private static SilacLabel AssignValidHeavyCharacter(SilacLabel originalLabel, char heavyLabel)
{
double massDifference = Convert.ToDouble(originalLabel.MassDifference.Substring(1));
if (originalLabel.MassDifference[0] == '-')
{
massDifference *= -1;
}
//Add the silac residues to the dictionary
Residue.AddNewResiduesToDictionary(new List <Residue> {
new Residue(originalLabel.MassDifference, heavyLabel, heavyLabel.ToString(), Chemistry.ChemicalFormula.ParseFormula(originalLabel.LabelChemicalFormula), ModificationSites.All)
});
return(new SilacLabel(originalLabel.OriginalAminoAcid, heavyLabel, originalLabel.LabelChemicalFormula, massDifference));
}
public static void RefreshAminoAcidDictionary()
{
//read in all the amino acids (they already exist in mzlib, but there might be synthetic amino acids that need to be included)
string aminoAcidPath = Path.Combine(DataDir, @"CustomAminoAcids", @"CustomAminoAcids.txt");
if (File.Exists(aminoAcidPath)) //if it already exists
{
string[] aminoAcidLines = File.ReadAllLines(aminoAcidPath);
List <Residue> residuesToAdd = new List <Residue>();
for (int i = 1; i < aminoAcidLines.Length; i++)
{
string[] line = aminoAcidLines[i].Split('\t').ToArray(); //tsv Name, one letter, monoisotopic, chemical formula
if (line.Length >= 4) //check something is there (not a blank line)
{
char letter = line[1][0];
if (InvalidAminoAcids.Contains(letter))
{
throw new ProteaseGuruException("Error while reading 'CustomAminoAcids.txt'. Line " + (i + 1).ToString() + " contains an invalid amino acid. (Ex: " + string.Join(", ", InvalidAminoAcids.Select(x => x.ToString())) + ")");
}
try
{
ChemicalFormula formula = ChemicalFormula.ParseFormula(line[3]);
//if it doesn't already exist or it does exist but has a different mass, add the entry
if (!(Residue.TryGetResidue(letter, out Residue residue)) ||
!(formula.Formula.Equals(residue.ThisChemicalFormula.Formula)))
{
residuesToAdd.Add(new Residue(line[0], letter, line[1], formula, ModificationSites.Any));
}
}
catch
{
throw new ProteaseGuruException("Error while reading 'CustomAminoAcids.txt'. Line " + (i + 1).ToString() + " was not in the correct format.");
}
}
}
Residue.AddNewResiduesToDictionary(residuesToAdd);
}
else //create it so that it can be manipulated
{
WriteAminoAcidsFile();
}
}
private void SaveCustomAminoAcid_Click(object sender, RoutedEventArgs e)
{
//VALIDATE INPUT
if (AminoAcidTextBox.Text.Length == 0)
{
MessageBox.Show("Please specify the character that represents a synthetic amino acid in the database");
return;
}
char aminoAcidLetter = AminoAcidTextBox.Text.First();
ChemicalFormula formula;
try
{
formula = ChemicalFormula.ParseFormula(ChemicalFormulaTextBox.Text);
}
catch
{
MessageBox.Show("The checmical formula '" + ChemicalFormulaTextBox.Text + "' could not be parsed. Please try again.");
return;
}
if (GlobalVariables.InvalidAminoAcids.Contains(aminoAcidLetter))
{
MessageBox.Show("The amino acid '" + aminoAcidLetter + "' cannot be assigned. " +
"\nThis character is used for modification motifs or as result delimiters. " +
"\nThe following amino acids are not allowed:" +
string.Join(", ", GlobalVariables.InvalidAminoAcids.Select(x => x.ToString())) + ")");
return;
}
//check if the specified amino acid already exists
if (Residue.TryGetResidue(aminoAcidLetter, out Residue residue))
{
MessageBox.Show("The amino acid '" + aminoAcidLetter + "' already exists." +
"\nMonoisotopic Mass: " + residue.MonoisotopicMass +
"\nChemical Formula: " + residue.ThisChemicalFormula.Formula +
"\n\nYou may overwrite this amino acid by manually deleting/modifying the current entry. " +
"\nThis can be done in MetaMorpheus by navigating to 'Data' in the top-left corner, " +
"selecting 'Open folder with mods/data files' from the drop down menu, " +
"opening the folder 'CustomAminoAcids', and opening the file 'CustomAminoAcids.txt." +
"\nMetaMorpheus will need to be restarted for these changes to take effect." +
"\n\nAmino acids can be reset to their default values by deleting the file 'CustomAminoAcids.txt' and restarting MetaMorpheus.");
return;
}
//Alright, the entry is valid
//Append the entry to the CustomAminoAcids.txt file
string aminoAcidDirectory = Path.Combine(GlobalVariables.DataDir, @"CustomAminoAcids");
string customAminoAcidPath = Path.Combine(aminoAcidDirectory, @"CustomAminoAcids.txt");
//check that the file exists and create it if it doesn't
if (!File.Exists(customAminoAcidPath))
{
GlobalVariables.WriteAminoAcidsFile();
}
//save it in the amino acid file
List <string> customAminoAcidsText = File.ReadAllLines(customAminoAcidPath).ToList();
customAminoAcidsText.Add(AminoAcidTextBox.Text + '\t' + aminoAcidLetter + '\t' + formula.MonoisotopicMass.ToString() + '\t' + formula.Formula); //tsv Name, one letter, monoisotopic, chemical formula
File.WriteAllLines(customAminoAcidPath, customAminoAcidsText);
//add the mod to the residue dictionary
Residue.AddNewResiduesToDictionary(new List <Residue> {
new Residue(AminoAcidTextBox.Text, aminoAcidLetter, AminoAcidTextBox.Text, formula, ModificationSites.Any)
});
MessageBox.Show("Success! Amino Acid '" + aminoAcidLetter + "' has been added to the dictionary." +
"\nMonoisotopic Mass: " + formula.MonoisotopicMass.ToString() +
"\nChemical Formula: " + formula.Formula);
DialogResult = true;
}
public static void TestSilacNoLightProtein()
{
//The concern with multiple mods per label is the conversions back and forth between "light" and "heavy" labels
Residue heavyArginine = new Residue("c", 'c', "c", Chemistry.ChemicalFormula.ParseFormula("C6H12N{15}4O"), ModificationSites.All); //+4 arginine
Residue heavierArginine = new Residue("d", 'd', "d", Chemistry.ChemicalFormula.ParseFormula("C{13}6H12N{15}4O"), ModificationSites.All); //+10 arginine
Residue.AddNewResiduesToDictionary(new List <Residue> {
heavyArginine
}); //These should be added in the search task, but we need to add this one earlier so that we can create a heavy pwsm
Residue lightArginine = Residue.GetResidue('R');
SilacLabel heavyLabel = new SilacLabel(lightArginine.Letter, heavyArginine.Letter, heavyArginine.ThisChemicalFormula.Formula, heavyArginine.MonoisotopicMass - lightArginine.MonoisotopicMass);
SilacLabel heavierLabel = new SilacLabel(lightArginine.Letter, heavierArginine.Letter, heavierArginine.ThisChemicalFormula.Formula, heavierArginine.MonoisotopicMass - lightArginine.MonoisotopicMass);
SearchTask task = new SearchTask
{
SearchParameters = new SearchParameters
{
SilacLabels = new List <SilacLabel> {
heavyLabel, heavierLabel
}
},
CommonParameters = new CommonParameters(digestionParams: new DigestionParams(generateUnlabeledProteinsForSilac: false)) //this is the important part of the unit test
};
PeptideWithSetModifications heavyPeptide = new PeptideWithSetModifications("PEPTIDEc", new Dictionary <string, Modification>());
List <double> massDifferences = new List <double> {
heavierArginine.MonoisotopicMass - heavyArginine.MonoisotopicMass
};
MsDataFile myMsDataFile1 = new TestDataFile(heavyPeptide, massDifferences);
string mzmlName = @"silac.mzML";
IO.MzML.MzmlMethods.CreateAndWriteMyMzmlWithCalibratedSpectra(myMsDataFile1, mzmlName, false);
string xmlName = "SilacDb.xml";
Protein theProtein = new Protein("PEPTIDER", "accession1");
ProteinDbWriter.WriteXmlDatabase(new Dictionary <string, HashSet <Tuple <int, Modification> > >(), new List <Protein> {
theProtein
}, xmlName);
string outputFolder = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestSilac");
Directory.CreateDirectory(outputFolder);
var theStringResult = task.RunTask(outputFolder, new List <DbForTask> {
new DbForTask(xmlName, false)
}, new List <string> {
mzmlName
}, "taskId1").ToString();
//test proteins
string[] output = File.ReadAllLines(TestContext.CurrentContext.TestDirectory + @"/TestSilac/AllProteinGroups.tsv");
Assert.AreEqual(output.Length, 2);
Assert.IsTrue(output[0].Contains("Modification Info List\tIntensity_silac(R+3.988)\tIntensity_silac(R+10.008)")); //test that two files were made and no light file
Assert.IsTrue(output[1].Contains("875000\t437500")); //test the heavier intensity is half that of the heavy (per the raw file)
//test peptides
output = File.ReadAllLines(TestContext.CurrentContext.TestDirectory + @"/TestSilac/AllQuantifiedPeptides.tsv");
Assert.AreEqual(output.Length, 2);
Assert.IsTrue(output[0].Contains("Organism\tIntensity_silac(R+3.988)\tIntensity_silac(R+10.008)")); //test the two files were made and no light file
Assert.IsTrue(output[1].Contains("875000\t437500")); //test intensity
//test peaks
output = File.ReadAllLines(TestContext.CurrentContext.TestDirectory + @"/TestSilac/AllQuantifiedPeaks.tsv");
Assert.AreEqual(output.Length, 3);
Assert.IsTrue(output[1].Contains("silac\t")); //test the filename was NOT modified (it was for proteins, but we don't want it for peptides)
Assert.IsTrue(output[2].Contains("silac\t")); //test the filename was NOT modified (it was for proteins, but we don't want it for peptides)
Assert.IsTrue(output[1].Contains("PEPTIDER(+3.988)\t")); //test light sequence was not modified
Assert.IsTrue(output[2].Contains("PEPTIDER(+10.008)\t")); //test heavy sequence was output correctly (do NOT want "PEPTIDEa")
Assert.IsTrue(output[1].Contains("959.44")); //test light mass
Assert.IsTrue(output[2].Contains("965.46")); //test heavy mass
//test PSMs
output = File.ReadAllLines(TestContext.CurrentContext.TestDirectory + @"/TestSilac/AllPSMs.psmtsv");
Assert.IsTrue(output[1].Contains("959.44")); //test the correct monoisotopic mass
Assert.IsTrue(output[1].Contains("PEPTIDER(+3.988)")); //test the correct psm
Assert.IsTrue(output[1].Contains("silac\t")); //test the filename was NOT modified (it was for proteins, but we don't want it for peptides)
//Clear the old files
Directory.Delete(outputFolder, true);
File.Delete(xmlName);
File.Delete(mzmlName);
}
public void SilacLabelTest()
{
Protein originalProtein = new Protein("ACDEFGHIKAKAK", "TEST");
List <PeptideWithSetModifications> originalDigest = originalProtein.Digest(new DigestionParams(), new List <Modification>(), new List <Modification>()).ToList();
//Multiple SILAC labels
Residue lysine = Residue.GetResidue('K');
Residue arginine = Residue.GetResidue('R');
Residue heavyLabel = new Residue("heavy", 'a', "aaa", ChemicalFormula.ParseFormula("C{13}6H12N2O"), ModificationSites.All); //Lysine +6
Residue heavierLabel = new Residue("heavier", 'b', "bbb", ChemicalFormula.ParseFormula("C{13}6H12N{15}2O"), ModificationSites.All); //Lysine +8
Residue heavyArginine = new Residue("heavyR", 'c', "ccc", ChemicalFormula.ParseFormula("C{13}6H5N{15}4O"), ModificationSites.All); //Arginine +10
List <Residue> residuesToAdd = new List <Residue> {
heavyLabel, heavierLabel, heavyArginine
};
Residue.AddNewResiduesToDictionary(residuesToAdd);
List <SilacLabel> silacLabels = new List <SilacLabel>
{
new SilacLabel('K', 'a', heavyLabel.ThisChemicalFormula.Formula, heavyLabel.MonoisotopicMass - lysine.MonoisotopicMass),
new SilacLabel('K', 'b', heavierLabel.ThisChemicalFormula.Formula, heavierLabel.MonoisotopicMass - lysine.MonoisotopicMass)
};
List <PeptideWithSetModifications> silacDigest = originalProtein.Digest(new DigestionParams(), new List <Modification>(), new List <Modification>(), silacLabels).ToList();
Assert.IsTrue(originalDigest.Count * 3 == silacDigest.Count); //check that each peptide now has a light, heavy, and heavier compliment
double silacPeptideLightMonoisotopicMass = silacDigest.Where(x => x.BaseSequence.Contains("K")).First().MonoisotopicMass;
double silacPeptideHeavyMonoisotopicMass = silacDigest.Where(x => x.BaseSequence.Contains("a")).First().MonoisotopicMass;
double silacPeptideHeavierMonoisotopicMass = silacDigest.Where(x => x.BaseSequence.Contains("b")).First().MonoisotopicMass;
Assert.IsTrue(silacPeptideLightMonoisotopicMass != double.NaN); //if both NaN, then the mass comparison statements will always be true, because NaN + double = NaN
Assert.IsTrue(silacPeptideHeavyMonoisotopicMass != double.NaN); //if both NaN, then the mass comparison statements will always be true, because NaN + double = NaN
Assert.IsTrue(silacPeptideHeavierMonoisotopicMass != double.NaN); //if both NaN, then the mass comparison statements will always be true, because NaN + double = NaN
Assert.IsTrue(Math.Round(silacPeptideLightMonoisotopicMass + heavyLabel.MonoisotopicMass, 5).Equals(Math.Round(silacPeptideHeavyMonoisotopicMass + lysine.MonoisotopicMass, 5))); //check that the residue masses were succesfully added
Assert.IsTrue(Math.Round(silacPeptideHeavyMonoisotopicMass + heavierLabel.MonoisotopicMass, 5).Equals(Math.Round(silacPeptideHeavierMonoisotopicMass + heavyLabel.MonoisotopicMass, 5))); //check that the residue masses were succesfully added
//code coverage
SilacLabel testParameterlessConstructorForTomlsWithoutAnyRealTestAndMoreJustForCodeCoverage = new SilacLabel();
Assert.IsTrue(testParameterlessConstructorForTomlsWithoutAnyRealTestAndMoreJustForCodeCoverage != null);
Assert.IsTrue(silacLabels[0].AdditionalLabels == null);
//The zero index label is K to a with a mass diff of 6
//the one index label is K to b with a mass diff of 8
silacLabels[0].AddAdditionalSilacLabel(new SilacLabel('D', 'c', heavyLabel.ThisChemicalFormula.Formula, heavyLabel.MonoisotopicMass - lysine.MonoisotopicMass - 1));
Assert.IsTrue(silacLabels[0].AdditionalLabels.Count == 1);
silacLabels[0].AddAdditionalSilacLabel(new SilacLabel('E', 'd', heavyLabel.ThisChemicalFormula.Formula, heavyLabel.MonoisotopicMass - lysine.MonoisotopicMass + 1));
Assert.IsTrue(silacLabels[0].AdditionalLabels.Count == 2);
silacDigest = originalProtein.Digest(new DigestionParams(), new List <Modification>(), new List <Modification>(), silacLabels).ToList();
Assert.IsTrue(silacDigest.Count == 9);
//Turnover
silacLabels = new List <SilacLabel>
{
new SilacLabel('K', 'b', heavierLabel.ThisChemicalFormula.Formula, heavierLabel.MonoisotopicMass - lysine.MonoisotopicMass)
};
silacDigest = originalProtein.Digest(new DigestionParams(), new List <Modification>(), new List <Modification>(), silacLabels, (null, silacLabels[0])).ToList();
Assert.IsTrue(silacDigest.Count == 14);
silacDigest = originalProtein.Digest(new DigestionParams(), new List <Modification>(), new List <Modification>(), silacLabels, (silacLabels[0], null)).ToList();
Assert.IsTrue(silacDigest.Count == 14);
silacLabels = new List <SilacLabel>
{
new SilacLabel('K', 'a', heavyLabel.ThisChemicalFormula.Formula, heavyLabel.MonoisotopicMass - lysine.MonoisotopicMass),
new SilacLabel('K', 'b', heavierLabel.ThisChemicalFormula.Formula, heavierLabel.MonoisotopicMass - lysine.MonoisotopicMass)
};
silacDigest = originalProtein.Digest(new DigestionParams(generateUnlabeledProteinsForSilac: false), new List <Modification>(), new List <Modification>(), silacLabels, (silacLabels[1], silacLabels[0])).ToList();
Assert.IsTrue(silacDigest.Count == 14);
originalProtein = new Protein("ACDEFGHIKARAK", "TEST");
silacLabels[1].AddAdditionalSilacLabel(new SilacLabel('R', 'c', heavyArginine.ThisChemicalFormula.Formula, heavyArginine.MonoisotopicMass - arginine.MonoisotopicMass));
silacDigest = originalProtein.Digest(new DigestionParams(generateUnlabeledProteinsForSilac: false), new List <Modification>(), new List <Modification>(), silacLabels, (silacLabels[1], silacLabels[0])).ToList();
Assert.IsTrue(silacDigest.Count == 14);
silacLabels = new List <SilacLabel>
{
new SilacLabel('K', 'a', heavyLabel.ThisChemicalFormula.Formula, heavyLabel.MonoisotopicMass - lysine.MonoisotopicMass),
new SilacLabel('K', 'b', heavierLabel.ThisChemicalFormula.Formula, heavierLabel.MonoisotopicMass - lysine.MonoisotopicMass)
};
silacLabels[0].AddAdditionalSilacLabel(new SilacLabel('R', 'c', heavyArginine.ThisChemicalFormula.Formula, heavyArginine.MonoisotopicMass - arginine.MonoisotopicMass));
silacDigest = originalProtein.Digest(new DigestionParams(generateUnlabeledProteinsForSilac: false), new List <Modification>(), new List <Modification>(), silacLabels, (silacLabels[1], silacLabels[0])).ToList();
Assert.IsTrue(silacDigest.Count == 14);
}