private void PopulateProteaseList()
{
string proteaseDirectory = System.IO.Path.Combine(GlobalVariables.DataDir, @"ProteolyticDigestion");
string proteaseFilePath = System.IO.Path.Combine(proteaseDirectory, @"proteases.tsv");
var myLines = File.ReadAllLines(proteaseFilePath);
myLines = myLines.Skip(1).ToArray();
Dictionary <string, Protease> dict = new Dictionary <string, Protease>();
foreach (string line in myLines)
{
if (line.Trim() != string.Empty) // skip empty lines
{
string[] fields = line.Split('\t');
List <DigestionMotif> motifList = DigestionMotif.ParseDigestionMotifsFromString(fields[1]);
string name = fields[0];
var cleavageSpecificity = ((CleavageSpecificity)Enum.Parse(typeof(CleavageSpecificity), fields[4], true));
string psiMsAccessionNumber = fields[5];
string psiMsName = fields[6];
var protease = new Protease(name, cleavageSpecificity, psiMsAccessionNumber, psiMsName, motifList);
dict.Add(protease.Name, protease);
}
}
foreach (Protease protease in dict.Values)
{
ProteaseSelectedForUse.Items.Add(protease);
}
}
public static void TestWrongSyntax()
{
Assert.Throws <MzLibException>(() =>
{
var protease = DigestionMotif.ParseDigestionMotifsFromString("X[Y,P]");
Assert.Fail("Exception shold be thrown for incorrect syntax.");
});
}
public static void TestParseProtease()
{
var argn = DigestionMotif.ParseDigestionMotifsFromString("|D");
Assert.AreEqual(argn.Count, 1);
var c = argn[0];
Assert.AreEqual(c.InducingCleavage, "D");
Assert.AreEqual(c.PreventingCleavage, null);
Assert.AreEqual(c.CutIndex, 0);
var chymotrypsin = DigestionMotif.ParseDigestionMotifsFromString("F[P]|,W[P]|,Y[P]|");
Assert.AreEqual(chymotrypsin.Count, 3);
}
public static void MultipleProteaseSelectionTestPreventCleavage()
{
Protein ParentProtein = new Protein("MOAT", "accession1");
var motifList = DigestionMotif.ParseDigestionMotifsFromString("O[A]|,|T");
var protease = new Protease("TestProtease3", CleavageSpecificity.Full, null, null, motifList);
ProteaseDictionary.Dictionary.Add(protease.Name, protease);
DigestionParams multiProtease = new DigestionParams(protease: protease.Name, maxMissedCleavages: 0, minPeptideLength: 1, initiatorMethionineBehavior: InitiatorMethionineBehavior.Retain);
var digestedList = ParentProtein.Digest(multiProtease, new List <Modification>(), new List <Modification>()).ToList();
var sequences = digestedList.Select(p => p.BaseSequence).ToList();
Assert.That(sequences.Count == 2);
Assert.That(sequences.Contains("MOA"));
Assert.That(sequences.Contains("T"));
}
public static void TestGlycoPeptide()
{
var prot = new Protein("MNNNYTKQQQQKS", null);
var motifList = DigestionMotif.ParseDigestionMotifsFromString("K|");
var protease = new Protease("CustomizedProtease", CleavageSpecificity.Full, null, null, motifList);
ProteaseDictionary.Dictionary.Add(protease.Name, protease);
DigestionParams digestionParams = new DigestionParams(
protease: protease.Name,
maxMissedCleavages: 0,
minPeptideLength: 1,
initiatorMethionineBehavior: InitiatorMethionineBehavior.Retain,
keepNGlycopeptide: true,
keepOGlycopeptide: true);
List <Modification> variableModifications = new List <Modification>();
var ye = prot.Digest(digestionParams, new List <Modification>(), variableModifications).ToList();
Assert.AreEqual(2, ye.Count);
}
public static void TestBadPeptide()
{
var prot = new Protein("MNNNKQQXQ", null);
var motifList = DigestionMotif.ParseDigestionMotifsFromString("K|");
var protease = new Protease("Custom Protease7", CleavageSpecificity.Full, null, null, motifList);
ProteaseDictionary.Dictionary.Add(protease.Name, protease);
DigestionParams digestionParams = new DigestionParams(
protease: protease.Name,
maxMissedCleavages: 0,
minPeptideLength: 1,
initiatorMethionineBehavior: InitiatorMethionineBehavior.Retain);
var ye = prot.Digest(digestionParams, new List <Modification>(), new List <Modification>()).ToList();
Assert.AreEqual(2, ye.Count);
var pep1 = ye[0];
Assert.IsTrue(pep1.MonoisotopicMass > 0);
var fragments = new List <Product>();
pep1.Fragment(DissociationType.HCD, FragmentationTerminus.Both, fragments);
foreach (var huh in fragments)
{
Assert.IsTrue(huh.NeutralMass > 0);
}
var pep2 = ye[1];
Assert.IsNaN(pep2.MonoisotopicMass);
var cool = new List <Product>();
pep2.Fragment(DissociationType.HCD, FragmentationTerminus.Both, cool);
Assert.IsTrue(cool[0].NeutralMass > 0);
Assert.IsTrue(cool[1].NeutralMass > 0);
Assert.IsTrue(cool[2].NeutralMass > 0);
Assert.IsTrue(double.IsNaN(cool[3].NeutralMass));
Assert.IsTrue(double.IsNaN(cool[4].NeutralMass));
Assert.IsTrue(double.IsNaN(cool[5].NeutralMass));
Assert.IsTrue(cool.Count == 6);
}
public static void TestWildCardExclusion()
{
var empty = new List <Modification>();
var digestionmotifs = DigestionMotif.ParseDigestionMotifsFromString("RX{P}|");
Protease multiletter = new Protease("multiletter", CleavageSpecificity.Full, "", "", digestionmotifs);
ProteaseDictionary.Dictionary.Add(multiletter.Name, multiletter);
DigestionParams myDigestionParams = new DigestionParams("multiletter", minPeptideLength: 1, maxMissedCleavages: 0);
// create a protein
Protein myProtein = new Protein("PROPRPPM", "myAccession");
// digest it into peptides
var myPeptides = myProtein.Digest(myDigestionParams, empty, empty).ToList();
string first = myPeptides.First().ToString();
string last = myPeptides.Last().ToString();
Assert.AreEqual(first, "PRO");
Assert.AreEqual(last, "PRPPM");
}
public static void TestOneMotifMultiplePreventing()
{
var empty = new List <Modification>();
var digestionmotifs = DigestionMotif.ParseDigestionMotifsFromString("N[M]|,N[C]|,N[A]|");
Protease customProtease = new Protease("custom", CleavageSpecificity.Full, "", "", digestionmotifs);
ProteaseDictionary.Dictionary.Add(customProtease.Name, customProtease);
DigestionParams myDigestionParams = new DigestionParams("custom", minPeptideLength: 1, maxMissedCleavages: 0);
// create a protein
Protein myProtein = new Protein("PRONFNMMHFHAA", "myAccession");
// digest it into peptides
var myPeptides = myProtein.Digest(myDigestionParams, empty, empty).ToList();
string first = myPeptides.First().ToString();
string last = myPeptides.Last().ToString();
Assert.AreEqual(myPeptides.Count, 2);
Assert.AreEqual(first, "PRON");
}
public static void TestCutIndexDifferentSyntax()
{
var empty = new List <Modification>();
var digestionmotifs = DigestionMotif.ParseDigestionMotifsFromString("K|[P]"); // same as K[P]|
Protease protease = new Protease("lys-c", CleavageSpecificity.Full, "", "", digestionmotifs);
ProteaseDictionary.Dictionary.Add(protease.Name, protease);
DigestionParams myDigestionParams = new DigestionParams("lys-c", minPeptideLength: 1, maxMissedCleavages: 0);
// create a protein
Protein myProtein = new Protein("PROKPKMKP", "myAccession");
// digest it into peptides
var myPeptides = myProtein.Digest(myDigestionParams, empty, empty).ToList();
string first = myPeptides.First().ToString();
string last = myPeptides.Last().ToString();
Assert.AreEqual(first, "PROKPK");
Assert.AreEqual(last, "MKP");
}
public static void TestGoodPeptide()
{
var prot = new Protein("MNNNKQQQQ", null);
var motifList = DigestionMotif.ParseDigestionMotifsFromString("K|");
var protease = new Protease("CustomizedProtease", CleavageSpecificity.Full, null, null, motifList);
ProteaseDictionary.Dictionary.Add(protease.Name, protease);
DigestionParams digestionParams = new DigestionParams(
protease: protease.Name,
maxMissedCleavages: 0,
minPeptideLength: 1,
initiatorMethionineBehavior: InitiatorMethionineBehavior.Retain);
List <Modification> variableModifications = new List <Modification>();
var ye = prot.Digest(digestionParams, new List <Modification>(), variableModifications).ToList();
Assert.AreEqual(2, ye.Count);
var pep1 = ye[0];
Assert.IsTrue(pep1.MonoisotopicMass > 0);
var test = new List <Product>();
pep1.Fragment(DissociationType.HCD, FragmentationTerminus.Both, test);
foreach (var huh in test)
{
Assert.IsTrue(huh.NeutralMass > 0);
}
var pep2 = ye[1];
pep1.Fragment(DissociationType.HCD, FragmentationTerminus.Both, test);
Assert.IsTrue(pep2.MonoisotopicMass > 0);
foreach (var huh in test)
{
Assert.IsTrue(huh.NeutralMass > 0);
}
}