/// <summary>
/// Check if iso cyanic acid loss is present in the spectrum's MS1 scan.
/// </summary>
/// <param name="spectrum">The spectrum to be checked.</param>
/// <returns>True, if isocyanic acid is present; Otherwise, false.</returns>
private static bool IsIsoCyanicAcidLossPresentMs1(MsSpectrum spectrum)
{
// Get the precursor m/z value
double precursorMz = spectrum.PreCursorMz;
// Loop through all of the M/Z-values
foreach (double mzVal in spectrum.ParentScan.MzValues)
{
// Check that the m/z is not greater than the precursor, because the code is looking for an loss i.e. a value less than the precursor
// TODO: Maybe insert to increase speed.
//if(mzVal > precursorMz) { break; }
// Check if the isocyanic neutral loss is present.
if (HelperUtilities.IsApproximately(mzVal, precursorMz - 43, ScoreSettings.CyanicLossTolerance))
{
// The isocyanic netural loss ion is found
// If that is the case set the M/Z value of the ion
spectrum.IsoCyanicMzMs1 = mzVal;
// Return true, because the ion was found
return(true);
}
}
// No loss was found. Set the m/z value for the loss ion to an impossible value
spectrum.IsoCyanicMzMs1 = -1;
// Return false, because no ion was found
return(false);
}
/// <summary>
/// Check weather the spectrum has the correct mass shift.
/// </summary>
/// <param name="citMz">The m/z value for the citrullinated spectrum.</param>
/// <param name="argMz">The m/z value for the arginine spectrum.</param>
/// <param name="fragMassError">The fragment mass error. Used to calculate the tolerance.</param>
/// <param name="containsCit">Indicates that the ion contains the citrullination.</param>
/// <returns>True, if has correct mass shift; Otherwise, false.</returns>
private static bool HasCorrectCitMassShift(double citMz, double argMz, double fragMassError, bool containsCit)
{
// Determine whether the ion contains the citrullination
if (containsCit)
{
// Citrullination. The cit M/Z should be 0.984 heavier than Arg M/Z
return(HelperUtilities.IsApproximately(citMz - 0.984, argMz, fragMassError / 5));
}
else
{
// No citrullination. The cit M/Z and Arg M/Z should be equal
return(HelperUtilities.IsApproximately(citMz, argMz, fragMassError / 5));
}
}
/// <summary>
/// Check if list of isocyanic loss contains a certain m/z-value.
/// </summary>
/// <param name="cyanlossMz">The list of isocyanic losses.</param>
/// <param name="mzVal">The M/Z-value to be checked.</param>
/// <returns>True, if list contains the iso cyanic loss; Otherwise, false.</returns>
private static bool IsoListContains(List <double> cyanlossMz, double mzVal)
{
// Loop through all of the values
foreach (double cyanLossMz in cyanlossMz)
{
// If an loss m/z is approx. equal to the M/Z-value to be checked, return true
if (HelperUtilities.IsApproximately(cyanLossMz + 43, mzVal, ScoreSettings.CyanicLossTolerance))
{
return(true);
}
}
// If the item is not found
return(false);
}
/// <summary>
/// Update the window
/// </summary>
/// <param name="result"></param>
internal void UpdateWindow(QuantResult result)
{
_result = result;
GetSpectra(_result);
SetCitInfo();
ValidationUIUtilities.ClearChart(chartMS1);
ValidationUIUtilities.ClearChart(chartMS2);
ValidationUIUtilities.CreateMS1Chart(chartMS1, citSpectrum);
ValidationUIUtilities.CreateLoneCitMs2Chart(chartMS2, citSpectrum);
ValidationUIUtilities.FillIonGridGeneral(metroGridCitIons, citSpectrum, HelperUtilities.CreateAAArray(_result.Sequence));
if (Quantification.QuantificationResults.Contains(result))
{
metroButtonAddQuant.Enabled = false;
metroButtonRemoveQuant.Enabled = true;
}
else
{
metroButtonAddQuant.Enabled = true;
metroButtonRemoveQuant.Enabled = false;
}
}
/// <summary>
/// Update the quantification window.
/// </summary>
/// <param name="result">The quantification result.</param>
internal void UpdateWindow(QuantResult result)
{
// Set the result
_result = result;
// Get the spectra
GetSpectra(_result);
// Add the info
SetCitInfo();
SetArgInfo();
// Clear the charts
ValidationUIUtilities.ClearChart(chartArgMS1);
ValidationUIUtilities.ClearChart(chartCitMS1);
ValidationUIUtilities.ClearChart(chartMS2);
// Create the charts
ValidationUIUtilities.CreateMS1Chart(chartArgMS1, argSpectrum);
ValidationUIUtilities.CreateMS1Chart(chartCitMS1, citSpectrum);
ValidationUIUtilities.CreatePairedMs2Chart(chartMS2, citSpectrum, argSpectrum);
// Create the ion grid
ValidationUIUtilities.FillIonGridGeneral(metroGridArgIons, argSpectrum, HelperUtilities.CreateAAArray(_result.Sequence));
ValidationUIUtilities.FillIonGridGeneral(metroGridCitIons, citSpectrum, HelperUtilities.CreateAAArray(_result.Sequence));
// Set the title and spectrum ID
labelTitel.Text = string.Format("Quantification - Paired (By {0})", _result.ValidationBy);
metroLabelCitSpectrumID.Text = _result.CitSpectrumID.ToString();
metroLabelArgSpectrumID.Text = _result.ArgSpectrumID.ToString();
if (Quantification.QuantificationResults.Contains(result))
{
metroButtonAddQuant.Enabled = false;
metroButtonRemoveQuant.Enabled = true;
}
else
{
metroButtonAddQuant.Enabled = true;
metroButtonRemoveQuant.Enabled = false;
}
}
/// <summary>
/// Count the presence of isocyanic acid loss on MS2.
/// </summary>
/// <param name="citSpectrum">The citrullinated spectrum.</param>
/// <param name="citIndex">The index of the citrullinated arginine.</param>
/// <param name="aaSeq">The amino acid sequence.</param>
/// <returns>The number of isocyanic acid losses.</returns>
private static double CountIsoCyanicAcidLossPresentMs2(MsSpectrum citSpectrum, int citIndex, string[] aaSeq)
{
// Create temporay list of isocyanic loss M/Z
List <double> cyanlossMz = new List <double>();
// Create scores
int aIonCount = 0;
int bIonCount = 0;
int b17IonCount = 0;
int b18IonCount = 0;
int yIonCount = 0;
int y17IonCount = 0;
int y18IonCount = 0;
List <double> mzValues = citSpectrum.MzValues.ToList();
mzValues.Reverse();
foreach (double mzVal in mzValues)
{
// Loop through the all of amino acid sequence.However only the index is used.
for (int i = 0; i < aaSeq.Length; i++)
{
if (IsoListContains(cyanlossMz, mzVal))
{
continue;
}
// Check that the this is the citrullinated a- or b-ions. The aa index is greater than or equal to the index of the citrullination.
if (i >= citIndex)
{
// Check that both spectra contains the A-ion at this specific amino acid
if (citSpectrum.AIonIndex.Contains(i))
{
/* Calculate A-ion */
// Get the M/Z value for A-ion on the complementary citrullinated spectrum
double citMz = citSpectrum.SpectrumPossibleAIons[i];
// If the spectrum has an ion that is 43 Da less than the cit spectrum, add the spectrum m/z to the list
if (HelperUtilities.IsApproximately(mzVal, citMz - 43, ScoreSettings.CyanicLossTolerance))
{
cyanlossMz.Add(mzVal);
aIonCount++;
continue;
}
}
// Check that both spectra contains the B-ion at this specific amino acid
if (citSpectrum.BIonIndex.Contains(i))
{
/* Calculate B-ion */
// Get the M/Z value for B-ion on the complementary citrullinated spectrum
double citMz = citSpectrum.SpectrumPossibleBIons[i];
// If the spectrum has an ion that is 43 Da less than the cit spectrum, add the spectrum m/z to the list
if (HelperUtilities.IsApproximately(mzVal, citMz - 43, ScoreSettings.CyanicLossTolerance))
{
cyanlossMz.Add(mzVal);
bIonCount++;
continue;
}
}
// Check that both spectra contains the B-17 ion at this specific amino acid
if (citSpectrum.B17IonIndex.Contains(i))
{
/* Calculate B-17 ion */
// Get the M/Z value for B-17 ion on the complementary citrullinated spectrum
double citMz = citSpectrum.SpectrumPossibleBm17Ions[i];
// If the spectrum has an ion that is 43 Da less than the cit spectrum, add the spectrum m/z to the list
if (HelperUtilities.IsApproximately(mzVal, citMz - 43, ScoreSettings.CyanicLossTolerance))
{
cyanlossMz.Add(mzVal);
b17IonCount++;
continue;
}
}
// Check that both spectra contains the B-18 ion at this specific amino acid
if (citSpectrum.B18IonIndex.Contains(i))
{
/* Calculate B-18 ion */
// Get the M/Z value for B-18 ion on the complementary citrullinated spectrum
double citMz = citSpectrum.SpectrumPossibleBm18Ions[i];
// If the spectrum has an ion that is 43 Da less than the cit spectrum, add the spectrum m/z to the list
if (HelperUtilities.IsApproximately(mzVal, citMz - 43, ScoreSettings.CyanicLossTolerance))
{
cyanlossMz.Add(mzVal);
b18IonCount++;
continue;
}
}
}
// Check that the this is the citrullinated y-ion. The aa index is less than or equal to the index of the citrullination.
if (i <= citIndex)
{
// Check that both spectra contains the Y-ion at this specific amino acid
if (citSpectrum.YIonIndex.Contains(i))
{
/* Calculate Y-ion */
// Get the M/Z value for Y-ion on the complementary citrullinated spectrum
double citMz = citSpectrum.SpectrumPossibleYIons[i];
// If the spectrum has an ion that is 43 Da less than the cit spectrum, add the spectrum m/z to the list
if (HelperUtilities.IsApproximately(mzVal, citMz - 43, ScoreSettings.CyanicLossTolerance))
{
cyanlossMz.Add(mzVal);
yIonCount++;
continue;
}
}
// Check that both spectra contains the Y-17 ion at this specific amino acid
if (citSpectrum.Y17IonIndex.Contains(i))
{
/* Calculate Y-17 ion */
// Get the M/Z value for Y-17 ion on the complementary citrullinated spectrum
double citMz = citSpectrum.SpectrumPossibleYm17Ions[i];
// If the spectrum has an ion that is 43 Da less than the cit spectrum, add the spectrum m/z to the list
if (HelperUtilities.IsApproximately(mzVal, citMz - 43, ScoreSettings.CyanicLossTolerance))
{
cyanlossMz.Add(mzVal);
y17IonCount++;
continue;
}
}
// Check that both spectra contains the Y-18 ion at this specific amino acid
if (citSpectrum.Y18IonIndex.Contains(i))
{
/* Calculate Y-18 ion */
// Get the M/Z value for Y-18 ion on the complementary citrullinated spectrum
double citMz = citSpectrum.SpectrumPossibleYm18Ions[i];
// If the spectrum has an ion that is 43 Da less than the cit spectrum, add the spectrum m/z to the list
if (HelperUtilities.IsApproximately(mzVal, citMz - 43, ScoreSettings.CyanicLossTolerance))
{
cyanlossMz.Add(mzVal);
y18IonCount++;
continue;
}
}
}
}
}
// Set collection
citSpectrum.IsoCyanicLossMzMs2 = cyanlossMz.ToArray();
// Calculate score
double score = aIonCount * ScoreSettings.MS2IsoCyanLossAScore;
score += bIonCount * ScoreSettings.MS2IsoCyanLossBScore;
score += b17IonCount * (ScoreSettings.MS2IsoCyanLossBScore / ScoreSettings.MS2IsoCyanOnLossScoreDivider);
score += b18IonCount * (ScoreSettings.MS2IsoCyanLossBScore / ScoreSettings.MS2IsoCyanOnLossScoreDivider);
score += yIonCount * ScoreSettings.MS2IsoCyanLossYScore;
score += y17IonCount * (ScoreSettings.MS2IsoCyanLossYScore / ScoreSettings.MS2IsoCyanOnLossScoreDivider);
score += y18IonCount * (ScoreSettings.MS2IsoCyanLossYScore / ScoreSettings.MS2IsoCyanOnLossScoreDivider);
// TODO: Set score instead of count
//return cyanlossMz.Count;
return(score);
}
/// <summary>
/// Create the image.
/// </summary>
/// <param name="directory">The directory the image should be saved to.</param>
/// <param name="result">The result the image should be created from.</param>
private void CreateImage(string directory, KeyValuePair <QuantResult, KeyValuePair <MsSpectrum, MsSpectrum> > result)
{
KeyValuePair <MsSpectrum, MsSpectrum> spectraData = result.Value;
// Get the filename
string baseFilename = string.Format("{0}_{1}_{2}", result.Key.Protein.Split('|')[0], result.Key.Sequence, result.Key.ValidationBy);
string filename = FileReader.GenerateFileName(directory, baseFilename, "tiff");
// Append the file to the annotation writer
if (_createAnnotationFile)
{
_annotationWriter.AppendLine($"** {filename.Split(new string[] { @"\" }, System.StringSplitOptions.None).Last() } **");
}
// From the validation type, create the graph
if (result.Key.ValidationBy == "Lone")
{
ValidationUIUtilities.CreateLoneCitMs2Chart(chartMS2, spectraData.Key);
ValidationUIUtilities.AnnotateSingleSpectra(chartMS2, spectraData.Key, HelperUtilities.CreateAAArray(result.Key.Sequence), true, _createAnnotationFile, _annotationWriter);
}
else
{
ValidationUIUtilities.CreatePairedMs2Chart(chartMS2, spectraData.Key, spectraData.Value);
ValidationUIUtilities.AnnotatePairedSpectra(chartMS2, spectraData.Key, spectraData.Value, HelperUtilities.CreateAAArray(result.Key.Sequence), _createAnnotationFile, _annotationWriter);
}
// Clear the old titles
chartMS2.Titles.Clear();
// And add a new one
chartMS2.Titles.Add(string.Format("{0}_{1}_{2}", result.Key.Protein.Split('|')[0], result.Key.Sequence, result.Key.ValidationBy));
chartMS2.Titles[0].Font = new Font(chartMS2.Titles[0].Font.FontFamily, 13F);
chartMS2.Titles[0].IsDockedInsideChartArea = false;
chartMS2.Titles[0].Docking = Docking.Top;
chartMS2.Titles[0].DockingOffset = 10;
chartMS2.SaveImage(filename, ChartImageFormat.Tiff);
ValidationUIUtilities.ClearChart(chartMS2);
chartMS2.Annotations.Clear();
}