Version 2.37, Build 74

 - Added support for c and z ions in function GetFragmentationMasses()

MwtWinDll/MwtWinDll.vbw

@@ -1,4 +1,4 @@
-MolecularWeightCalculator = 22, 24, 746, 516, 
+MolecularWeightCalculator = 22, 24, 746, 516, Z
 MWCompoundClass = 132, 144, 856, 636, C
 MWPeptideClass = 132, 144, 856, 636, 
 ElementAndMassRoutines = 154, 168, 891, 660, 

MwtWinDll/MwtWinDll_MergeModule/EditMwtWinDll_Installer.bat

@@ -1 +1 @@
-"C:\Program Files\Microsoft Visual Studio\Common\IDE\IDE98\DEVENV.EXE" "D:\My Documents\Projects\DataMining\MwtWin\MwtWinDll\MwtWinDll_MergeModule\MwtWinDll_MergeModule.sln"
+"C:\Program Files (x86)\Microsoft Visual Studio\Common\IDE\IDE98\DEVENV.EXE" "F:\My Documents\Projects\DataMining\MwtWin\MwtWinDll\MwtWinDll_MergeModule\MwtWinDll_MergeModule.sln"

MwtWinDll/MwtWindll.vbp

@@ -1,6 +1,6 @@
 Type=OleDll
 Reference=*\G{00020430-0000-0000-C000-000000000046}#2.0#0#C:\WINDOWS\system32\stdole2.tlb#OLE Automation
-Reference=*\G{F935DC20-1CF0-11D0-ADB9-00C04FD58A0B}#1.0#0#C:\WINDOWS\system32\wshom.ocx#Windows Script Host Object Model
+Reference=*\G{F935DC20-1CF0-11D0-ADB9-00C04FD58A0B}#1.0#0#C:\WINDOWS\SysWOW64\wshom.ocx#Windows Script Host Object Model
 Class=MolecularWeightCalculator; clsMwtWin.cls
 Class=MWCompoundClass; clsCompound.cls
 Class=MWPeptideClass; clsPeptideClass.cls
@@ -20,8 +20,8 @@ Description="Molecular Weight Calculator - Dll Version"
 CompatibleMode="0"
 CompatibleEXE32="MwtWindll.dll"
 MajorVer=2
-MinorVer=36
-RevisionVer=72
+MinorVer=37
+RevisionVer=75
 AutoIncrementVer=1
 ServerSupportFiles=0
 VersionComments="Written by Matthew Monroe"

MwtWinDll/RevisionHistory.txt

@@ -1,6 +1,8 @@
 MwtWin.Dll Change Log
 
-Future: Changed blnShowCharge() from type Integer to type Boolean in the GetFragmentationMasses() function
+Version 2.37, Build 74
+	- Added support for c and z ions in function GetFragmentationMasses()
+	- Changed blnShowCharge() from type Integer to type Boolean in the GetFragmentationMasses() function
 
 Version 2.36, Build 70; February 23, 2007
 	 - Added option to include 3+ fragmentation ions in the GetFragmentationMasses() function

MwtWinDll/clsMwtWin.cls

@@ -23,7 +23,7 @@ Option Explicit
 '
 ' Project started: November 12, 2002
 
-Private Const PROGRAM_DATE = "February 23, 2007"
+Private Const PROGRAM_DATE = "October 16, 2009"
 Private Const PROGRAM_VERSION = "2.37"
 
 ' Duplicate of enum statements in ElementAndMassRoutines.bas

MwtWinDll/clsPeptideClass.cls

@@ -45,11 +45,13 @@ Public Enum ntgNTerminusGroupConstants
     ntgNone = 6
 End Enum
 
-Private Const ION_TYPE_MAX As Integer = 2
+Private Const ION_TYPE_MAX As Integer = 4
 Public Enum itIonTypeConstants
     itAIon = 0
     itBIon = 1
     itYIon = 2
+    itCIon = 3
+    itZIon = 4
 End Enum
 
 Private Type udtModificationSymbolType
@@ -274,7 +276,8 @@ Private Function ComputeMaxIonsPerResidue() As Integer
                 intIonCount = intIonCount + 1
 
                 If Abs(.IntensityOptions.BYIonShoulder) > 0 Then
-                    If eIonIndex = itIonTypeConstants.itBIon Or eIonIndex = itIonTypeConstants.itYIon Then
+                    If eIonIndex = itIonTypeConstants.itBIon Or eIonIndex = itIonTypeConstants.itYIon Or _
+                       eIonIndex = itIonTypeConstants.itCIon Or eIonIndex = itIonTypeConstants.itZIon Then
                         intIonCount = intIonCount + 2
                     End If
                 End If
@@ -406,7 +409,7 @@ Public Function GetFragmentationMasses(ByRef udtFragSpectrum() As udtFragmentati
 
             For eIonType = 0 To ION_TYPE_MAX
                 If mFragSpectrumOptions.IonTypeOptions(eIonType).ShowIon Then
-                    If (lngResidueIndex = 1 Or lngResidueIndex = ResidueCount) And (eIonType = itIonTypeConstants.itAIon Or eIonType = itIonTypeConstants.itBIon) Then
+                    If (lngResidueIndex = 1 Or lngResidueIndex = ResidueCount) And (eIonType = itIonTypeConstants.itAIon Or eIonType = itIonTypeConstants.itBIon Or eIonType = itIonTypeConstants.itCIon) Then
                         ' Don't include a or b ions in the output masses
                     Else
 
@@ -432,10 +435,10 @@ Public Function GetFragmentationMasses(ByRef udtFragSpectrum() As udtFragmentati
                                 Else
                                     ' Add ion to Predicted Spectrum
 
-                                    ' Y Ions are numbered in decreasing order: y5, y4, y3, y2, y1
-                                    ' A and B ions are numbered in increasing order: a1, a2, etc.  or b1, b2, etc.
+                                    ' Y and Z Ions are numbered in decreasing order: y5, y4, y3, y2, y1
+                                    ' A and B, C ions are numbered in increasing order: a1, a2, etc.  or b1, b2, etc.
                                     strIonSymbolGeneric = LookupIonTypeString(eIonType)
-                                    If eIonType = itIonTypeConstants.itYIon Then
+                                    If eIonType = itIonTypeConstants.itYIon Or eIonType = itIonTypeConstants.itZIon Then
                                         strIonSymbol = strIonSymbolGeneric & Trim(Str(ResidueCount - lngResidueIndex + 1))
                                     Else
                                         strIonSymbol = strIonSymbolGeneric & Trim(Str(lngResidueIndex))
@@ -448,10 +451,9 @@ Public Function GetFragmentationMasses(ByRef udtFragSpectrum() As udtFragmentati
 
                                     AppendDataToFragSpectrum lngIonCount, FragSpectrumWork(), sngConvolutedMass, sngIntensity, strIonSymbol, strIonSymbolGeneric, lngResidueIndex, .Symbol, intChargeIndex, eIonType, False
 
-                                    ' Add shoulder ions to PredictedSpectrum()
-                                    '   if a B or Y ion and the shoulder intensity is > 0
+                                    ' Add shoulder ions to PredictedSpectrum() if a B or Y ion and the shoulder intensity is > 0
                                     ' Need to use Abs() here since user can define negative theoretical intensities (which allows for plotting a spectrum inverted)
-                                    If Abs(sngIonShoulderIntensity) > 0 And (eIonType = itIonTypeConstants.itBIon Or eIonType = itIonTypeConstants.itYIon) Then
+                                    If Abs(sngIonShoulderIntensity) > 0 And (eIonType = itIonTypeConstants.itBIon Or eIonType = itIonTypeConstants.itYIon Or eIonType = itIonTypeConstants.itCIon Or eIonType = itIonTypeConstants.itZIon) Then
                                         For intShoulderIndex = -1 To 1 Step 2
                                             sngObservedMass = sngConvolutedMass + intShoulderIndex * (1 / intChargeIndex)
                                             AppendDataToFragSpectrum lngIonCount, FragSpectrumWork(), sngObservedMass, sngIonShoulderIntensity, SHOULDER_ION_PREFIX & strIonSymbol, SHOULDER_ION_PREFIX & strIonSymbolGeneric, lngResidueIndex, .Symbol, intChargeIndex, eIonType, True
@@ -549,8 +551,8 @@ End Function
 
 Private Function GetInternalResidues(lngCurrentResidueIndex As Long, eIonType As itIonTypeConstants, Optional ByRef blnPhosphorylated As Boolean) As String
     ' Determines the residues preceding or following the given residue (up to and including the current residue)
-    ' If eIonType is a or b ions, then returns residues from the N terminus
-    ' If eIonType is y ion, then returns residues from the C terminus
+    ' If eIonType is a, b, or c ions, then returns residues from the N terminus
+    ' If eIonType is y or z ions, then returns residues from the C terminus
     ' Also, set blnPhosphorylated to true if any of the residues is Ser, Thr, or Tyr and is phosphorylated
     '
     ' Note that the residue symbols are separated by a space to avoid accidental matching by the InStr() function
@@ -560,7 +562,7 @@ Private Function GetInternalResidues(lngCurrentResidueIndex As Long, eIonType As
 
     strInternalResidues = ""
     blnPhosphorylated = False
-    If eIonType = itIonTypeConstants.itYIon Then
+    If eIonType = itIonTypeConstants.itYIon Or eIonType = itIonTypeConstants.itZIon Then
         For lngResidueIndex = lngCurrentResidueIndex To ResidueCount
             With Residues(lngResidueIndex)
                 strInternalResidues = strInternalResidues & .Symbol & " "
@@ -1320,6 +1322,8 @@ Public Function LookupIonTypeString(eIonType As itIonTypeConstants) As String
     Case itIonTypeConstants.itAIon: LookupIonTypeString = "a"
     Case itIonTypeConstants.itBIon: LookupIonTypeString = "b"
     Case itIonTypeConstants.itYIon: LookupIonTypeString = "y"
+    Case itIonTypeConstants.itCIon: LookupIonTypeString = "c"
+    Case itIonTypeConstants.itZIon: LookupIonTypeString = "z"
     Case Else: LookupIonTypeString = ""
     End Select
 
@@ -1575,6 +1579,8 @@ On Error GoTo SetDefaultOptionsErrorHandler
             .IonType(itIonTypeConstants.itAIon) = 20
             .IonType(itIonTypeConstants.itBIon) = 100
             .IonType(itIonTypeConstants.itYIon) = 100
+            .IonType(itIonTypeConstants.itCIon) = 100
+            .IonType(itIonTypeConstants.itZIon) = 100
             .BYIonShoulder = 50
             .NeutralLoss = 20
         End With
@@ -1587,7 +1593,7 @@ On Error GoTo SetDefaultOptionsErrorHandler
             .NeutralLossWater = False
         End With
 
-        For intIonIndex = itIonTypeConstants.itBIon To itIonTypeConstants.itYIon
+        For intIonIndex = itIonTypeConstants.itBIon To itIonTypeConstants.itZIon
             With .IonTypeOptions(intIonIndex)
                 .ShowIon = True
                 .NeutralLossAmmonia = True
@@ -2074,6 +2080,9 @@ Private Sub UpdateResidueMasses()
 
                 .IonMass(itIonTypeConstants.itAIon) = dblRunningTotal - dblImmoniumMassDifference - dblChargeCarrierMass
                 .IonMass(itIonTypeConstants.itBIon) = dblRunningTotal
+
+                ' Add NH3 (ammonia) to the B ion mass to get the C ion mass
+                .IonMass(itIonTypeConstants.itCIon) = .IonMass(itIonTypeConstants.itBIon) + dblNH3Mass
             Else
                 .Mass = 0
                 .MassWithMods = 0
@@ -2093,7 +2102,7 @@ Private Sub UpdateResidueMasses()
         mTotalMass = 0
     End If
 
-    ' Now compute the y-ion masses
+    ' Now compute the y-ion and z-ion masses
     dblRunningTotal = mCTerminus.Mass + dblChargeCarrierMass
 
     For lngIndex = ResidueCount To 1 Step -1
@@ -2112,6 +2121,9 @@ Private Sub UpdateResidueMasses()
                         .IonMass(itIonTypeConstants.itYIon) = .IonMass(itIonTypeConstants.itYIon) - dblHydrogenMass
                     End If
                 End If
+
+                ' Subtract NH2 (amide) from the Y ion mass to get the Z ion mass
+                .IonMass(itIonTypeConstants.itZIon) = .IonMass(itIonTypeConstants.itYIon) - (dblNH3Mass - dblHydrogenMass)
             End If
         End With
     Next lngIndex