private void UpdateProteins()
{
tvResult.BeginUpdate();
try
{
tvResult.Nodes.Clear();
foreach (var g in proteins)
{
var subNode = tvResult.Nodes.Add(string.Format("{0} ({1})", g[0].Name, g[0].Peptides.Count));
subNode.Tag = g;
var uniquePeptides = g[0].Peptides.GroupBy(m => PeptideUtils.GetMatchedSequence(m.Sequence)).OrderByDescending(n => n.Count()).ThenBy(n => n.Key);
foreach (var up in uniquePeptides)
{
var subPNode = subNode.Nodes.Add(string.Format("{0} ({1})", up.Key, up.Count()));
subPNode.Tag = new List <IIdentifiedSpectrum>(from p in up select p.Spectrum);
var peps = (from p in up
orderby p.Spectrum.Query.FileScan.Experimental, p.Spectrum.Query.FileScan.FirstScan
select p).ToList();
foreach (var p in peps)
{
var ppNode = subPNode.Nodes.Add(string.Format("{0}, {1:0.##}", p.Spectrum.Query.FileScan.LongFileName, p.Spectrum.Score));
ppNode.Tag = p.Spectrum;
}
}
}
}
finally
{
tvResult.EndUpdate();
}
}
private ResultCorrelationItem BuildResult(IIdentifiedResult ir)
{
var result = new ResultCorrelationItem();
result.ClassificationTitles = ClassificationSet.Keys.ToArray();
foreach (var g in ir)
{
var pro = g[0];
var protein = new ProteinCorrelationItem();
result.Add(protein);
protein.Index = g.Index;
protein.Protein = ParseItem(pro.Peptides, result.ClassificationTitles);
protein.Protein.Name = pro.Name;
var peps = pro.Peptides.GroupBy(m => PeptideUtils.GetMatchedSequence(m.Sequence));
foreach (var pep in peps)
{
var pepitem = ParseItem(pep.ToList(), result.ClassificationTitles);
protein.Peptides.Add(pepitem);
pepitem.Name = pep.Key;
pepitem.Correlation = Correlation.Pearson(pepitem.Values, protein.Protein.Values);
}
}
result.ForEach(m =>
{
m.Peptides.Sort((m1, m2) => m2.Correlation.CompareTo(m1.Correlation));
});
return(result);
}
/**
* 根据给定的sphc、pephits，以及classifiedNames进行统计各个classifiedNames对应的肽段个数。
*/
public void ClassifyPeptideHit(Func <IIdentifiedPeptide, string> classifyFunc, string[] classifiedNames)
{
classifications = new Dictionary <string, Count>();
if (classifiedNames != null)
{
foreach (string name in classifiedNames)
{
classifications[name] = new Count();
}
}
var s = from p in Peptides
let key = classifyFunc(p)
let seq = PeptideUtils.GetPureSequence(p.Sequence)
group seq by key into ss
select new { Key = ss.Key, PeptideCount = ss.Count(), UniquePeptideCount = ss.Distinct().Count() };
foreach (var item in s)
{
classifications[item.Key] = new Count()
{
PeptideCount = item.PeptideCount,
UniquePeptideCount = item.UniquePeptideCount
};
}
}
protected override void DoRealGo()
{
Aminoacids aas = Aminoacids.ParseModificationFromOutFileLine(modification.Text);
IPeptideMassCalculator calc;
if (isMonoisotopic.Checked)
{
calc = new MonoisotopicPeptideMassCalculator(aas);
}
else
{
calc = new AveragePeptideMassCalculator(aas);
}
string seq = PeptideUtils.GetMatchedSequence(sequence.Text);
double value;
if (isMH.Checked)
{
value = calc.GetMz(seq, 1);
}
else
{
value = calc.GetMass(seq);
}
txtResult.Text = value.ToString();
}
private void init(String modifiedAminoacids, String sequence,
char modifiedSign)
{
String matchSequence = PeptideUtils.GetMatchedSequence(sequence);
this.pureSequence = PeptideUtils.GetPureSequence(matchSequence);
modifiedCount = 0;
for (int i = 0; i < matchSequence.Length; i++)
{
char c = matchSequence[i];
if (char.IsLetter(c) && char.IsUpper(c))
{
sites.Add(new Pair <char, char>(c, ' '));
}
else if (isCandidateModifiedAminoacid(modifiedAminoacids,
getLastPair().First))
{
if (modifiedSign == ' ')
{
getLastPair().Second = c;
}
else
{
getLastPair().Second = modifiedSign;
}
modifiedCount++;
}
}
calculate();
}
public override IEnumerable <string> Process(string fileName)
{
MascotResultTextFormat format = new MascotResultTextFormat();
IIdentifiedResult ir = format.ReadFromFile(fileName);
List <IIdentifiedSpectrum> spectra = ir.GetSpectra();
spectra.ForEach(m =>
{
for (int i = m.Peptides.Count - 1; i >= 0; i--)
{
IIdentifiedPeptide peptide = m.Peptides[i];
string seq = PeptideUtils.GetMatchedSequence(peptide.Sequence);
if (!validator.Validate(seq))
{
m.RemovePeptideAt(i);
peptide.Spectrum = null;
}
}
});
ir.Filter(m =>
{
return(m.Spectrum != null);
});
string result = fileName + ".Labeled";
format.WriteToFile(result, ir);
return(new[] { result });
}
public void CreateTargetsFromEmpiricalFormulaOnlyLargePeptideTest1()
{
var util = new IqTargetUtilities();
var peptideSequence =
"PEPITIDEPEPITIDEPEPITIDEPEPITIDEPEPITIDEPEPITIDEPEPITIDEPEPITIDEPEPITIDEPEPITIDEPEPITIDEPEPITIDEPEPITIDEPEPITIDEPEPITIDEPEPITIDEPEPITIDEPEPITIDEPEPITIDEPEPITIDEPEPITIDEPEPITIDEPEPITIDEPEPITIDEPEPITIDE";
var peptideUtil = new PeptideUtils();
var empiricalFormula = peptideUtil.GetEmpiricalFormulaForPeptideSequence(peptideSequence);
var formulas = new string[] { empiricalFormula };
var targets = util.CreateTargets(formulas);
foreach (var parentTarget in targets)
{
Console.WriteLine(parentTarget.ID + "\t" + parentTarget.MonoMassTheor.ToString("0.00000") + "\tNumChildren= " + parentTarget.ChildTargets().Count());
if (parentTarget.HasChildren())
{
foreach (var childTarget in parentTarget.ChildTargets())
{
Console.WriteLine("\t\t\t" + childTarget.ID + "\t" + childTarget.MonoMassTheor.ToString("0.00000") + "\t" +
childTarget.MZTheor.ToString("0.00000") + "\t" + childTarget.ChargeState + "\t" + (1.00235d / childTarget.ChargeState).ToString("0.0000"));
}
}
}
}
/// <summary>
/// 根据序列构建氨基酸信息列表。该信息列表中已将修饰质量加到氨基酸上，可方便地用于构建离子列表。
/// </summary>
/// <param name="sequence">氨基酸序列，包含修饰字符。</param>
/// <returns>氨基酸信息列表</returns>
public List <AminoacidInfo> BuildInfo(string sequence)
{
var matchedSequence = PeptideUtils.GetMatchedSequence(sequence);
var result = new List <AminoacidInfo>();
foreach (char c in matchedSequence)
{
if (char.IsLetter(c) && char.IsUpper(c))
{
var aai = new AminoacidInfo();
aai.Aminoacid = c;
aai.Modification = ' ';
aai.Mass = this[c].MonoMass;
result.Add(aai);
}
else
{
AminoacidInfo aai = result.Last();
aai.Modification = c;
aai.Mass += this[c].MonoMass;
}
}
return(result);
}
public override IEnumerable <string> Process(string fileName)
{
var peptides = new MascotPeptideTextFormat().ReadFromFile(fileName);
var seqs = (from p in peptides
let pep = p.Peptide
select PeptideUtils.GetMatchedSequence(pep.Sequence)).ToList();
var nmod = (from seq in seqs
where !char.IsLetter(seq[0])
select seq).Count();
var kseqs = (from seq in seqs
where seq.Contains(modificationAminoacid)
select seq).Count();
var kmod = (from seq in seqs
where seq.Contains(modificationAminoacid) && IsFullModifiedK(seq)
select seq).Count();
var result = fileName + ".labelingEfficiency";
using (StreamWriter sw = new StreamWriter(result))
{
sw.WriteLine("Total PSMs\t{0}", peptides.Count);
sw.WriteLine("N-terminal modified PSMs\t{0}", nmod);
sw.WriteLine("{0}-contained PSMs\t{1}", modificationAminoacid, kseqs);
sw.WriteLine("{0}-full-modified PSMs\t{2}", modificationAminoacid, kmod);
}
return(new string[] { result });
}
public void checkModImport_Test1()
{
var importer = new MassTagFromSqlDbImporter("MT_Shewanella_ProdTest_P352", "porky", _targetIDList);
var targetCollection = importer.Import();
var testPeptide1 = (PeptideTarget)targetCollection.TargetList[70];
Assert.AreEqual(72, targetCollection.TargetList.Count);
Assert.AreEqual(189684639, testPeptide1.ID);
Assert.AreEqual("QALYEAENVLRDEQIALQK", testPeptide1.Code);
Assert.AreEqual(2213.1326995m, (decimal)testPeptide1.MonoIsotopicMass);
Assert.AreEqual(1, testPeptide1.ModCount);
Assert.AreEqual("NH3_Loss:1", testPeptide1.ModDescription);
Assert.AreEqual(true, testPeptide1.ContainsMods);
Assert.AreEqual(696, testPeptide1.ObsCount);
var peptideUtils = new PeptideUtils();
Assert.AreEqual("C97H159N27O33", peptideUtils.GetEmpiricalFormulaForPeptideSequence(testPeptide1.Code));
Assert.AreNotEqual("C97H159N27O33", testPeptide1.EmpiricalFormula);
Assert.AreEqual("C97H156N26O33", testPeptide1.EmpiricalFormula);
}
public void GetEmpiricalFormulaForAminoAcidTest1()
{
var utils = new PeptideUtils();
var testAminoAcid = 'A';
Assert.AreEqual("C3H5NO", utils.GetEmpiricalFormulaForAminoAcidResidue(testAminoAcid));
}
public string GetMatchSequence()
{
if (this.Peptides.Count == 0)
{
return("");
}
return(PeptideUtils.GetMatchedSequence(this.Peptides[0].Sequence));
}
public void GenerateIsotopicProfileTest1()
{
var peptideUtils = new PeptideUtils();
var empiricalFormula = peptideUtils.GetEmpiricalFormulaForPeptideSequence("SAMPLERSAMPLER");
var featureGenerator = new JoshTheorFeatureGenerator();
}
public void GetIsotopicProfileTest2()
{
var peptideUtils = new PeptideUtils();
var empFormula = "S3";
var isoCalc = IsotopicDistributionCalculator.Instance;
var iso = isoCalc.GetIsotopePattern(empFormula);
TestUtilities.DisplayIsotopicProfileData(iso);
}
public void GetIsotopicProfileTest1()
{
var peptideUtils = new PeptideUtils();
var empFormula = peptideUtils.GetEmpiricalFormulaForPeptideSequence("SAMPLERSAMPLER");
var isoCalc = IsotopicDistributionCalculator.Instance;
var iso = isoCalc.GetIsotopePattern(empFormula);
TestUtilities.DisplayIsotopicProfileData(iso);
}
private void InitTheoreticalPeaks()
{
Aminoacids aas = new Aminoacids();
aas.SetModification(StaticModification);
aas.SetModification(DynamicModification);
CIDFragmentationBuilder <MatchedPeak> builder = new CIDFragmentationBuilder <MatchedPeak> (ExperimentalPeakList.PrecursorCharge, aas);
ionSeries = builder.GetIonSeries(PeptideUtils.GetMatchedSequence(Peptide));
}
public void GetMonoisotopicMassFromEmpiricalFormulaTest1()
{
var testPeptide = "SAMPLER";
var peptideUtils = new PeptideUtils();
var formula = peptideUtils.GetEmpiricalFormulaForPeptideSequence(testPeptide);
var monomass = EmpiricalFormulaUtilities.GetMonoisotopicMassFromEmpiricalFormula(formula);
Assert.IsTrue(monomass > 0);
Console.WriteLine("SAMPLER monoisotopic mass= \t" + monomass);
Assert.AreEqual(802.40072m, (decimal)Math.Round(monomass, 5)); //note that Peptide Util reports 802.40071, as does MacCoss's lab: http://proteome.gs.washington.edu/cgi-bin/aa_calc.pl
}
protected void CheckTerminalExtension(List <SapPredicted> predicted, MS2Item query, MS2Item libms2, SapMatchedCount ms3match)
{
var bNterminalValid = libms2.Peptide.StartsWith("-");
var bCterminalValid = libms2.Peptide.EndsWith("-");
if (bNterminalValid || bCterminalValid)
{
foreach (var ne in options.ExtensionDeltaMassList)
{
var neMz = libms2.Precursor + ne.DeltaMass / libms2.Charge;
if (neMz >= query.MinPrecursorMz && neMz <= query.MaxPrecursorMz)
{
var seq = PeptideUtils.GetPureSequence(libms2.Peptide);
if (bNterminalValid)
{
predicted.Add(new SapPredicted()
{
Ms2 = query,
LibMs2 = libms2,
Matched = ms3match,
Target = new TargetVariant()
{
Source = PeptideUtils.GetPureSequence(libms2.Peptide),
Target = new HashSet <string>(from t in ne.Target select t + seq),
DeltaMass = ne.DeltaMass,
TargetType = VariantType.NTerminalExtension
}
});
}
if (bCterminalValid)
{
predicted.Add(new SapPredicted()
{
Ms2 = query,
LibMs2 = libms2,
Matched = ms3match,
Target = new TargetVariant()
{
Source = PeptideUtils.GetPureSequence(libms2.Peptide),
Target = new HashSet <string>(from t in ne.Target select seq + t),
DeltaMass = ne.DeltaMass,
TargetType = VariantType.CTerminalExtension
}
});
}
}
}
}
}
private void ValidateModifications(string seq)
{
char[] modifiedChars = PeptideUtils.GetModifiedChar(seq);
if (modifiedChars.Length > 0)
{
foreach (char c in modifiedChars)
{
if (!_sciBuilder.IsModificationDefined(c))
{
throw new ArgumentException(MyConvert.Format("Modification {0} was not defined in SILAC configuration file : {1}.", c, option.SilacParamFile));
}
}
}
}
private List <string> GetIdentifiedSpectrumKey(IIdentifiedSpectrum spectrum, SilacCompoundInfo sci)
{
int theoreticalMass = (int)(sci.Light.Mz * sci.Light.Charge + 0.5);
int charge = spectrum.Charge;
List <string> keys = new List <string>();
foreach (IIdentifiedPeptide peptide in spectrum.Peptides)
{
string sequenceCharge = PeptideUtils.GetPureSequence(peptide.Sequence) + "." + charge + "." + theoreticalMass;
keys.Add(sequenceCharge);
}
return(keys);
}
public void addUnimodFormulaTest1()
{
var testPeptide = "SAMPLER";
var peptideUtils = new PeptideUtils();
var baseFormula = peptideUtils.GetEmpiricalFormulaForPeptideSequence(testPeptide);
var mod = "H3 C2 N O";
var modFormula = EmpiricalFormulaUtilities.AddFormula(baseFormula, mod);
Console.WriteLine("Unmodified peptide= " + baseFormula);
Console.WriteLine("Modified peptide= " + modFormula);
Assert.AreEqual("C35H61N11O12S", modFormula);
}
private string GetModificationCount(IIdentifiedPeptide pep, string p)
{
var result = 0;
var matchedSeq = PeptideUtils.GetMatchedSequence(pep.Sequence);
for (int i = 0; i < matchedSeq.Length - 1; i++)
{
if (p.Contains(matchedSeq[i]) && !Char.IsLetter(matchedSeq[i + 1]))
{
result++;
i++;
}
}
return(result.ToString());
}
public void InitTerminalLoss(Aminoacids aa, int maxTerminalLossLength, int minSequenceLength)
{
this.TerminalLoss = new List <TerminalLossItem>();
var seq = PeptideUtils.GetMatchedSequence(this.Peptide);
var pureseq = PeptideUtils.GetPureSequence(this.Peptide);
var pos = 0;
var index = 0;
var maxIndex = Math.Min(maxTerminalLossLength, pureseq.Length - minSequenceLength);
var deltaMass = 0.0;
while (index < maxIndex)
{
deltaMass += aa[seq[pos]].MonoMass;
if (!char.IsUpper(seq[pos + 1]))
{
pos++;
continue;
}
index++;
pos++;
var precursorLoss = this.Precursor - deltaMass / this.Charge;
this.TerminalLoss.Add(new TerminalLossItem(true, pureseq.Substring(index), precursorLoss));
}
index = 0;
pos = seq.Length - 1;
deltaMass = 0.0;
while (index < maxIndex)
{
deltaMass += aa[seq[pos]].MonoMass;
if (!char.IsUpper(seq[pos]))
{
pos--;
continue;
}
index++;
pos--;
var precursorLoss = this.Precursor - deltaMass / this.Charge;
this.TerminalLoss.Add(new TerminalLossItem(false, pureseq.Substring(0, pureseq.Length - index), precursorLoss));
}
}
public void getN15IsotopicProfileTest1()
{
var isIt = isotopicDistributionCalculator.IsSetToLabeled;
var utils = new PeptideUtils();
//string formula = utils.GetEmpiricalFormulaForPeptideSequence("SAMPLERPAMPLERSAMPLERPAMPLERSAMPLERPAMPLERSAMPLERPAMPLER");
var formula = utils.GetEmpiricalFormulaForPeptideSequence("SAMPLERPAMPLERSAMPLERPAMPLER");
var numNitrogens = utils.GetNumAtomsForElement("N", formula);
var iso1 = isotopicDistributionCalculator.GetIsotopePattern(formula);
PeakUtilities.TrimIsotopicProfile(iso1, 0.001);
TestUtilities.DisplayIsotopicProfileData(iso1);
isotopicDistributionCalculator.SetLabeling("N", 14, 0.02, 15, 0.98);
var iso2 = isotopicDistributionCalculator.GetIsotopePattern(formula);
//PeakUtilities.TrimIsotopicProfile(iso2, 0.001);
isotopicDistributionCalculator.ResetToUnlabeled();
var iso3 = isotopicDistributionCalculator.GetIsotopePattern(formula);
PeakUtilities.TrimIsotopicProfile(iso3, 0.001);
Console.WriteLine();
TestUtilities.DisplayIsotopicProfileData(iso2);
for (var i = 0; i < iso1.Peaklist.Count; i++)
{
Assert.AreEqual((decimal)Math.Round(iso1.Peaklist[i].Height, 4), (decimal)Math.Round(iso3.Peaklist[i].Height, 4));
}
Console.WriteLine();
TestUtilities.DisplayIsotopicProfileData(iso3);
Console.WriteLine("Num nitrogens= " + numNitrogens);
}
public void GetEmpiricalFormulaForPeptideSequenceTest2()
{
var utils = new PeptideUtils();
var testSequence1 = "IPNFWVTTFVNHPQVSALLGEEDEEALHYLTR";
var testSequence2 = "K.IPNFWVTTFVNHPQVSALLGEEDEEALHYLTR*.V";
var empiricalFormula1 = utils.GetEmpiricalFormulaForPeptideSequence(testSequence1);
var empiricalFormula2 = utils.GetEmpiricalFormulaForPeptideSequence(testSequence2);
Assert.AreEqual(empiricalFormula1, empiricalFormula2);
Assert.AreEqual((decimal)Math.Round(utils.GetMonoIsotopicMassForPeptideSequence(testSequence1), 5), (decimal)Math.Round(utils.GetMonoIsotopicMassForPeptideSequence(testSequence2), 5));
}
public List <IqTarget> Import()
{
var targets = GetMassTagDataFromDb();
if (IsEmpiricalFormulaExtracted)
{
GetModDataFromDb(_targetsContainingMods);
var peptideUtils = new PeptideUtils();
foreach (IqTargetDms iqTarget in targets)
{
var baseEmpiricalFormula = peptideUtils.GetEmpiricalFormulaForPeptideSequence(iqTarget.Code);
if (!string.IsNullOrEmpty(iqTarget.ModDescription))
{
var target = iqTarget;
var mods = (from n in _massTagModData where n.Item1 == target.ID select n);
foreach (var tuple in mods)
{
var modString = tuple.Item4;
try
{
baseEmpiricalFormula = EmpiricalFormulaUtilities.AddFormula(baseEmpiricalFormula, modString);
}
catch (Exception ex)
{
IqLogger.Log.Debug("Failed to calculate empirical formula for the Target " + target.ID + " (" + ex.Message + ")" +
"; Having trouble with the mod: " + modString + "; This Target was NOT imported!!");
}
}
}
iqTarget.EmpiricalFormula = baseEmpiricalFormula;
if (IsMonoMassCalculatedFromEmpiricalFormula)
{
iqTarget.MonoMassTheor = EmpiricalFormulaUtilities.GetMonoisotopicMassFromEmpiricalFormula(iqTarget.EmpiricalFormula);
}
}
}
return(targets);
}
public string GetPhosphoModificationString(string peptide)
{
string matchedSequence = PeptideUtils.GetMatchedSequence(peptide);
StringBuilder result = new StringBuilder();
for (int i = 0; i < matchedSequence.Length; i++)
{
if (!PeptideUtils.IsAminoacid(matchedSequence[i]))
{
continue;
}
if (IsPhospho(matchedSequence, i))
{
result.Append(matchedSequence[i]);
}
}
return(result.ToString());
}
/// <summary>
/// 根据原始蛋白质的序列，替换搜库结果中突变序列中对应位置的L为I
/// </summary>
/// <param name="mutSeq">搜库结果突变序列</param>
/// <param name="oriPureSeq">原始蛋白质纯序列</param>
/// <returns>修正后的突变序列</returns>
public static string ReplaceLToI(string mutSeq, string oriPureSeq)
{
if (!oriPureSeq.Contains('I'))
{
return(mutSeq);
}
string mutPureSeq = PeptideUtils.GetPureSequence(mutSeq);
StringBuilder mutPureSeqSb = new StringBuilder(mutPureSeq);
for (int i = 0; i < oriPureSeq.Length && i < mutPureSeq.Length; i++)
{
if (oriPureSeq[i] == 'I' && mutPureSeqSb[i] == 'L')
{
mutPureSeqSb[i] = oriPureSeq[i];
}
}
StringBuilder mutSeqSb = new StringBuilder(mutSeq);
int curIndex = 0;
if (mutSeq.Contains('.'))
{
for (int i = 2; i < mutSeqSb.Length - 2; i++)
{
if (char.IsLetter(mutSeqSb[i]) && char.IsUpper(mutSeqSb[i]))
{
mutSeqSb[i] = mutPureSeqSb[curIndex++];
}
}
}
else
{
for (int i = 0; i < mutSeqSb.Length; i++)
{
if (char.IsLetter(mutSeqSb[i]) && char.IsUpper(mutSeqSb[i]))
{
mutSeqSb[i] = mutPureSeqSb[curIndex++];
}
}
}
return(mutSeqSb.ToString());
}
public void AddPhosphorylationTest1()
{
const string testPeptide = "SAMPLER";
var peptideUtils = new PeptideUtils();
var formula = peptideUtils.GetEmpiricalFormulaForPeptideSequence(testPeptide);
const string phosphorylationMod = "HPO3";
var empiricalFormula = EmpiricalFormulaUtilities.AddFormula(formula, phosphorylationMod);
var massUnmodified = EmpiricalFormulaUtilities.GetMonoisotopicMassFromEmpiricalFormula(formula);
var massModified = EmpiricalFormulaUtilities.GetMonoisotopicMassFromEmpiricalFormula(empiricalFormula);
var diff = Math.Round(massModified - massUnmodified, 1, MidpointRounding.AwayFromZero);
Console.WriteLine(formula + "\t" + massUnmodified);
Console.WriteLine(empiricalFormula + "\t" + massModified);
Console.WriteLine("diff= " + diff);
Assert.AreEqual(80.0, diff);
}
public void PyroglutamateTest1()
{
const string testPeptide = "SAMPLER";
var peptideUtils = new PeptideUtils();
var formula = peptideUtils.GetEmpiricalFormulaForPeptideSequence(testPeptide);
const string pyroglutamateMod = "H3N1";
var empiricalFormula = EmpiricalFormulaUtilities.SubtractFormula(formula, pyroglutamateMod);
var massUnmodified = EmpiricalFormulaUtilities.GetMonoisotopicMassFromEmpiricalFormula(formula);
var massModified = EmpiricalFormulaUtilities.GetMonoisotopicMassFromEmpiricalFormula(empiricalFormula);
var diff = Math.Round(massModified - massUnmodified, 1, MidpointRounding.AwayFromZero);
Console.WriteLine(formula + "\t" + massUnmodified);
Console.WriteLine(empiricalFormula + "\t" + massModified);
Console.WriteLine("diff= " + diff);
Assert.AreEqual(-17.0, diff);
}
