/// <summary>
/// Basic overview of how peptides can be used and modified
/// </summary>
private static void PeptideExamples()
{
Console.WriteLine("**Peptide Examples**");
// Simple Peptide creation
Peptide peptide1 = new Peptide("ACDEFGHIKLMNPQRSTVWY");
WritePeptideToConsole(peptide1);
// Fragmenting a peptide is simple, you can include as many fragment types as you want
Console.WriteLine("{0,-4} {1,-20} {2,-10} {3,-10} {4,-5}", "Type", "Formula", "Mass", "m/z +1", "Sequence");
foreach (Fragment fragment in peptide1.Fragment(FragmentTypes.b | FragmentTypes.y))
{
WriteFragmentToConsole(fragment);
}
// Modifications can be applied to any residue or termini
Console.WriteLine("Lets add some Iron to our peptide...");
peptide1.SetModification(new ChemicalFormula("Fe"), Terminus.C | Terminus.N);
WritePeptideToConsole(peptide1);
// A chemicalmodification is a simple wrapper for a chemical formula. You can name your mods if you want
Console.WriteLine("Add a modification of Oxygen with the name \"Oxidation\" to all Methionines");
ChemicalFormulaModification oxMod = new ChemicalFormulaModification("O", "Oxidation");
peptide1.SetModification(oxMod, 'M');
WritePeptideToConsole(peptide1);
// If you fragment a modified peptide, the modifications stay part of the fragments
Console.WriteLine("{0,-4} {1,-20} {2,-20} {3,-5}", "Type", "Formula", "Mass", "m/z +1");
foreach (Fragment fragment in peptide1.Fragment(FragmentTypes.b | FragmentTypes.y, 2))
{
WriteFragmentToConsole(fragment);
}
}
public void PeptideCloneWithModification()
{
Peptide pepA = new Peptide("DEREK");
pepA.SetModification(new OldSchoolChemicalFormulaModification(ChemicalFormula.ParseFormula("H2O")), 'R');
Peptide pepB = new Peptide(pepA);
Assert.AreEqual(pepB, pepA);
}
public void PeptideInEqualityAminoAcidModification()
{
Peptide pepA = new Peptide("DEREK");
Peptide pepB = new Peptide("DEREK");
pepB.SetModification(new ChemicalFormula("H2O"), 'R');
Assert.AreNotEqual(pepA, pepB);
}
public void GenerateIsotopologues()
{
Peptide pep = new Peptide("DERLEK");
var a = pep.GenerateAllModificationCombinations().ToArray();
Assert.AreEqual(0, a.Count());
var i = new ModificationWithMultiplePossibilitiesCollection("My Iso Mod", ModificationSites.E);
i.AddModification(new OldSchoolModification(1, "My Mod1a", ModificationSites.E));
i.AddModification(new OldSchoolModification(2, "My Mod2b", ModificationSites.E));
pep.SetModification(i);
var i2 = new ModificationWithMultiplePossibilitiesCollection("My Iso Mod2", ModificationSites.R);
i2.AddModification(new OldSchoolModification(1, "My Mod2a", ModificationSites.R));
i2.AddModification(new OldSchoolModification(2, "My Mod2b", ModificationSites.R));
i2.AddModification(new OldSchoolModification(3, "My Mod2c", ModificationSites.R));
pep.SetModification(i2);
a = pep.GenerateAllModificationCombinations().ToArray();
// Only 6 and not 12, because in the first modification, it is one choice that is substituted across all modification sites
Assert.AreEqual(6, a.Count());
}
public void PeptideParitalCloneInternalWithCTerminusModification()
{
Peptide pepA = new Peptide("DEREK");
pepA.SetModification(new OldSchoolChemicalFormulaModification(ChemicalFormula.ParseFormula("H2O")), Terminus.C);
Peptide pepB = new Peptide(pepA, 2, 3);
Peptide pepC = new Peptide("REK");
pepC.SetModification(new OldSchoolChemicalFormulaModification(ChemicalFormula.ParseFormula("H2O")), Terminus.C);
Assert.AreEqual(pepC, pepB);
}
private static void IsotopologueExample()
{
var iso1 = new Isotopologue("One", ModificationSites.K);
iso1.AddModification(new ChemicalFormulaModification("C1", "Sample 1"));
iso1.AddModification(new ChemicalFormulaModification("C2", "Sample 2"));
var iso2 = new Isotopologue("Two", ModificationSites.R);
iso2.AddModification(new ChemicalFormulaModification("C3", "Sample 3"));
iso2.AddModification(Modification.Empty);
Peptide peptide = new Peptide("DEREK");
peptide.SetModification(iso1);
peptide.SetModification(iso2);
foreach (var iso in peptide.GenerateIsotopologues())
{
Console.WriteLine(iso + ", " + iso.MonoisotopicMass);
}
}
public void ParseCTerminalChemicalFormulaWithLastResidueModStringRepresentation()
{
Peptide peptide = new Peptide("TTGSSSSSSSK[H2O]-[C2H3NO]");
Assert.AreEqual("TTGSSSSSSSK[H2O]-[C2H3NO]", peptide.GetSequenceWithModifications());
peptide.NTerminus = new ChemicalFormulaTerminus(ChemicalFormula.ParseFormula("N"));
Assert.AreEqual("TTGSSSSSSSK[H2O]-[C2H3NO]", peptide.GetSequenceWithModifications());
ChemicalFormula formulaA = new ChemicalFormula(ChemicalFormula.ParseFormula("C39H70N14O23"));
var formulaB = peptide.GetChemicalFormula();
Assert.AreEqual(formulaA, formulaB);
peptide.AddModification(new ObjectWithMass100(), 0);
Assert.AreEqual("[mass: 100]-TTGSSSSSSSK[H2O]-[C2H3NO]", peptide.GetSequenceWithModifications());
Assert.AreEqual(1, peptide.AddModification(new ObjectWithMass100(), Terminus.C));
Assert.AreEqual(3, peptide.ModificationCount());
Assert.AreEqual(0, peptide.ReplaceModification(new ObjectWithMass100(), new ObjectWithMass100()));
Assert.That(() => peptide.ReplaceModification(null, new ObjectWithMass100()),
Throws.TypeOf <MzLibException>()
.With.Property("Message")
.EqualTo("Cannot replace a null modification"));
peptide.SetModification(new ObjectWithMass100(), new int[] { 1, 11 });
Assert.AreEqual(4, peptide.ModificationCount());
OldSchoolModification mod1 = new OldSchoolModification(5, "mass 5 on T", ModificationSites.T);
peptide.SetModifications(new List <OldSchoolModification> {
mod1
});
Assert.AreEqual(5, peptide.ModificationCount());
}
public void PeptideParitalCloneInternalWithCTerminusModification()
{
Peptide pepA = new Peptide("DEREK");
pepA.SetModification(new ChemicalFormula("H2O"), Terminus.C);
Peptide pepB = new Peptide(pepA, 2, 3);
Peptide pepC = new Peptide("REK");
pepC.SetModification(new ChemicalFormula("H2O"), Terminus.C);
Assert.AreEqual(pepB,pepC);
}
public void PeptideInEqualityAminoAcidModification()
{
Peptide pepA = new Peptide("DEREK");
Peptide pepB = new Peptide("DEREK");
pepB.SetModification(new ChemicalFormula("H2O"), 'R');
Assert.AreNotEqual(pepA,pepB);
}
public void PeptideCloneWithModification()
{
Peptide pepA = new Peptide("DEREK");
pepA.SetModification(new ChemicalFormula("H2O"), 'R');
Peptide pepB = new Peptide(pepA);
Assert.AreEqual(pepB, pepA);
}
public static IEnumerable <Peptide> GetUniquePeptides(Peptide peptide)
{
HashSet <QuantitationChannelSet> sets = new HashSet <QuantitationChannelSet>();
Dictionary <IQuantitationChannel, HashSet <int> > locations = new Dictionary <IQuantitationChannel, HashSet <int> >();
IMass[] mods = peptide.Modifications;
int modLength = mods.Length;
for (int i = 0; i < modLength; i++)
{
if (mods[i] != null)
{
IMass mod = mods[i];
List <QuantitationChannelSet> channelsets = new List <QuantitationChannelSet>();
QuantitationChannelSet quantSetMod;
ModificationCollection modCol;
if ((modCol = mod as ModificationCollection) != null)
{
foreach (IMass mod2 in modCol)
{
if ((quantSetMod = mod2 as QuantitationChannelSet) != null)
{
channelsets.Add(quantSetMod);
}
}
}
else if ((quantSetMod = mod as QuantitationChannelSet) != null)
{
channelsets.Add(quantSetMod);
}
foreach (QuantitationChannelSet channelset in channelsets)
{
sets.Add(channelset);
foreach (IQuantitationChannel channel in channelset.GetChannels())
{
HashSet <int> residues;
if (locations.TryGetValue(channel, out residues))
{
residues.Add(i);
}
else
{
residues = new HashSet <int> {
i
};
locations.Add(channel, residues);
}
}
}
}
}
if (sets.Count == 0)
{
yield return(new Peptide(peptide, true));
}
else if (sets.Count == 1)
{
foreach (QuantitationChannelSet set in sets)
{
foreach (IQuantitationChannel channel in set.GetChannels())
{
Peptide toReturn = new Peptide(peptide, true);
foreach (int residue in locations[channel])
{
toReturn.SetModification(channel, residue);
}
yield return(toReturn);
}
}
}
else
{
List <HashSet <IQuantitationChannel> > quantChannels = new List <HashSet <IQuantitationChannel> >();
GetUniquePeptides_helper(sets.ToList(), 0, new HashSet <IQuantitationChannel>(), quantChannels);
foreach (HashSet <IQuantitationChannel> channelset in quantChannels)
{
Peptide toReturn = new Peptide(peptide, true);
Dictionary <int, IMass> modsToAdd = new Dictionary <int, IMass>();
foreach (IQuantitationChannel channel in channelset)
{
foreach (int residue in locations[channel])
{
IMass modToAdd;
if (modsToAdd.TryGetValue(residue, out modToAdd))
{
ModificationCollection col = new ModificationCollection(channel, modToAdd);
modsToAdd[residue] = col;
}
else
{
modsToAdd.Add(residue, channel);
}
}
}
foreach (KeyValuePair <int, IMass> kvp in modsToAdd)
{
toReturn.SetModification(kvp.Value, kvp.Key);
}
yield return(toReturn);
}
}
}
/// <summary>
/// Basic overview of how peptides can be used and modified
/// </summary>
private static void PeptideExamples()
{
Console.WriteLine("**Peptide Examples**");
// Simple Peptide creation
Peptide peptide1 = new Peptide("ACDEFGHIKLMNPQRSTVWY");
WritePeptideToConsole(peptide1);
// Fragmenting a peptide is simple, you can include as many fragment types as you want
Console.WriteLine("{0,-4} {1,-20} {2,-10} {3,-10} {4,-5}", "Type", "Formula", "Mass", "m/z +1", "Sequence");
foreach (Fragment fragment in peptide1.Fragment(FragmentTypes.b | FragmentTypes.y))
{
WriteFragmentToConsole(fragment);
}
// Modifications can be applied to any residue or termini
Console.WriteLine("Lets add some Iron to our peptide...");
peptide1.SetModification(new ChemicalFormula("Fe"), Terminus.C | Terminus.N);
WritePeptideToConsole(peptide1);
// A chemicalmodification is a simple wrapper for a chemical formula. You can name your mods if you want
Console.WriteLine("Add a modification of Oxygen with the name \"Oxidation\" to all Methionines");
ChemicalFormulaModification oxMod = new ChemicalFormulaModification("O", "Oxidation");
peptide1.SetModification(oxMod, 'M');
WritePeptideToConsole(peptide1);
// If you fragment a modified peptide, the modifications stay part of the fragments
Console.WriteLine("{0,-4} {1,-20} {2,-20} {3,-5}", "Type", "Formula", "Mass", "m/z +1");
foreach (Fragment fragment in peptide1.Fragment(FragmentTypes.b | FragmentTypes.y, 2))
{
WriteFragmentToConsole(fragment);
}
}
private static void IsotopologueExample()
{
var iso1 = new Isotopologue("One", ModificationSites.K);
iso1.AddModification(new ChemicalFormulaModification("C1", "Sample 1"));
iso1.AddModification(new ChemicalFormulaModification("C2", "Sample 2"));
var iso2 = new Isotopologue("Two", ModificationSites.R);
iso2.AddModification(new ChemicalFormulaModification("C3", "Sample 3"));
iso2.AddModification(Modification.Empty);
Peptide peptide = new Peptide("DEREK");
peptide.SetModification(iso1);
peptide.SetModification(iso2);
foreach (var iso in peptide.GenerateIsotopologues())
{
Console.WriteLine(iso + ", " + iso.MonoisotopicMass);
}
}
public void SetAminoAcidModification()
{
ChemicalFormula formula = new ChemicalFormula("Fe");
_mockPeptideEveryAminoAcid.SetModification(formula, AminoAcid.Asparagine);
Assert.AreEqual("ACDEFGHIKLMN[Fe]PQRSTVWY", _mockPeptideEveryAminoAcid.ToString());
}
public static IEnumerable<Peptide> GetUniquePeptides(Peptide peptide)
{
QuantitationChannelSet quantSetMod;
IMass mod;
ModificationCollection modCol;
HashSet<QuantitationChannelSet> sets = new HashSet<QuantitationChannelSet>();
Dictionary<IQuantitationChannel, HashSet<int>> locations = new Dictionary<IQuantitationChannel, HashSet<int>>();
HashSet<int> residues;
IMass[] mods = peptide.Modifications;
int modLength = mods.Length;
for (int i = 0; i < modLength; i++)
{
if (mods[i] != null)
{
mod = mods[i];
List<QuantitationChannelSet> channelsets = new List<QuantitationChannelSet>();
if ((modCol = mod as ModificationCollection) != null)
{
foreach (IMass mod2 in modCol)
{
if ((quantSetMod = mod2 as QuantitationChannelSet) != null)
{
channelsets.Add(quantSetMod);
}
}
}
else if ((quantSetMod = mod as QuantitationChannelSet) != null)
{
channelsets.Add(quantSetMod);
}
foreach (QuantitationChannelSet channelset in channelsets)
{
sets.Add(channelset);
foreach (IQuantitationChannel channel in channelset.GetChannels())
{
if (locations.TryGetValue(channel, out residues))
{
residues.Add(i);
}
else
{
residues = new HashSet<int>() { i };
locations.Add(channel, residues);
}
}
}
}
}
if (sets.Count == 0)
{
yield return new Peptide(peptide, true);
}
else if (sets.Count == 1)
{
foreach (QuantitationChannelSet set in sets)
{
foreach (IQuantitationChannel channel in set.GetChannels())
{
Peptide toReturn = new Peptide(peptide, true);
foreach (int residue in locations[channel])
{
toReturn.SetModification(channel, residue);
}
yield return toReturn;
}
}
}
else
{
List<HashSet<IQuantitationChannel>> quantChannels = new List<HashSet<IQuantitationChannel>>();
GetUniquePeptides_helper(sets.ToList(), 0, new HashSet<IQuantitationChannel>(), quantChannels);
foreach (HashSet<IQuantitationChannel> channelset in quantChannels)
{
Peptide toReturn = new Peptide(peptide, true);
Dictionary<int, IMass> modsToAdd = new Dictionary<int, IMass>();
IMass modToAdd;
foreach (IQuantitationChannel channel in channelset)
{
foreach (int residue in locations[channel])
{
if (modsToAdd.TryGetValue(residue, out modToAdd))
{
ModificationCollection col = new ModificationCollection(channel, modToAdd);
col.Add(channel);
col.Add(modToAdd);
modsToAdd[residue] = col;
}
else
{
modsToAdd.Add(residue, channel);
}
}
}
foreach (KeyValuePair<int, IMass> kvp in modsToAdd)
{
toReturn.SetModification(kvp.Value, kvp.Key);
}
yield return toReturn;
}
}
yield break;
}
