public static void TestIonCalculator()
{
ModifiedPeptide pep = new ModifiedPeptide();
pep.Sequence = "KDEPAEESDGDLGFGLFD";
pep.NTerminus = "H";
pep.CTerminus = "OH";
pep.addModification(new PepMod(){
accession = 21,
index = 7
});
string strIon = "b";
IonCalculator ic = new IonCalculator(new Hashtable(){
{"peptide",pep},
{"maxcharge", 3},
{"weighttype", "monoisotopic"},
{"neutralloss", new List<string>() {"H2O", "NH3"}},
{"customtemplate", "mass: {mass}, charge: {charge}"}
});
Console.WriteLine("** Testing **");
Console.WriteLine("Peptide: "+pep.Sequence+"\n");
Console.WriteLine("*** Result for "+strIon+"-Ions ***");
List<Ms2Ion> arrResult = ic.calculateIon(strIon);
foreach (Ms2Ion o in arrResult) {
Console.WriteLine(
o.mass.ToString()+"\t"+
o.ion.ToString()+
o.index.ToString()+"\t+"+
o.charge.ToString()+"\t"+
o.flag+"\t"+
o.custom+"\n"
);
}
Console.WriteLine("*** Testing ***");
Console.WriteLine("Peptide: "+pep.Sequence+"\n");
strIon = "y";
Console.WriteLine("*** Result for "+strIon+"-Ions ***");
arrResult = ic.calculateIon(strIon);
foreach (Ms2Ion o in arrResult) {
Console.WriteLine(
o.mass.ToString()+"\t"+
o.ion.ToString()+
o.index.ToString()+"\t+"+
o.charge.ToString()+"\t"+
o.flag+"\t"+
o.custom+"\n"
);
}
}
public static void TestPeptide()
{
Peptide pep = new Peptide();
string seq = "HGYIGEFEYVDDHR";
Console.WriteLine("** Test validation **");
Console.WriteLine("Peptide: "+pep.Sequence);
if (pep.validateSequence(seq) == true) {
Console.WriteLine("TRUE");
} else {
Console.WriteLine("FALSE");
}
seq = "HXGYIGEFEYVDDHR";
Console.WriteLine("Peptide: "+seq+"");
if (pep.validateSequence(seq) == true) {
Console.WriteLine("TRUE");
} else {
Console.WriteLine("FALSE");
}
seq = "HGYIGEF4EYVDDHR";
Console.WriteLine("Peptide: "+seq+"");
if (pep.validateSequence(seq) == true) {
Console.WriteLine("TRUE");
} else {
Console.WriteLine("FALSE");
}
seq = "HGYIGEFEYV*DDHR";
Console.WriteLine("Peptide: "+seq+"");
if (pep.validateSequence(seq) == true) {
Console.WriteLine("TRUE");
} else {
Console.WriteLine("FALSE");
}
pep = new Peptide();
pep.Sequence = "HGYIGEFEYVDDHR";
pep.NTerminus = "H";
pep.CTerminus = "OH";
Console.WriteLine("** Testing naked peptide **");
Console.WriteLine("Peptide: "+pep.Sequence+"");
Console.WriteLine("N-Terminus: "+pep.NTerminus+"");
Console.WriteLine("C-Terminus: "+pep.CTerminus+"");
Console.WriteLine("*** Masses monoisotopic ***");
Console.WriteLine("Mass C-Terminus: "+pep.getCTerminusMass("monoisotopic").ToString()+"");
Console.WriteLine("Mass N-Terminus: "+pep.getNTerminusMass("monoisotopic").ToString()+"");
Console.WriteLine("Peptide mass: "+pep.getMass("monoisotopic").ToString()+"");
Console.WriteLine("Calculated MCR 2: "+pep.getTheoreticalMCR("monoisotopic", 2).ToString()+"");
Console.WriteLine("*** Masses average ***");
Console.WriteLine("Mass C-Terminus: "+pep.getCTerminusMass("average").ToString()+"");
Console.WriteLine("Mass N-Terminus: "+pep.getNTerminusMass("average").ToString()+"");
Console.WriteLine("Peptide mass: "+pep.getMass("average").ToString()+"");
Console.WriteLine("Calculated MCR 3: "+pep.getTheoreticalMCR("monoisotopic", 3).ToString()+"");
ModifiedPeptide modpep = new ModifiedPeptide();
modpep.Plugins.Add("mpimp.sharprot.plugins.ModPlugins");
modpep.Sequence = "ITLLEELQEKTEEDEENKPSVIEK";
modpep.NTerminus = "H";
modpep.CTerminus = "OH";
PepMod objMod1 = new PepMod(){
accession = 21,
index = 1
};
Console.WriteLine("** Testing phosphat modification **");
Console.WriteLine("Peptide: "+modpep.Sequence+"");
Console.WriteLine("N-Terminus: "+modpep.NTerminus+"");
Console.WriteLine("C-Terminus: "+modpep.CTerminus+"");
Console.WriteLine("Modification 1: "+objMod1.accession.ToString()+"");
Console.WriteLine("*** Masses monoisotopic without Modifications ***");
Console.WriteLine("Mass C-Terminus: "+modpep.getCTerminusMass("monoisotopic").ToString()+"");
Console.WriteLine("Mass N-Terminus: "+modpep.getNTerminusMass("monoisotopic").ToString()+"");
Console.WriteLine("Peptide mass: "+modpep.getMass("monoisotopic").ToString()+"");
Console.WriteLine("Calculated MCR 2: "+modpep.getTheoreticalMCR("monoisotopic", 2).ToString()+"");
Console.WriteLine("*** Masses average without Modifications ***");
Console.WriteLine("Mass C-Terminus: "+modpep.getCTerminusMass("average").ToString()+"");
Console.WriteLine("Mass N-Terminus: "+modpep.getNTerminusMass("average").ToString()+"");
Console.WriteLine("Peptide mass: "+modpep.getMass("average").ToString()+"");
Console.WriteLine("Calculated MCR 3: "+modpep.getTheoreticalMCR("monoisotopic", 3).ToString()+"");
modpep.addModification(objMod1);
Console.WriteLine("*** Masses monoisotopic with Phosphat - Modifications ***");
Console.WriteLine("Mass C-Terminus: "+modpep.getCTerminusMass("monoisotopic").ToString()+"");
Console.WriteLine("Mass N-Terminus: "+modpep.getNTerminusMass("monoisotopic").ToString()+"");
Console.WriteLine("Peptide mass: "+modpep.getMass("monoisotopic").ToString()+"");
Console.WriteLine("Calculated MCR 2: "+modpep.getTheoreticalMCR("monoisotopic", 2).ToString()+"");
Console.WriteLine("*** Masses average with Phosphat - Modifications ***");
Console.WriteLine("Mass C-Terminus: "+modpep.getCTerminusMass("average").ToString()+"");
Console.WriteLine("Mass N-Terminus: "+modpep.getNTerminusMass("average").ToString()+"");
Console.WriteLine("Peptide mass: "+modpep.getMass("average").ToString()+"");
Console.WriteLine("Calculated MCR 3: "+modpep.getTheoreticalMCR("monoisotopic", 3).ToString()+"");
modpep = new ModifiedPeptide();
modpep.Plugins.Add("mpimp.sharprot.plugins.ModPlugins");
modpep.Sequence = "ITLLEELQ";
modpep.NTerminus = "H";
modpep.CTerminus = "OH";
Console.WriteLine("** Testing 15N Modification **");
Console.WriteLine("Peptide: "+modpep.Sequence+"");
Console.WriteLine("N-Terminus: "+modpep.NTerminus+"");
Console.WriteLine("C-Terminus: "+modpep.CTerminus+"");
Console.WriteLine("Modification X: 15N");
Console.WriteLine("*** Masses monoisotopic without 15N - Modifications ***");
Console.WriteLine("Mass C-Terminus: "+modpep.getCTerminusMass("monoisotopic").ToString()+"");
Console.WriteLine("Mass N-Terminus: "+modpep.getNTerminusMass("monoisotopic").ToString()+"");
Console.WriteLine("Peptide mass: "+modpep.getMass("monoisotopic").ToString()+"");
Console.WriteLine("Calculated MCR 2: "+modpep.getTheoreticalMCR("monoisotopic", 2).ToString()+"");
Console.WriteLine("*** Masses average without 15N - Modifications ***");
Console.WriteLine("Mass C-Terminus: "+modpep.getCTerminusMass("average").ToString()+"");
Console.WriteLine("Mass N-Terminus: "+modpep.getNTerminusMass("average").ToString()+"");
Console.WriteLine("Peptide mass: "+modpep.getMass("average").ToString()+"");
Console.WriteLine("Calculated MCR 3: "+modpep.getTheoreticalMCR("monoisotopic", 3).ToString()+"");
modpep.add15NModifications();
Console.WriteLine("*** Masses monoisotopic with 15N - Modifications ***");
Console.WriteLine("Mass C-Terminus: "+modpep.getCTerminusMass("monoisotopic").ToString()+"");
Console.WriteLine("Mass N-Terminus: "+modpep.getNTerminusMass("monoisotopic").ToString()+"");
Console.WriteLine("Peptide mass: "+modpep.getMass("monoisotopic").ToString()+"");
Console.WriteLine("Calculated MCR 2: "+modpep.getTheoreticalMCR("monoisotopic", 2).ToString()+"");
Console.WriteLine("*** Masses average with 15N - Modifications ***");
Console.WriteLine("Mass C-Terminus: "+modpep.getCTerminusMass("average").ToString()+"");
Console.WriteLine("Mass N-Terminus: "+modpep.getNTerminusMass("average").ToString()+"");
Console.WriteLine("Peptide mass: "+modpep.getMass("average").ToString()+"");
Console.WriteLine("Calculated MCR 3: "+modpep.getTheoreticalMCR("monoisotopic", 3).ToString()+"");
modpep = new ModifiedPeptide();
modpep.Plugins.Add("mpimp.sharprot.plugins.ModPlugins");
modpep.Sequence = "KDEPAEESDGDLGFGLFD";
modpep.NTerminus = "H";
modpep.CTerminus = "OH";
objMod1 = new PepMod(){
accession = 21,
index = 7
};
Console.WriteLine("** Testing phosphat data **");
Console.WriteLine("Peptide: "+modpep.Sequence+"");
Console.WriteLine("N-Terminus: "+modpep.NTerminus+"");
Console.WriteLine("C-Terminus: "+modpep.CTerminus+"");
Console.WriteLine("Modification 1: "+objMod1.accession.ToString()+" at "+objMod1.index.ToString()+"");
Console.WriteLine("*** Masses monoisotopic without Phospho mod ***");
Console.WriteLine("Mass C-Terminus: "+modpep.getCTerminusMass("monoisotopic").ToString()+"");
Console.WriteLine("Mass N-Terminus: "+modpep.getNTerminusMass("monoisotopic").ToString()+"");
Console.WriteLine("Peptide mass: "+modpep.getMass("monoisotopic").ToString()+"");
Console.WriteLine("Calculated MCR 2: "+modpep.getTheoreticalMCR("monoisotopic", 2).ToString()+"");
Console.WriteLine("*** Masses average without Phospho mod ***");
Console.WriteLine("Mass C-Terminus: "+modpep.getCTerminusMass("average").ToString()+"");
Console.WriteLine("Mass N-Terminus: "+modpep.getNTerminusMass("average").ToString()+"");
Console.WriteLine("Peptide mass: "+modpep.getMass("average").ToString()+"");
Console.WriteLine("Calculated MCR 3: "+modpep.getTheoreticalMCR("monoisotopic", 3).ToString()+"");
modpep.addModification(objMod1);
Console.WriteLine("*** Masses monoisotopic with Phospho mod ***");
Console.WriteLine("Mass C-Terminus: "+modpep.getCTerminusMass("monoisotopic").ToString()+"");
Console.WriteLine("Mass N-Terminus: "+modpep.getNTerminusMass("monoisotopic").ToString()+"");
Console.WriteLine("Peptide mass: "+modpep.getMass("monoisotopic").ToString()+"");
Console.WriteLine("Calculated MCR 2: "+modpep.getTheoreticalMCR("monoisotopic", 2).ToString()+"");
Console.WriteLine("*** Masses average with Phospho mod ***");
Console.WriteLine("Mass C-Terminus: "+modpep.getCTerminusMass("average").ToString()+"");
Console.WriteLine("Mass N-Terminus: "+modpep.getNTerminusMass("average").ToString()+"");
Console.WriteLine("Peptide mass: "+modpep.getMass("average").ToString()+"");
Console.WriteLine("Calculated MCR 3: "+modpep.getTheoreticalMCR("monoisotopic", 3).ToString()+"");
modpep = new ModifiedPeptide();
modpep.Plugins.Add("mpimp.sharprot.plugins.ModPlugins");
modpep.setModifiedSequence("KDEPAEE(pS)DGDLGFGLFD");
modpep.NTerminus = "H";
modpep.CTerminus = "OH";
Console.WriteLine("** Testing phosphat data (using the modseq detector) **");
Console.WriteLine("*** Masses monoisotopic with Phospho mod ***");
Console.WriteLine("Mass C-Terminus: "+modpep.getCTerminusMass("monoisotopic").ToString()+"");
Console.WriteLine("Mass N-Terminus: "+modpep.getNTerminusMass("monoisotopic").ToString()+"");
Console.WriteLine("Peptide mass: "+modpep.getMass("monoisotopic").ToString()+"");
Console.WriteLine("Calculated MCR 2: "+modpep.getTheoreticalMCR("monoisotopic", 2).ToString()+"");
Console.WriteLine("*** Masses average with Phospho mod ***");
Console.WriteLine("Mass C-Terminus: "+modpep.getCTerminusMass("average").ToString()+"");
Console.WriteLine("Mass N-Terminus: "+modpep.getNTerminusMass("average").ToString()+"");
Console.WriteLine("Peptide mass: "+modpep.getMass("average").ToString()+"");
Console.WriteLine("Calculated MCR 3: "+modpep.getTheoreticalMCR("monoisotopic", 3).ToString()+"");
Console.WriteLine("** Other tests **");
pep = new Peptide();
pep.Sequence ="LSNSGDAKVR";
pep.NTerminus = "H";
pep.CTerminus = "OH";
Console.WriteLine("*** Test for "+pep.Sequence+" ***");
Console.WriteLine("Mass C-Terminus: "+modpep.getCTerminusMass("monoisotopic").ToString()+"");
Console.WriteLine("Mass N-Terminus: "+modpep.getNTerminusMass("monoisotopic").ToString()+"");
Console.WriteLine("Peptide mass: "+modpep.getMass("monoisotopic").ToString()+"");
Console.WriteLine("Calculated MCR 2: "+modpep.getTheoreticalMCR("monoisotopic", 2).ToString()+"");
modpep = new ModifiedPeptide();
modpep.setModifiedSequence("LSN(pS)GDAKVR");
modpep.NTerminus = "H";
modpep.CTerminus = "OH";
Console.WriteLine("*** Test for "+modpep.Sequence+" with Phosphosite ***");
Console.WriteLine("Mass C-Terminus: "+modpep.getCTerminusMass("monoisotopic").ToString()+"");
Console.WriteLine("Mass N-Terminus: "+modpep.getNTerminusMass("monoisotopic").ToString()+"");
Console.WriteLine("Peptide mass: "+modpep.getMass("monoisotopic").ToString()+"");
Console.WriteLine("Calculated MCR 2: "+modpep.getTheoreticalMCR("monoisotopic", 2).ToString()+"");
modpep = new ModifiedPeptide();
modpep.setModifiedSequence("(pS)YTNLLDLASGNFPVMGR");
modpep.NTerminus = "H";
modpep.CTerminus = "OH";
Console.WriteLine("*** Test for "+modpep.Sequence+" with Phosphosite ***");
Console.WriteLine("Mass C-Terminus: "+modpep.getCTerminusMass("monoisotopic").ToString()+"");
Console.WriteLine("Mass N-Terminus: "+modpep.getNTerminusMass("monoisotopic").ToString()+"");
Console.WriteLine("Peptide mass: "+modpep.getMass("monoisotopic").ToString()+"");
Console.WriteLine("Calculated MCR 2: "+modpep.getTheoreticalMCR("monoisotopic", 2).ToString()+"");
modpep = new ModifiedPeptide();
modpep.setModifiedSequence("VNIKAPGD(pS)PNTDGIK");
modpep.NTerminus = "H";
modpep.CTerminus = "OH";
Console.WriteLine("*** Test for "+modpep.Sequence+" with Phosphosite ***");
Console.WriteLine("Mass C-Terminus: "+modpep.getCTerminusMass("monoisotopic").ToString()+"");
Console.WriteLine("Mass N-Terminus: "+modpep.getNTerminusMass("monoisotopic").ToString()+"");
Console.WriteLine("Peptide mass: "+modpep.getMass("monoisotopic").ToString()+"");
Console.WriteLine("Calculated MCR 2: "+modpep.getTheoreticalMCR("monoisotopic", 2).ToString()+"");
}
