\n6. Each time you redistribute the Program (or any work based on the Program), the recipient automatically receives a license from the original licensor to copy, distribute or modify the Program subject to these terms and conditions.  You may not impose any further restrictions on the recipients' exercise of the rights granted herein.  You are not responsible for enforcing compliance by third parties to this License.\n\n7. If, as a consequence of a court judgment or allegation of patent infringement or for any other reason (not limited to patent issues), conditions are imposed on you (whether by court order, agreement or otherwise) that contradict the conditions of this License, they do not excuse you from the conditions of this License.  If you cannot distribute so as to satisfy simultaneously your obligations under this License and any other pertinent obligations, then as a consequence you may not distribute the Program at all.  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Many people have made generous contributions to the wide range of software distributed through that system in reliance on consistent application of that system; it is up to the author/donor to decide if he or she is willing to distribute software through any other system and a licensee cannot impose that choice.\n\nThis section is intended to make thoroughly clear what is believed to be a consequence of the rest of this License.\n\n8. If the distribution and/or use of the Program is restricted in certain countries either by patents or by copyrighted interfaces, the original copyright holder who places the Program under this License may add an explicit geographical distribution limitation excluding those countries, so that distribution is permitted only in or among countries not thus excluded.  In such case, this License incorporates the limitation as if written in the body of this License.\n\n9. 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["How to Apply These Terms to Your New Programs","How to Apply These Terms to Your New Programs\n\nIf you develop a new program, and you want it to be of the greatest possible use to the public, the best way to achieve this is to make it free software which everyone can redistribute and change under these terms.\n\nTo do so, attach the following notices to the program.  It is safest to attach them to the start of each source file to most effectively convey the exclusion of warranty; and each file should have at least the \"copyright\" line and a pointer to where the full notice is found.\n\n<one line to give the program's name and a brief idea of what it does.>\nCopyright (C) <year>  <name of author>\n\nThis program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.  This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more details.\n\nYou should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.\n\nAlso add information on how to contact you by electronic and paper mail.  If the program is interactive, make it output a short notice like this when it starts in an interactive mode:\n\nGnomovision version 69, Copyright (C) year name of author\nGnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'.  This is free software, and you are welcome to redistribute it under certain conditions; type `show c' for details. \n\nThe hypothetical commands `show w' and `show c' should show the appropriate parts of the General Public License.  Of course, the commands you use may be called something other than `show w' and `show c'; they could even be mouse-clicks or menu items--whatever suits your program. \n\nYou should also get your employer (if you work as a programmer) or your school, if any, to sign a \"copyright disclaimer\" for the program, if necessary.  Here is a sample; alter the names: \n\nYoyodyne, Inc., hereby disclaims all copyright interest in the program `Gnomovision' (which makes passes at compilers) written by James Hacker. \n<signature of Ty Coon>, 1 April 1989\nTy Coon, President of Vice\n\nThis General Public License does not permit incorporating your program into proprietary programs.  If your program is a subroutine library, you may consider it more useful to permit linking proprietary applications with the library.  If this is what you want to do, use the GNU Lesser General Public License instead of this License.\n"]

{"sheet":"Error Log","index":11,"n_rows":1,"n_cols":4,"rows_kept":1,"cut":false,"hidden":true,"merged":[]}
["Date","Location","Error Number","Error Message"]

{"sheet":"Analyze Binomial Help","index":12,"n_rows":11,"n_cols":2,"rows_kept":11,"cut":false,"hidden":true,"merged":[]}
["Binomial Fitting","The binomial fitting algorythm relies on the \"Solver\", \"Analysis ToolPak\", and \"Analysis TooPak - VBA\" add-ins within Excel. This can be installed from the Microsoft Office CD through Excel \"Tools\" \"Add-Ins\". If it is not present a \"module not found\" error will pop up during fitting. To include Solver as a reference for HX-Express open HX-Express and go to VBA (Alt+F11),. then under \"Tools\" and \"References\" Check the \"Solver\" and \"atpvbaen.xls\" boxes. If it is not listed try running solver in excel before adding it as a reference in HX-Express. On some systems it is necessary to run solver once before HX-express recognizes it. "]
["Number of Amides","The number of slow exchanging amides needs to be specified for the binomial function. Changing the number of amides will affect the width of the binomial distribution. If the peptide sequence is provided and used for calculating the natural abundance isotopic distribution then this value can be left \"0\" and HX-Express will automatically calculate the number of amides based on the peptide sequence (and glycans). "]
["Number of Amides","In some cases the number of amides for optimal fits will deviate from that predicted from the sequence. Some highly protected peptides may have residues that have yet to exchange at early timepoints, thereby not contributing to the binomial distribution. Alternatively, the presence of fast back-exchanging residues will also warrant a slightly lower number of amides for the best fits. Checking the \"Optimize Fit\" box for Number of Amides will float the value for the number of amides to find the best fit for each time point. If this is used then the final width plot will report the number of amides used for each spectrum. Using both the \"Optimize Fit\" and \"Auto Estimate\" functions at the same time is not recommended as it often results in strange binomial fits. "]
["Asymmetric Fitting","Adjusting this term results in asymmetric weighted least-squares fitting in which the error for values below the resulting fit are scaled by the asymmetry value. For clean (non overlapped) data this term should be left at 1 (no asymmetry). In many cases a higher charged mass envelope will have a lower charge state overlapping contaminant. For this type of overlap a higher asymmetry  value can be used to get a more accurate fit by forcing the binomial function to fit to the lower values (thus minimizing contribution of the overlapped peaks). The ideal value depends on the severity of the overlap, but typically the range is 2-10 (for raw spectral fitting it may be higher). The \"Auto Estimate\" option will perform iterative fits, steadily increasing the assymetry term until the fit no longer improves. \n\nThe AutoAssymetry option will automatically repeat the fitting process while scaling the assymetry term, until the p value converges. For raw spectral fitting this may add significant time to the calculations.  "]
["Natural Isotopic Distribution","The fitting algorythm requires the distribution of the undeuterated spectra to calculate final resulting isotopic distrbutions for each binomial fit. This can either be obtained from the undeuterated spectrum (faster) or calculated from the peptide sequence. If there is evidence of overlap within the undeuterated mass list, or the signal is poor, the later option should be used. The calculation of the natural abundance isotopic distribution utilizes the \"Analysis ToolPak - VBA\" add-in within excel, therefore this needs to be enabled within Excel. In Excel File, \"Options\", \"Add-Ins\", \"Manage Excel Add-ins\" and add both \"Analysis ToolPaks\". For HX-express (Alt+F11 to enter VBA; select HXToolsProject; Then under \"Tools\" click \"References\" and check the \"atpvbaen.xla\" add-in.  "]
["Glycopeptides","The natural isotopic distribution can also be calculated for glycopeptides. For this check the \"Add Glycosylation\" box and add the appropriate number of Hexose (Mannose, Galactose, etc.), HexNAc (GlcNAc, GalNAc), DeoxyHexose (Fucose), and NeuAc (neuraminic acid) groups. For example, if the glycopeptide had a Man9 high-mannose glycan then you would need to add '9' in the hexose box and '2' in the HexNAc box, and check the \"add glycosylation\" box. These values are ignored if the \"Caculate undeuterated mass envelope from peptide sequence\" box is unchecked. "]
["Peptide Modifications","For peptides that contain modifications, the \"custom modification box\" should be checked, and the chemical formula entered into the next field. Modications that add atoms can be entered directly, while modifications resulting in a loss of atoms should have a \"-\" as the first character followed by the chemical formula. Currenlyt only H, C, N, O, S, P, and Na atoms are supported, others will no be recognized.  "]
["Fitting to the Raw Data","Instead of fitting the binomial function to the isotopically peaked peaks, it is possible to fit the binomial to the raw spectra. This uses the natural abundance calculation from the sequence, guesses the binomial p from the centroid, reconstructs the theoretical spectra making each peak a guassian and uses Solver to minimize the fit to the raw data. For this, first analyse all spectra without the \"use isotopic peak detection\" option. The m/z threshold and instrument resolution will be adjusted slightly during fitting, but an initial guess is required. For a well calibrated Q-TOF these two values are in the range of 0.1 and 10,000 but is highly insrument dependent. Fitting to raw data is about 20 times slower, and should only be used for very noisy spectra where isotope recognition fails. Only minimal smoothing of the raw data is recommended for this analysis (4 x 2 Savitzky-Golay).  "]
["Multiple Binomials","When performing binomial fitting with the 'optimize fits\" option, HX Express will automatically check to see if the best value for the number of amides. If this value is larger that either the number expected for the peptide sequence, or the number of amides obtained from a fully deuterated spectra, then it will atuomatically flag the spectra as bimodal and label the plot with red font. For data showing bimodal distributions a double or triple binomial can be used for the fitting. This can be used to re-fit spectra with multiple binomial distributions but only after a single binomial has been applied to all the data. (See Bimodal Help)"]
["Summary of Binomials","The new Summary sheet will include the probabilities (p) and the relative deuterium uptake (or percent) calculated from the binomial fit. The relative deuterium uptake plot will show the fits with the conventional centroid fitting and the binomial fit. If you need to adjust anything among the worksheets to optimize the binomial fit you will need to first unlock the worksheets using the \"unlock worksheets\" in the HX Express menu otpions, perform the new optimization within the worksheets, and lastly to use the 're-summarize binomials\" option from the main HX Express menu options to update the summary sheet. "]
["Cleaning up Raw Fitting","The raw fitting routine generates dozens of columns of data, which can result in large file sizes (>10 MGBytes). It can also cause calculations to get sluggish on some systems. To keep the final resulting file low apply the \"Clean up Raw Fitting\" option under HXExpress after the fitting is complete. This also re-summarizes all the results, so it should be applied if any manual re-fitting was performed.\nIf the \"Compress worksheets\" is checked then each worksheet will be immediately cleaned up right after the fitting procedure (recommended).   "]