public static void TestCompIons_MatchIonsScore()
{
TestDataFile t = new TestDataFile();
Tolerance productMassTolerance = new AbsoluteTolerance(0.01);
double precursorMass = 300;
//The below theoretical does not accurately represent B-Y ions
double[] sorted_theoretical_product_masses_for_this_peptide = new double[] { precursorMass + (2 * Constants.ProtonMass) - 275.1350, precursorMass + (2 * Constants.ProtonMass) - 258.127, precursorMass + (2 * Constants.ProtonMass) - 257.1244, 50, 60, 70, 147.0764, precursorMass + (2 * Constants.ProtonMass) - 147.0764, precursorMass + (2 * Constants.ProtonMass) - 70, precursorMass + (2 * Constants.ProtonMass) - 60, precursorMass + (2 * Constants.ProtonMass) - 50, 257.1244, 258.127, 275.1350 }; //{ 50, 60, 70, 147.0764, 257.1244, 258.127, 275.1350 }
List <Product> productsWithLocalizedMassDiff = new List <Product>();
foreach (double d in sorted_theoretical_product_masses_for_this_peptide)
{
NeutralTerminusFragment frag = new NeutralTerminusFragment(FragmentationTerminus.Both, d, 1, 1);
productsWithLocalizedMassDiff.Add(new Product(ProductType.b, frag, 0));
}
CommonParameters commonParametersNoComp = new CommonParameters {
ProductMassTolerance = new AbsoluteTolerance(0.01)
};
CommonParameters commonParametersWithComp = new CommonParameters(productMassTolerance: new AbsoluteTolerance(0.01), addCompIons: true);
MsDataScan scan = t.GetOneBasedScan(2);
var scanWithMass = new Ms2ScanWithSpecificMass(scan, precursorMass.ToMz(1), 1, "", new CommonParameters());
List <MatchedFragmentIon> matchedIons = MetaMorpheusEngine.MatchFragmentIons(scanWithMass, productsWithLocalizedMassDiff, commonParametersNoComp);
List <MatchedFragmentIon> matchedCompIons = MetaMorpheusEngine.MatchFragmentIons(scanWithMass, productsWithLocalizedMassDiff, commonParametersWithComp);
matchedCompIons.AddRange(matchedIons);
// score when the mass-diff is on this residue
double localizedScore = MetaMorpheusEngine.CalculatePeptideScore(scan, matchedIons);
double scoreNormal = MetaMorpheusEngine.CalculatePeptideScore(scan, matchedIons);
double scoreComp = MetaMorpheusEngine.CalculatePeptideScore(scan, matchedCompIons);
Assert.IsTrue(scoreNormal * 2 == scoreComp && scoreComp > scoreNormal + 1);
}
/// <summary>
/// A product is the individual neutral fragment from an MS dissociation. A fragmentation product here contains one of the two termini (N- or C-).
/// The ProductType describes where along the backbone the fragmentaiton occurred (e.g. b-, y-, c-, zdot-). The neutral loss mass (if any) that
/// occurred from a mod on the fragment is listed as a mass. Finally the neutral mass of the whole fragment is provided.
/// </summary>
public Product(ProductType productType, NeutralTerminusFragment terminusFragment, double neutralLoss)
{
TerminusFragment = terminusFragment;
ProductType = productType;
this.NeutralLoss = neutralLoss;
NeutralMass = DissociationTypeCollection.ProductTypeSpecificFragmentNeutralMass(terminusFragment.NeutralMass, productType) - neutralLoss;
}
private static List <MatchedFragmentIon> ReadFragmentIonsFromString(string matchedMzString, string peptideBaseSequence)
{
var peaks = matchedMzString.Split(MzSplit, StringSplitOptions.RemoveEmptyEntries).Select(v => v.Trim())
.ToList();
peaks.RemoveAll(p => p.Contains("\""));
List <MatchedFragmentIon> matchedIons = new List <MatchedFragmentIon>();
foreach (var peak in peaks)
{
var split = peak.Split(new char[] { '+', ':' });
string ionTypeAndNumber = split[0];
Match result = IonParser.Match(ionTypeAndNumber);
ProductType productType = (ProductType)Enum.Parse(typeof(ProductType), result.Groups[1].Value);
int fragmentNumber = int.Parse(result.Groups[2].Value);
int z = int.Parse(split[1]);
double mz = double.Parse(split[2], CultureInfo.InvariantCulture);
double neutralLoss = 0;
// check for neutral loss
if (ionTypeAndNumber.Contains("-"))
{
string temp = ionTypeAndNumber.Replace("(", "");
temp = temp.Replace(")", "");
var split2 = temp.Split('-');
neutralLoss = double.Parse(split2[1], CultureInfo.InvariantCulture);
}
FragmentationTerminus terminus = FragmentationTerminus.None;
if (TerminusSpecificProductTypes.ProductTypeToFragmentationTerminus.ContainsKey(productType))
{
terminus = TerminusSpecificProductTypes.ProductTypeToFragmentationTerminus[productType];
}
int aminoAcidPosition = fragmentNumber;
if (terminus == FragmentationTerminus.C)
{
aminoAcidPosition = peptideBaseSequence.Length - fragmentNumber;
}
var t = new NeutralTerminusFragment(terminus, mz.ToMass(z) - DissociationTypeCollection.GetMassShiftFromProductType(productType), fragmentNumber, aminoAcidPosition);
Product p = new Product(productType, t, neutralLoss);
matchedIons.Add(new MatchedFragmentIon(p, mz, 1.0, z));
}
return(matchedIons);
}
