public static void Figure_EffectOfTemperature_Simple()
{
var ionTable = new IonTable();
double[] temps = ScottPlot.DataGen.Consecutive(50);
double[] ljps = new double[temps.Length];
for (int i = 0; i < temps.Length; i++)
{
Console.WriteLine($"Calculating for {temps[i]}C...");
var ionSet = new List <Ion> {
new Ion("Zn", 9, 0.0284), new Ion("K", 0, 3), new Ion("Cl", 18, 3.0568)
};
ljps[i] = Calculate.Ljp(ionTable.Lookup(ionSet), temps[i]).mV;
}
var plt = new ScottPlot.Plot(800, 600);
plt.PlotScatter(temps, ljps);
plt.Title("JLJP Screenshot Ion Set");
plt.YLabel("LJP (mV)");
plt.XLabel("Temperature (C)");
string filePath = System.IO.Path.GetFullPath("Figure_EffectOfTemperatureSimple.png");
plt.SaveFig(filePath);
Console.WriteLine($"Saved: {filePath}");
}
public IonLookup()
{
var mdTableBytes = Properties.Resources.IonTable;
string mdTableString = System.Text.Encoding.Default.GetString(mdTableBytes);
string[] mdTableLines = mdTableString.Split("\n");
Table = new IonTable(mdTableLines);
}
public void Test_KnownIonSets_LjpWithinExpectedRange()
{
var ionTable = new IonTable();
var knownSets = new KnownIonSets(ionTable);
foreach (var ionSet in knownSets.ionSets)
{
Console.WriteLine($"Testing known ion set: {ionSet.name}");
var ljp = Calculate.Ljp(ionSet.ions, ionSet.temperatureC);
Assert.AreEqual(ionSet.expectedLjp_mV, ljp.mV, ionSet.expectedAccuracy_mV);
}
}
public void Test_LjpCalculationMatches_ExampleFromSourceCode()
{
/* From JLJP: https://github.com/swharden/JLJP/blob/2.0.0/src/Example.java */
Ion Zn = new Ion("Zn", MolsPerCubicMeter(9), MolsPerCubicMeter(0.0284));
Ion K = new Ion("K", MolsPerCubicMeter(0), MolsPerCubicMeter(3));
Ion Cl = new Ion("Cl", MolsPerCubicMeter(18), MolsPerCubicMeter(3.0568));
var ionSet = new List <Ion> {
Zn, K, Cl
};
var ionTable = new IonTable();
ionSet = ionTable.Lookup(ionSet);
var ljp = Calculate.Ljp(ionSet);
Assert.AreEqual(-20.79558643, ljp.mV, 1e-6);
}
public void Test_LjpCalculationMatches_Harper003()
{
// ion set from Harper (1985) Table I
// https://pubs.acs.org/doi/pdf/10.1021/j100255a022
var ionSet = new List <Ion>
{
new Ion("Ca", .29, .00545),
new Ion("Cl", .29 * 2, .00545 * 2)
};
var ionTable = new IonTable();
ionSet = ionTable.Lookup(ionSet);
var ljp = Calculate.Ljp(ionSet);
Assert.AreEqual(-35, ljp.mV, 0.5);
}
public void Test_LjpCalculationMatches_Harper004()
{
// ion set from Harper (1985) Table I
// https://pubs.acs.org/doi/pdf/10.1021/j100255a022
var ionSet = new List <Ion>
{
new Ion("Zn", .4, .0186),
new Ion("SO4", .4, .0186),
};
var ionTable = new IonTable();
ionSet = ionTable.Lookup(ionSet);
var ljp = Calculate.Ljp(ionSet);
Assert.AreEqual(-8.1, ljp.mV, 0.5);
}
public void Test_LjpCalculationMatches_ExampleFromScreenshot()
{
/* Test came from screenshot on original JLJP website */
var ionSet = new List <Ion>
{
new Ion("Zn", 9, 0.0284),
new Ion("K", 0, 3),
new Ion("Cl", 18, 3.0568)
};
var ionTable = new IonTable();
ionSet = ionTable.Lookup(ionSet);
var ljp = Calculate.Ljp(ionSet);
Assert.AreEqual(-20.79558643, ljp.mV, 1e-6);
}
public void Test_LjpCalculationMatches_NgAndBarry001()
{
/* LJP for this test came from Ng and Barry (1994) Table 2 */
// 50 mM NaCl : 50 mM KCl
var ionSet = new List <Ion>
{
new Ion("Na", 50, 0),
new Ion("K", 0, 50),
new Ion("Cl", 50, 50)
};
var ionTable = new IonTable();
ionSet = ionTable.Lookup(ionSet);
var ljp = Calculate.Ljp(ionSet);
Assert.AreEqual(-4.3, ljp.mV, 0.5);
}
public void Test_LjpCalculationMatches_NgAndBarry005()
{
/* LJP for this test came from Ng and Barry (1994) Table 2 */
// 100 CaCl2 : 100 MgCl2
// Ca (100), Cl (200) : Mg (100) Cl (200)
var ionSet = new List <Ion>
{
new Ion("Ca", 100, 0),
new Ion("Mg", 0, 100),
new Ion("Cl", 200, 200)
};
var ionTable = new IonTable();
ionSet = ionTable.Lookup(ionSet);
var ljp = Calculate.Ljp(ionSet);
Assert.AreEqual(+0.6, ljp.mV, 0.5);
}
public void Test_LjpCalculationMatches_JPWin002()
{
// ion set shown in JPCalcWin manual (page 10)
// https://tinyurl.com/wk7otn7
var ionSet = new List <Ion>
{
new Ion("Cs", 145, 0),
new Ion("Na", 0, 145),
new Ion("F", 125, 0),
new Ion("Cl", 20, 145)
};
var ionTable = new IonTable();
ionSet = ionTable.Lookup(ionSet);
var ljp = Calculate.Ljp(ionSet);
Assert.AreEqual(+8.71, ljp.mV, 0.5);
}
public void Test_LjpCalculationMatches_NgAndBarry007()
{
/* LJP for this test came from Ng and Barry (1994) Table 2 */
// 50 CaCl2 + 50 MgCl2 : 100 LiCl
// Ca (50), Cl (200), Mg (50) : Li (100), Cl (100)
var ionSet = new List <Ion>
{
new Ion("Ca", 50, 0),
new Ion("Cl", 200, 100),
new Ion("Mg", 50, 0),
new Ion("Li", 0, 100)
};
var ionTable = new IonTable();
ionSet = ionTable.Lookup(ionSet);
var ljp = Calculate.Ljp(ionSet);
Assert.AreEqual(-8.2, ljp.mV, 0.5);
}
public void Test_LjpCalculationMatches_NgAndBarry006()
{
/* LJP for this test came from Ng and Barry (1994) Table 2 */
// 100 KCl + 2 CaCl2 : 100 LiCl + 2 CaCl2
// K (100), Cl (104), Ca (2) : Li (100), Cl (104), Ca (2)
var ionSet = new List <Ion>
{
new Ion("Ca", 2, 2),
new Ion("K", 100, 0),
new Ion("Li", 0, 100),
new Ion("Cl", 104, 104)
};
var ionTable = new IonTable();
ionSet = ionTable.Lookup(ionSet);
var ljp = Calculate.Ljp(ionSet);
Assert.AreEqual(+6.4, ljp.mV, 0.5);
}
private void LoadIonTable()
{
IonTableListbox.Items.Clear();
try
{
ionTable = new IonTable();
foreach (var ion in ionTable.ions)
{
IonTableListbox.Items.Add(ion.nameWithCharge);
}
}
catch
{
IonTableListbox.Items.Add("ERROR");
IonTableListbox.IsEnabled = false;
MessageBox.Show(
"The ion table failed to load. Calculations will work, but ion values cannot be looked up and example ion sets will not be available.",
"Ion Table Error",
MessageBoxButton.OK,
MessageBoxImage.Warning);
}
}
public IonMasses(TypedMass precursorMass, IonTable <TypedMass> fragmentMasses)
{
PrecursorMass = precursorMass;
FragmentMasses = fragmentMasses;
}
public static void Figure_EffectOfTemperature_SeveralSets()
{
/* this study calculates one of several known ionSets at every temperature between 0C and 50C */
var ionTable = new IonTable();
double[] temps = ScottPlot.DataGen.Consecutive(50);
double[] jljpResults = new double[temps.Length];
double[] ngAndBarryResults = new double[temps.Length];
double[] HarperResults = new double[temps.Length];
double[] jpWinResults = new double[temps.Length];
List <Ion> ionSet;
for (int i = 0; i < temps.Length; i++)
{
Console.WriteLine($"Calculating for {temps[i]}C...");
// see LjpCalculationTests.cs for ion set citations
// create a new ion set for each iteration to prevent modifications due to solving from carrying to the next solve
ionSet = new List <Ion> {
new Ion("Zn", 9, 0.0284), new Ion("K", 0, 3), new Ion("Cl", 18, 3.0568)
};
jljpResults[i] = Calculate.Ljp(ionTable.Lookup(ionSet), temps[i]).mV;
ionSet = new List <Ion> {
new Ion("Ca", 2, 2), new Ion("K", 100, 0), new Ion("Li", 0, 100), new Ion("Cl", 104, 104)
};
ngAndBarryResults[i] = Calculate.Ljp(ionTable.Lookup(ionSet), temps[i]).mV;
ionSet = new List <Ion> {
new Ion("Ca", .29, .00545), new Ion("Cl", .29 * 2, .00545 * 2)
};
HarperResults[i] = Calculate.Ljp(ionTable.Lookup(ionSet), temps[i]).mV;
ionSet = new List <Ion> {
new Ion("Na", 10, 145), new Ion("Cl", 10, 145), new Ion("Cs", 135, 0), new Ion("F", 135, 0)
};
jpWinResults[i] = Calculate.Ljp(ionTable.Lookup(ionSet), temps[i]).mV;
}
var mplt = new ScottPlot.MultiPlot(800, 600, 2, 2);
mplt.subplots[0].PlotScatter(temps, jljpResults);
mplt.subplots[0].Title("JLJP screenshot");
mplt.subplots[1].PlotScatter(temps, ngAndBarryResults);
mplt.subplots[1].Title("Ng and Barry (1994)");
mplt.subplots[2].PlotScatter(temps, HarperResults);
mplt.subplots[2].Title("Harper (1985)");
mplt.subplots[3].PlotScatter(temps, jpWinResults);
mplt.subplots[3].Title("JPWin screenshot");
for (int i = 0; i < 4; i++)
{
mplt.subplots[i].YLabel("LJP (mV)");
mplt.subplots[i].XLabel("Temperature (C)");
}
string filePath = System.IO.Path.GetFullPath("Figure_EffectOfTemperature.png");
mplt.SaveFig(filePath);
Console.WriteLine($"Saved: {filePath}");
}
public static Adduct CalcProductCharge(TypedMass productPrecursorMass,
Adduct precursorCharge,
IList <IonType> acceptedIonTypes,
IonTable <TypedMass> productMasses,
IList <IList <ExplicitLoss> > potentialLosses,
double productMz,
double tolerance,
MassType massType,
MassShiftType massShiftType,
out IonType?ionType,
out int?ordinal,
out TransitionLosses losses,
out int massShift)
{
// Get length of fragment ion mass array
int len = productMasses.GetLength(1);
// Check all possible ion types and offsets
double? minDelta = null;
var bestCharge = Adduct.EMPTY;
IonType? bestIonType = null;
int? bestOrdinal = null;
TransitionLosses bestLosses = null;
int bestMassShift = 0;
// Check to see if it is the precursor
foreach (var lossesTrial in TransitionGroup.CalcTransitionLosses(IonType.precursor, 0, massType, potentialLosses))
{
var productMass = productPrecursorMass - (lossesTrial != null ? lossesTrial.Mass : 0);
int potentialMassShift;
int nearestCharge;
var charge = CalcProductCharge(productMass, productMz, tolerance, false, precursorCharge,
massShiftType, out potentialMassShift, out nearestCharge);
if (Equals(charge, precursorCharge))
{
double potentialMz = SequenceMassCalc.GetMZ(productMass, charge) + potentialMassShift;
double delta = Math.Abs(productMz - potentialMz);
if (CompareIonMatch(delta, lossesTrial, potentialMassShift, minDelta, bestLosses, bestMassShift) < 0)
{
bestCharge = charge;
bestIonType = IonType.precursor;
bestOrdinal = len + 1;
bestLosses = lossesTrial;
bestMassShift = potentialMassShift;
minDelta = delta;
}
}
}
var categoryLast = -1;
foreach (var typeAccepted in GetIonTypes(acceptedIonTypes))
{
var type = typeAccepted.IonType;
var category = typeAccepted.IonCategory;
// Types have priorities. If changing type category, and there is already a
// suitable answer stop looking.
if (category != categoryLast && minDelta.HasValue && MatchMz(minDelta.Value, tolerance))
{
break;
}
categoryLast = category;
for (int offset = 0; offset < len; offset++)
{
foreach (var lossesTrial in TransitionGroup.CalcTransitionLosses(type, offset, massType, potentialLosses))
{
// Look for the closest match.
var productMass = productMasses[type, offset];
if (lossesTrial != null)
{
productMass -= lossesTrial.Mass;
}
int potentialMassShift;
int nearestCharge;
var chargeFound = CalcProductCharge(productMass, productMz, tolerance, false, precursorCharge,
massShiftType, out potentialMassShift, out nearestCharge);
if (!chargeFound.IsEmpty)
{
var charge = chargeFound;
double potentialMz = SequenceMassCalc.GetMZ(productMass, charge) + potentialMassShift;
double delta = Math.Abs(productMz - potentialMz);
if (CompareIonMatch(delta, lossesTrial, potentialMassShift, minDelta, bestLosses, bestMassShift) < 0)
{
bestCharge = charge;
bestIonType = type;
// The peptide length is 1 longer than the mass array
bestOrdinal = Transition.OffsetToOrdinal(type, offset, len + 1);
bestLosses = lossesTrial;
bestMassShift = potentialMassShift;
minDelta = delta;
}
}
}
}
}
ionType = bestIonType;
ordinal = bestOrdinal;
losses = bestLosses;
massShift = bestMassShift;
return(bestCharge);
}
public static Adduct CalcProductCharge(TypedMass productPrecursorMass,
int?productZ,
Adduct precursorCharge,
IList <IonType> acceptedIonTypes,
IonTable <TypedMass> productMasses,
IList <IList <ExplicitLoss> > potentialLosses,
double productMz,
double tolerance,
MassType massType,
MassShiftType massShiftType,
out IonType?ionType,
out int?ordinal,
out TransitionLosses losses,
out int massShift)
{
// Get length of fragment ion mass array
int len = productMasses.GetLength(1);
// Check all possible ion types and offsets
double?minDelta = null;
double?minFragmentMass = null, maxFragmentMass = null, maxLoss = null;
if (massShiftType == MassShiftType.none)
{
if (!productZ.HasValue)
{
minFragmentMass = productMz - tolerance;
}
else
{
minFragmentMass = SequenceMassCalc.GetMH(productMz - tolerance, productZ.Value);
maxFragmentMass = SequenceMassCalc.GetMH(productMz + tolerance, productZ.Value);
}
}
var bestCharge = Adduct.EMPTY;
IonType? bestIonType = null;
int? bestOrdinal = null;
TransitionLosses bestLosses = null;
int bestMassShift = 0;
// Check to see if it is the precursor
foreach (var lossesTrial in TransitionGroup.CalcTransitionLosses(IonType.precursor, 0, massType, potentialLosses))
{
var productMass = productPrecursorMass;
if (lossesTrial != null)
{
productMass -= lossesTrial.Mass;
maxLoss = Math.Max(maxLoss ?? 0, lossesTrial.Mass);
}
int potentialMassShift;
int nearestCharge;
var charge = CalcProductCharge(productMass, productZ, productMz, tolerance, false, precursorCharge,
massShiftType, out potentialMassShift, out nearestCharge);
if (Equals(charge, precursorCharge))
{
double potentialMz = SequenceMassCalc.GetMZ(productMass, charge) + potentialMassShift;
double delta = Math.Abs(productMz - potentialMz);
if (CompareIonMatch(delta, lossesTrial, potentialMassShift, minDelta, bestLosses, bestMassShift) < 0)
{
bestCharge = charge;
bestIonType = IonType.precursor;
bestOrdinal = len + 1;
bestLosses = lossesTrial;
bestMassShift = potentialMassShift;
minDelta = delta;
}
}
}
if (maxLoss.HasValue)
{
maxFragmentMass += maxLoss.Value;
}
var categoryLast = -1;
foreach (var typeAccepted in GetIonTypes(acceptedIonTypes))
{
var type = typeAccepted.IonType;
var category = typeAccepted.IonCategory;
// Types have priorities. If changing type category, and there is already a
// suitable answer stop looking.
if (category != categoryLast && minDelta.HasValue && MatchMz(minDelta.Value, tolerance))
{
break;
}
categoryLast = category;
// The peptide length is 1 longer than the mass array
for (int ord = len; ord > 0; ord--)
{
int offset = Transition.OrdinalToOffset(type, ord, len + 1);
var productMassBase = productMasses[type, offset];
// Until below the maximum fragment mass no possible matches
if (maxFragmentMass.HasValue && productMassBase > maxFragmentMass.Value)
{
continue;
}
// Once below the minimum fragment mass no more possible matches, so stop
if (minFragmentMass.HasValue && productMassBase < minFragmentMass.Value)
{
break;
}
foreach (var lossesTrial in TransitionGroup.CalcTransitionLosses(type, offset, massType, potentialLosses))
{
// Look for the closest match.
var productMass = productMassBase;
if (lossesTrial != null)
{
productMass -= lossesTrial.Mass;
}
int potentialMassShift;
int nearestCharge;
var chargeFound = CalcProductCharge(productMass, productZ, productMz, tolerance, false, precursorCharge,
massShiftType, out potentialMassShift, out nearestCharge);
if (!chargeFound.IsEmpty)
{
var charge = chargeFound;
double potentialMz = SequenceMassCalc.GetMZ(productMass, charge) + potentialMassShift;
double delta = Math.Abs(productMz - potentialMz);
if (CompareIonMatch(delta, lossesTrial, potentialMassShift, minDelta, bestLosses, bestMassShift) < 0)
{
bestCharge = charge;
bestIonType = type;
bestOrdinal = ord;
bestLosses = lossesTrial;
bestMassShift = potentialMassShift;
minDelta = delta;
}
}
}
}
}
ionType = bestIonType;
ordinal = bestOrdinal;
losses = bestLosses;
massShift = bestMassShift;
return(bestCharge);
}
public IonMasses ChangeFragmentMasses(IonTable <TypedMass> fragmentMasses)
{
return(ChangeProp(ImClone(this), im => im.FragmentMasses = fragmentMasses));
}
