Version 2.37, Build 78; May 15, 2012

 - Added parameter blnAddProtonChargeCarrier to ComputeIsotopicAbundances

Batch.txt

@@ -134,3 +134,7 @@ CH2(CH2)7CH2Br
 ; Change the charge state with the following command
 ISOTOPICDISTRIBUTIONCHARGE=2
 CH2(CH2)7CH2Br
+
+; Disable adding a proton when computing m/z
+ISOTOPICDISTRIBUTIONADDPROTON=False
+CH2(CH2)7CH2Br

BatchSimple.txt

@@ -6,3 +6,7 @@ CH2(CH2)7CH2Br
 ; Change the charge state with the following command
 ISOTOPICDISTRIBUTIONCHARGE=2
 CH2(CH2)7CH2Br
+
+; Disable adding a proton when computing m/z
+ISOTOPICDISTRIBUTIONADDPROTON=False
+CH2(CH2)7CH2Br

FileIOFunctions.bas

@@ -1358,6 +1358,7 @@ On Error GoTo LoadValuesAndFormulasErrorHandler
                             frmIsotopicDistribution.txtEffectiveResolution = strSettingInFile
                         Case "IONPLOTRESOLUTIONMASS": frmIsotopicDistribution.txtEffectiveResolutionMass = strSettingInFile
                         Case "IONPLOTGAUSSIANQUALITY": frmIsotopicDistribution.txtGaussianQualityFactor = strSettingInFile
+                        Case "IONPLOTADDPROTON": frmIsotopicDistribution.chkAddProtonChargeCarrier.value = lngSettingInFile
                         Case "IONCOMPARISONPLOTCOLOR": frmIsotopicDistribution.lblComparisonListPlotColor.BackColor = lngSettingInFile
                         Case "IONCOMPARISONPLOTTYPE"
                             ValidateValueLng lngSettingInFile, 0, 2, 0          ' ipmSticksToZero
@@ -2381,6 +2382,7 @@ On Error GoTo SaveValuesErrorHandler
                 Print #OutFileNum, "IonPlotResolution=" & Trim(.txtEffectiveResolution.Text)
                 Print #OutFileNum, "IonPlotResolutionMass=" & Trim(.txtEffectiveResolutionMass.Text)
                 Print #OutFileNum, "IonPlotGaussianQuality=" & Trim(.txtGaussianQualityFactor.Text)
+                Print #OutFileNum, "IonPlotAddProton=" & CheckBoxToIntegerString(.chkAddProtonChargeCarrier)
                 Print #OutFileNum, "IonComparisonPlotColor=" & Trim(.lblComparisonListPlotColor.BackColor)
                 Print #OutFileNum, "IonComparisonPlotType=" & Trim(.cboComparisonListPlotType.ListIndex)
                 Print #OutFileNum, "IonComparisonPlotNormalize=" & CheckBoxToIntegerString(.chkComparisonListNormalize)

MWTWIN.BAS

@@ -30,7 +30,7 @@ Option Explicit
 
 ' *** Be sure to update version in Project | Properties also ***
 Public Const PROGRAM_VERSION = "6.49"
-Public Const PROGRAM_DATE = "April 11, 2012"
+Public Const PROGRAM_DATE = "May 15, 2012"
 ' ***
 
 '
@@ -276,7 +276,7 @@ Public Sub AddToIntro(strAdd As String, Optional blnUseMsgBoxInstead As Boolean
         frmIntro.lblLoadStatus.Caption = frmIntro.lblLoadStatus.Caption & vbCrLf & strAdd
         If blnErrorMessage Then
             gBlnLoadStatusOK = False
-            frmIntro.CmdOK.Visible = True
+            frmIntro.cmdOK.Visible = True
         End If
     End If
 
@@ -519,6 +519,7 @@ Public Sub BatchProcessTextFile(Optional strInputFilename As String = "", Option
     Dim strHeaderMass As String
     Dim strHeaderFraction As String
     Dim strHeaderIntensity As String
+    Dim blnAddProtonChargeCarrier As Boolean
 
     Dim InFileNum As Integer, OutFileNum As Integer
 
@@ -551,6 +552,7 @@ Public Sub BatchProcessTextFile(Optional strInputFilename As String = "", Option
     strHeaderMass = LookupLanguageCaption(15210, "Mass/Charge")
     strHeaderFraction = LookupLanguageCaption(15220, "Fraction")
     strHeaderIntensity = LookupLanguageCaption(15230, "Intensity")
+    blnAddProtonChargeCarrier = True
 
     If strInputFilename = "" Then
         ' 1510 = Text Files, 1515 = .txt
@@ -617,6 +619,7 @@ Public Sub BatchProcessTextFile(Optional strInputFilename As String = "", Option
                 strSettingsUCase = UCase(strSettings)
 
                 Select Case Trim(strCommand)
+
             ' Output option commands
                 Case "VERBOSEMODE"
                     Select Case strSettingsUCase
@@ -968,6 +971,19 @@ Public Sub BatchProcessTextFile(Optional strInputFilename As String = "", Option
                         intIsotopicDistributionChargeState = CInt(strSettings)
                         If blnVerboseMode Then Print #OutFileNum, COMMENT_CHAR & " Isotopic Distribution charge set to " & Trim(intIsotopicDistributionChargeState)
                     End If
+
+                Case "ISOTOPICDISTRIBUTIONADDPROTON"
+                    ' Whether or not to add a proton whem charge is >=1 during Isotopic Distribution calculations
+                    If blnVerboseMode Then Print #OutFileNum, ""
+                    Select Case strSettingsUCase
+                    Case "TRUE", "1", "ON"
+                        If blnVerboseMode Then Print #OutFileNum, COMMENT_CHAR & " Isotopic Distribution calculations will add a proton when charge is >= 1"
+                        blnAddProtonChargeCarrier = True
+                    Case Else
+                        If blnVerboseMode Then Print #OutFileNum, COMMENT_CHAR & " Isotopic Distribution calculations will not add a proton when charge is >= 1"
+                        blnAddProtonChargeCarrier = False
+                    End Select
+
                 Case Else
                     Print #OutFileNum, COMMENT_CHAR & " Error: Unknown Command: " & strCommand
                 End Select
@@ -1044,7 +1060,7 @@ Public Sub BatchProcessTextFile(Optional strInputFilename As String = "", Option
                             intIsotopicDistributionChargeState = 1
                         End If
 
-                        lngErrorID = objMwtWin.ComputeIsotopicAbundances(strWork, intIsotopicDistributionChargeState, strResults, dblDummyArray, 0, strHeaderIsotopicAbundace, strHeaderMass, strHeaderFraction, strHeaderIntensity)
+                        lngErrorID = objMwtWin.ComputeIsotopicAbundances(strWork, intIsotopicDistributionChargeState, strResults, dblDummyArray, 0, strHeaderIsotopicAbundace, strHeaderMass, strHeaderFraction, strHeaderIntensity, blnAddProtonChargeCarrier)
 
                         If lngErrorID = 0 Then
                              ' Formula parsed successfuly
@@ -1814,7 +1830,7 @@ Public Sub Main()
 
     If Not gNonSaveExitApp Then
         If Not gBlnLoadStatusOK Then
-            frmIntro.CmdOK.SetFocus
+            frmIntro.cmdOK.SetFocus
         End If
     Else
         If gCommandLineInstructionsDisplayed Then
@@ -2889,6 +2905,8 @@ On Error GoTo SetDefaultValuesAndFormulasErrorHandler
 
         SetCheckBox .chkAutoLabelPeaks, False
         SetCheckBox .chkPlotResults, True
+
+        SetCheckBox .chkAddProtonChargeCarrier, True
     End With
 
     If blnShowDebugPrompts Then MsgBox "Call objMwtWin.Peptide.SetDefaultModificationSymbols"

MWT_ELEM.bak

@@ -1,4 +1,4 @@
-;       Elements File for MWTWIN program (v6.48)
+;       Elements File for MWTWIN program (v6.49)
 ;
 ; Comments may be added by preceding with a semicolon
 ; The heading [ELEMENTWEIGHTTYPE] 1 signifies that Average Elemental Weights are

MWT_VALU.bak

@@ -1,9 +1,9 @@
-;       Values File for MWTWIN Program (v6.48)
+;       Values File for MWTWIN Program (v6.49)
 ;
 ; File Automatically Created -- Select Save Values and Formulas under the Options Menu
 ;
-Formula0=C2H3NO
-Formula1=C2H2O
+Formula0=BrCH2(CH2)7CH2Br
+Formula1=FeCl3-6H2O
 Formula2=Co(Bpy)(CO)4
 Formula3=^13C6H6-.1H2O
 Formula4=HGlyLeuTyrOH
@@ -126,15 +126,16 @@ IonPlotType=1
 IonPlotResolution=5000
 IonPlotResolutionMass=1000
 IonPlotGaussianQuality=50
+IonPlotAddProton=1
 IonComparisonPlotColor=255
 IonComparisonPlotType=0
 IonComparisonPlotNormalize=1
 FinderAction=0
-FinderMWT=515.343
+FinderMWT=200
 FinderPercentMaxWeight=400
-FinderPPM=1
+FinderPPM=0
 FinderShowDeltaMass=1
-FinderWtTolerance=15
+FinderWtTolerance=0.05
 FinderPercentTolerance=1
 FinderMaxHits=100
 FinderSortResults=1
@@ -149,48 +150,48 @@ FinderHighlightText=0
 FinderAutoBoundsSet=1
 FinderSortMode=0
 FinderMin0=0
-FinderMax0=44
+FinderMax0=10
 FinderCheckElements0=1
 FinderPercentValue0=Percent
 FinderMin1=0
-FinderMax1=257
+FinderMax1=10
 FinderCheckElements1=1
 FinderPercentValue1=Percent
 FinderMin2=0
-FinderMax2=38
+FinderMax2=10
 FinderCheckElements2=1
 FinderPercentValue2=Percent
 FinderMin3=0
-FinderMax3=33
+FinderMax3=10
 FinderCheckElements3=1
 FinderPercentValue3=Percent
 FinderMin4=0
-FinderMax4=20
+FinderMax4=10
 FinderCheckElements4=0
 FinderPercentValue4=Percent
 FinderCustomWeight1=# or Element or Abbrev.
 FinderMin5=0
-FinderMax5=20
+FinderMax5=10
 FinderCheckElements5=0
 FinderPercentValue5=Percent
 FinderCustomWeight2=# or Element or Abbrev.
 FinderMin6=0
-FinderMax6=20
+FinderMax6=10
 FinderCheckElements6=0
 FinderPercentValue6=Percent
 FinderCustomWeight3=# or Element or Abbrev.
 FinderMin7=0
-FinderMax7=20
+FinderMax7=10
 FinderCheckElements7=0
 FinderPercentValue7=Percent
 FinderCustomWeight4=# or Element or Abbrev.
 FinderMin8=0
-FinderMax8=20
+FinderMax8=10
 FinderCheckElements8=0
 FinderPercentValue8=Percent
 FinderCustomWeight5=# or Element or Abbrev.
 FinderMin9=0
-FinderMax9=20
+FinderMax9=10
 FinderCheckElements9=0
 FinderPercentValue9=Percent
 FinderCustomWeight6=# or Element or Abbrev.
@@ -205,8 +206,8 @@ FragModelModificationSymbol7=$,227.127,False,Cleavable ICAT [(^12C10)H17N3O3]
 FragModelModificationSymbol8=%,236.127,False,Cleavable ICAT [(^13C9)(^12C)H17N3O3]
 FragModelModificationSymbol9=~,442.225,False,ICAT D0 [C20H34N4O5S]
 FragModelModificationSymbol10=`,450.274,False,ICAT D8 [C20H26D8N4O5S]
-FragModelNotationMode=0
-FragModelSequence=.FGAPPAGEISVDEGATAAILERGSSLLPK.G
+FragModelNotationMode=1
+FragModelSequence=Arg-His-Pro-Glu-Tyr-Ala-Val
 FragModelNTerminus=0
 FragModelCTerminus=0
 FragModelIonType0=0
@@ -220,14 +221,14 @@ FragModelIonsToModify2=1
 FragModelWaterLoss=1
 FragModelAmmoniaLoss=0
 FragModelPhosphateLoss=0
-FragModelDoubleCharge=1
+FragModelDoubleCharge=0
 FragModelDoubleChargeThreshold=8
 FragModelTripleCharge=0
 FragModelTripleChargeThreshold=9
 FragModelPrecursorIonRemove=1
-FragModelPrecursorIonMass=2808.52
+FragModelPrecursorIonMass=300
 FragModelPrecursorIonMassWindow=2
-FragModelIonMatchWindow=0.1
+FragModelIonMatchWindow=0.5
 FragModelIonIntensity0=10
 FragModelIonIntensity1=50
 FragModelIonIntensity2=50
@@ -1443,23 +1444,23 @@ FragModelIonAlignment=0
 SeriesPlotMode=1
 SeriesLineStyle=0
 SeriesLineWidth=1
-SeriesLineColor=16711680
-SeriesLineToBaseColor=16711680
-SeriesBarFillColor=16711680
+SeriesLineColor=255
+SeriesLineToBaseColor=255
+SeriesBarFillColor=255
 SeriesPointStyle=0
-SeriesPointColor=16711680
+SeriesPointColor=255
 AnnotationFontName=Arial
 AnnotationFontSize=10
 AnnotationFontColor=0
 [PlotOptions_Series2]
 SeriesPlotMode=1
 SeriesLineStyle=0
 SeriesLineWidth=1
-SeriesLineColor=32768
-SeriesLineToBaseColor=32768
-SeriesBarFillColor=32768
+SeriesLineColor=40960
+SeriesLineToBaseColor=40960
+SeriesBarFillColor=40960
 SeriesPointStyle=0
-SeriesPointColor=32768
+SeriesPointColor=40960
 AnnotationFontName=Arial
 AnnotationFontSize=10
 AnnotationFontColor=0
@@ -1494,7 +1495,7 @@ PrecisionY=1
 CursorVisible=True
 CursorSnapToData=False
 CursorColor=0
-CursorPositionX=100
+CursorPositionX=0
 CursorPositionY=0
 AutoLabelPeaksDisplayXPosition=True
 AutoLabelPeaksDisplayYPosition=False

MwtWinDll/MwtWinDll.vbw

@@ -1,7 +1,7 @@
 MolecularWeightCalculator = 22, 24, 746, 516, 
 MWCompoundClass = 132, 144, 856, 636, C
 MWPeptideClass = 132, 144, 856, 636, 
-ElementAndMassRoutines = 154, 168, 891, 660, 
+ElementAndMassRoutines = 154, 168, 891, 660, Z
 modSharedVBRoutines = 0, 0, 795, 492, C
 MWCapillaryFlowClass = 154, 168, 884, 660, C
 frmProgress = 115, 115, 784, 491, C, 23, 23, 670, 391, C

MwtWinDll/MwtWinDllTest.vbp

@@ -1,8 +1,8 @@
 Type=Exe
-Reference=*\G{00020430-0000-0000-C000-000000000046}#2.0#0#C:\WINDOWS\system32\stdole2.tlb#OLE Automation
-Reference=*\G{2779F0A5-153F-49E8-BDA8-2417488A54A3}#1.0#0#MwtWindll.dll#Molecular Weight Calculator - Dll Version
-Object={3B7C8863-D78F-101B-B9B5-04021C009402}#1.2#0; richtx32.Ocx
-Object={5E9E78A0-531B-11CF-91F6-C2863C385E30}#1.0#0; msflxgrd.ocx
+Reference=*\G{00020430-0000-0000-C000-000000000046}#2.0#0#C:\Windows\SysWOW64\stdole2.tlb#OLE Automation
+Reference=*\G{22E3BE8D-4CAB-4EA3-87EC-2B1C8512C0FD}#1.0#0#MwtWindll.dll#Molecular Weight Calculator - Dll Version
+Object={3B7C8863-D78F-101B-B9B5-04021C009402}#1.2#0; richtx32.ocx
+Object={5E9E78A0-531B-11CF-91F6-C2863C385E30}#1.0#0; MSFLXGRD.OCX
 Form=MwtWinDllTest.frm
 Module=modMwtWinDllTest; MwtWinDllTest.bas
 Form=frmresults.frm
@@ -17,7 +17,7 @@ HelpContextID="0"
 CompatibleMode="0"
 MajorVer=1
 MinorVer=0
-RevisionVer=2
+RevisionVer=3
 AutoIncrementVer=1
 ServerSupportFiles=0
 VersionCompanyName="PNNL"

MwtWinDll/MwtWinDllTest.vbw

@@ -1,3 +1,3 @@
-frmMwtWinDllTest = 75, 21, 514, 513, Z, 10, -7, 777, 590, C
+frmMwtWinDllTest = 75, 21, 514, 513, , 10, -7, 777, 590, C
 modMwtWinDllTest = 22, 24, 866, 533, 
 frmResults = 110, 120, 952, 647, , 66, 72, 908, 599, C

MwtWinDll/MwtWindll.vbp

@@ -21,7 +21,7 @@ CompatibleMode="0"
 CompatibleEXE32="MwtWindll.dll"
 MajorVer=2
 MinorVer=37
-RevisionVer=78
+RevisionVer=79
 AutoIncrementVer=1
 ServerSupportFiles=0
 VersionComments="Written by Matthew Monroe"

MwtWinDll/RevisionHistory.txt

@@ -1,5 +1,8 @@
 MwtWin.Dll Change Log
 
+Version 2.37, Build 78; May 15, 2012
+	- Added parameter blnAddProtonChargeCarrier to ComputeIsotopicAbundances
+
 Version 2.37, Build 77; August 5, 2011
 	- Recompiled due to new computer OS
 

MwtWinDll/WorkingRoutines.bas

@@ -330,9 +330,10 @@ Public Function TestComputeIsotopicAbundances(ByRef strFormulaIn As String, ByVa
 
 End Function
 
-Public Function ComputeIsotopicAbundancesInternal(ByRef strFormulaIn As String, ByVal intChargeState As Integer, ByRef strResults As String, ByRef ConvolutedMSData2DOneBased() As Double, ByRef ConvolutedMSDataCount As Long, Optional ByVal strHeaderIsotopicAbundances As String = "Isotopic Abundances for", Optional ByVal strHeaderMassToCharge As String = "Mass/Charge", Optional ByVal strHeaderFraction As String = "Fraction", Optional ByVal strHeaderIntensity As String = "Intensity", Optional blnUseFactorials As Boolean = False) As Integer
+Public Function ComputeIsotopicAbundancesInternal(ByRef strFormulaIn As String, ByVal intChargeState As Integer, ByRef strResults As String, ByRef ConvolutedMSData2DOneBased() As Double, ByRef ConvolutedMSDataCount As Long, Optional ByVal strHeaderIsotopicAbundances As String = "Isotopic Abundances for", Optional ByVal strHeaderMassToCharge As String = "Mass/Charge", Optional ByVal strHeaderFraction As String = "Fraction", Optional ByVal strHeaderIntensity As String = "Intensity", Optional blnUseFactorials As Boolean = False, Optional blnAddProtonChargeCarrier As Boolean = True) As Integer
     ' Computes the Isotopic Distribution for a formula, returns uncharged mass vlaues if intChargeState=0,
     '  M+H values if intChargeState=1, and convoluted m/z if intChargeState is > 1
+    ' If blnAddProtonChargeCarrier is False, then still convlutes by charge, but doesn't add a proton
     ' Updates strFormulaIn to the properly formatted formula
     ' Returns the results in strResults
     ' Returns 0 if success, or -1 if an error
@@ -907,7 +908,11 @@ On Error GoTo IsoAbundanceErrorHandler
             ConvolutedMSData2DOneBased(lngMassIndex, 1) = .Abundance / dblMaxAbundance * 100
 
             If intChargeState >= 1 Then
-                ConvolutedMSData2DOneBased(lngMassIndex, 0) = ConvoluteMassInternal(ConvolutedMSData2DOneBased(lngMassIndex, 0), 0, intChargeState)
+                If blnAddProtonChargeCarrier Then
+                    ConvolutedMSData2DOneBased(lngMassIndex, 0) = ConvoluteMassInternal(ConvolutedMSData2DOneBased(lngMassIndex, 0), 0, intChargeState)
+                Else
+                    ConvolutedMSData2DOneBased(lngMassIndex, 0) = ConvolutedMSData2DOneBased(lngMassIndex, 0) / intChargeState
+                End If
             End If
         End With
     Next lngMassIndex

MwtWinDll/clsMwtWin.cls

@@ -80,11 +80,14 @@ Public Function ComputeMass(ByVal strFormula As String) As Double
 
 End Function
 
-Public Function ComputeIsotopicAbundances(ByRef strFormulaIn As String, ByVal intChargeState As Integer, ByRef strResults As String, ByRef ConvolutedMSData2DOneBased() As Double, ByRef ConvolutedMSDataCount As Long, Optional ByVal strHeaderIsotopicAbundances As String = "Isotopic Abundances for", Optional ByVal strHeaderMass As String = "Mass", Optional ByVal strHeaderFraction As String = "Fraction", Optional ByVal strHeaderIntensity As String = "Intensity") As Integer
+Public Function ComputeIsotopicAbundances(ByRef strFormulaIn As String, ByVal intChargeState As Integer, ByRef strResults As String, ByRef ConvolutedMSData2DOneBased() As Double, ByRef ConvolutedMSDataCount As Long, Optional ByVal strHeaderIsotopicAbundances As String = "Isotopic Abundances for", Optional ByVal strHeaderMass As String = "Mass", Optional ByVal strHeaderFraction As String = "Fraction", Optional ByVal strHeaderIntensity As String = "Intensity", Optional blnAddProtonChargeCarrier As Boolean = True) As Integer
     ' Computes the Isotopic Distribution for a formula
     ' Returns 0 if success, or -1 if an error
 
-    ComputeIsotopicAbundances = ComputeIsotopicAbundancesInternal(strFormulaIn, intChargeState, strResults, ConvolutedMSData2DOneBased(), ConvolutedMSDataCount, strHeaderIsotopicAbundances, strHeaderMass, strHeaderFraction, strHeaderIntensity, False)
+    Dim blnUseFactorials As Boolean
+    blnUseFactorials = False
+
+    ComputeIsotopicAbundances = ComputeIsotopicAbundancesInternal(strFormulaIn, intChargeState, strResults, ConvolutedMSData2DOneBased(), ConvolutedMSDataCount, strHeaderIsotopicAbundances, strHeaderMass, strHeaderFraction, strHeaderIntensity, blnUseFactorials, blnAddProtonChargeCarrier)
 End Function
 
 Public Function ConvoluteMass(ByVal dblMassMZ As Double, ByVal intCurrentCharge As Integer, Optional ByVal intDesiredCharge As Integer = 1, Optional ByVal dblChargeCarrierMass As Double = 0) As Double