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clsITraqIntensityCorrection.cs
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clsITraqIntensityCorrection.cs
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using System;
namespace MASIC
{
// ReSharper disable CommentTypo
/// <summary>
/// <para>
/// This class corrects the intensities of iTraq or TMT data, based on the expected overlapping isotopic distributions
/// It supports 4-plex and 8-plex iTraq
/// It also supports TMT10, TMT11, and TMT16 (aka TMTpro)
/// </para>
/// <para>
/// The isotopic distribution weights are provided by the iTraq or TMT manufacturer
/// </para>
/// </summary>
/// <remarks>
/// There are two options for the iTRAQ 4-plex weights:
/// CorrectionFactorsiTRAQ4Plex.ABSciex
/// CorrectionFactorsiTRAQ4Plex.BroadInstitute
/// </remarks>
// ReSharper restore CommentTypo
public class clsITraqIntensityCorrection
{
// ReSharper disable CommentTypo
// Ignore Spelling: Biosystems, Da, Mertins, Philipp, plex, Proteomics, Sciex, Sickmann, Vaudel
private const int FOUR_PLEX_MATRIX_LENGTH = 4;
private const int EIGHT_PLEX_HIGH_RES_MATRIX_LENGTH = 8;
private const int EIGHT_PLEX_LOW_RES_MATRIX_LENGTH = 9;
private const int TEN_PLEX_TMT_MATRIX_LENGTH = 10;
private const int ELEVEN_PLEX_TMT_MATRIX_LENGTH = 11;
private const int SIXTEEN_PLEX_TMT_MATRIX_LENGTH = 16;
// ReSharper disable IdentifierTypo
/// <summary>
/// 4-plex iTRAQ correction factor type
/// </summary>
public enum CorrectionFactorsiTRAQ4Plex
{
/// <summary>
/// AB Sciex
/// </summary>
ABSciex = 0,
/// <summary>
/// Broad Institute
/// </summary>
/// <remarks>
/// Provided by Philipp Mertins at the Broad Institute ([email protected])
/// </remarks>
BroadInstitute = 1
}
// ReSharper restore IdentifierTypo
// ReSharper restore CommentTypo
private struct IsotopeContributionType
{
public float Minus2;
public float Minus1;
public float Zero;
public float Plus1;
public float Plus2;
public override string ToString()
{
return string.Format("{0:F2} {1:F2} {2:F2} {3:F2} {4:F2}", Minus2, Minus1, Zero, Plus1, Plus2);
}
}
/// <summary>
/// Matrix of coefficients, derived from the isotope contribution table
/// </summary>
// ReSharper disable once IdentifierTypo
private double[,] mCoeffs;
private readonly MatrixDecompositionUtility.LUDecomposition mMatrixUtility;
/// <summary>
/// Reporter ion mode
/// </summary>
public clsReporterIons.ReporterIonMassModeConstants ReporterIonMode { get; private set; }
/// <summary>
/// 4-plex iTRAQ correction factor type
/// </summary>
public CorrectionFactorsiTRAQ4Plex ITraq4PlexCorrectionFactorType { get; private set; }
/// <summary>
/// Constructor that assumes iTraqCorrectionFactorType = ABSciex
/// </summary>
/// <param name="reporterIonMode">iTRAQ or TMT mode</param>
public clsITraqIntensityCorrection(clsReporterIons.ReporterIonMassModeConstants reporterIonMode)
: this(reporterIonMode, CorrectionFactorsiTRAQ4Plex.ABSciex)
{
}
/// <summary>
/// Constructor
/// </summary>
/// <param name="reporterIonMode">iTRAQ or TMT mode</param>
/// <param name="iTraqCorrectionFactorType">Correction factor type for 4-plex iTRAQ</param>
/// <remarks>The iTraqCorrectionFactorType parameter is only used if reporterIonMode is ITraqFourMZ</remarks>
public clsITraqIntensityCorrection(clsReporterIons.ReporterIonMassModeConstants reporterIonMode, CorrectionFactorsiTRAQ4Plex iTraqCorrectionFactorType)
{
ReporterIonMode = reporterIonMode;
ITraq4PlexCorrectionFactorType = iTraqCorrectionFactorType;
mMatrixUtility = new MatrixDecompositionUtility.LUDecomposition();
if (ReporterIonMode == clsReporterIons.ReporterIonMassModeConstants.CustomOrNone)
{
return;
}
InitializeCoefficients(false);
}
/// <summary>
/// Change the reporter ion mode
/// </summary>
/// <param name="reporterIonMode"></param>
public void UpdateReporterIonMode(clsReporterIons.ReporterIonMassModeConstants reporterIonMode)
{
UpdateReporterIonMode(reporterIonMode, ITraq4PlexCorrectionFactorType);
}
/// <summary>
/// Change the reporter ion mode
/// </summary>
/// <param name="reporterIonMode"></param>
/// <param name="iTraqCorrectionFactorType"></param>
public void UpdateReporterIonMode(clsReporterIons.ReporterIonMassModeConstants reporterIonMode, CorrectionFactorsiTRAQ4Plex iTraqCorrectionFactorType)
{
if (ReporterIonMode != reporterIonMode || ITraq4PlexCorrectionFactorType != iTraqCorrectionFactorType)
{
ReporterIonMode = reporterIonMode;
ITraq4PlexCorrectionFactorType = iTraqCorrectionFactorType;
InitializeCoefficients(true);
}
}
/// <summary>
/// Apply the correction factors to the reporter ions
/// </summary>
/// <param name="reporterIonIntensities"></param>
/// <param name="debugShowIntensities">When true, show the old and new reporter ion intensities at the console</param>
public bool ApplyCorrection(float[] reporterIonIntensities, bool debugShowIntensities = false)
{
var dataCount = reporterIonIntensities.Length - 1;
var originalIntensities = new double[dataCount + 1];
for (var index = 0; index <= dataCount; index++)
{
originalIntensities[index] = reporterIonIntensities[index];
}
if (ApplyCorrection(originalIntensities, debugShowIntensities))
{
for (var index = 0; index <= dataCount; index++)
{
reporterIonIntensities[index] = (float)originalIntensities[index];
}
return true;
}
return false;
}
/// <summary>
/// Apply the correction factors to the reporter ions
/// </summary>
/// <param name="reporterIonIntensities"></param>
/// <param name="debugShowIntensities">When true, show the old and new reporter ion intensities at the console</param>
public bool ApplyCorrection(double[] reporterIonIntensities, bool debugShowIntensities = false)
{
var matrixSize = GetMatrixLength(ReporterIonMode);
var reporterIonMode = clsReporterIons.GetReporterIonModeDescription(ReporterIonMode);
if (reporterIonIntensities.Length != matrixSize)
{
throw new InvalidOperationException("Length of ReporterIonIntensities array must be " + matrixSize +
" when using the " + reporterIonMode + " mode");
}
var correctedIntensities = mMatrixUtility.ProcessData(mCoeffs, matrixSize, reporterIonIntensities);
var maxIntensity = 0.0;
for (var index = 0; index < matrixSize; index++)
{
maxIntensity = Math.Max(maxIntensity, reporterIonIntensities[index]);
}
if (debugShowIntensities)
{
Console.WriteLine();
Console.WriteLine("{0,-8} {1,-10} {2,-12} {3}", "Index", "Intensity", "NewIntensity", "% Change");
}
// Now update reporterIonIntensities
for (var index = 0; index < matrixSize; index++)
{
if (!(reporterIonIntensities[index] > 0))
{
continue;
}
double newIntensity;
if (correctedIntensities[index] < 0)
{
newIntensity = 0;
}
else
{
newIntensity = correctedIntensities[index];
}
if (debugShowIntensities)
{
// Compute percent change vs. the maximum reporter ion intensity
var percentChange = (newIntensity - reporterIonIntensities[index]) / maxIntensity * 100;
var percentChangeRounded = (int)Math.Round(percentChange, 0);
string visualPercentChange;
if (percentChangeRounded > 0)
{
visualPercentChange = new string('+', percentChangeRounded);
}
else if (percentChangeRounded < 0)
{
visualPercentChange = new string('-', -percentChangeRounded);
}
else
{
visualPercentChange = string.Empty;
}
Console.WriteLine("{0,-8} {1,-10:0.0} {2,-12:0.0}{3,7:0.0}% {4}", index, reporterIonIntensities[index], newIntensity, percentChange, visualPercentChange);
}
reporterIonIntensities[index] = newIntensity;
}
return true;
}
private int GetMatrixLength(clsReporterIons.ReporterIonMassModeConstants reporterIonMode)
{
return reporterIonMode switch
{
clsReporterIons.ReporterIonMassModeConstants.ITraqFourMZ => FOUR_PLEX_MATRIX_LENGTH,
clsReporterIons.ReporterIonMassModeConstants.ITraqEightMZHighRes => EIGHT_PLEX_HIGH_RES_MATRIX_LENGTH,
clsReporterIons.ReporterIonMassModeConstants.ITraqEightMZLowRes => EIGHT_PLEX_LOW_RES_MATRIX_LENGTH,
clsReporterIons.ReporterIonMassModeConstants.TMTTenMZ => TEN_PLEX_TMT_MATRIX_LENGTH,
clsReporterIons.ReporterIonMassModeConstants.TMTElevenMZ => ELEVEN_PLEX_TMT_MATRIX_LENGTH,
clsReporterIons.ReporterIonMassModeConstants.TMTSixteenMZ => SIXTEEN_PLEX_TMT_MATRIX_LENGTH,
_ => throw new ArgumentOutOfRangeException("Invalid value for reporterIonMode in GetMatrixLength: " + reporterIonMode)
};
}
/// <summary>
/// Initialize the coefficients
/// </summary>
/// <param name="debugShowMatrixTable">When true, show a table of the coefficients at the console</param>
private void InitializeCoefficients(bool debugShowMatrixTable)
{
// iTraq reporter ions
IsotopeContributionType udtIsoPct113;
IsotopeContributionType udtIsoPct114;
IsotopeContributionType udtIsoPct115;
IsotopeContributionType udtIsoPct116;
IsotopeContributionType udtIsoPct117;
IsotopeContributionType udtIsoPct118;
IsotopeContributionType udtIsoPct119;
IsotopeContributionType udtIsoPct120;
IsotopeContributionType udtIsoPct121;
// TMT reporter ions
IsotopeContributionType udtIsoPct126;
IsotopeContributionType udtIsoPct127N;
IsotopeContributionType udtIsoPct127C;
IsotopeContributionType udtIsoPct128N;
IsotopeContributionType udtIsoPct128C;
IsotopeContributionType udtIsoPct129N;
IsotopeContributionType udtIsoPct129C;
IsotopeContributionType udtIsoPct130N;
IsotopeContributionType udtIsoPct130C;
IsotopeContributionType udtIsoPct131N;
IsotopeContributionType udtIsoPct131C;
IsotopeContributionType udtIsoPct132N;
IsotopeContributionType udtIsoPct132C;
IsotopeContributionType udtIsoPct133N;
IsotopeContributionType udtIsoPct133C;
IsotopeContributionType udtIsoPct134N;
var matrixSize = GetMatrixLength(ReporterIonMode);
var maxIndex = matrixSize - 1;
switch (ReporterIonMode)
{
case clsReporterIons.ReporterIonMassModeConstants.ITraqFourMZ:
if (ITraq4PlexCorrectionFactorType == CorrectionFactorsiTRAQ4Plex.ABSciex)
{
// 4-plex ITraq, isotope contribution table
// Source percentages provided by Applied Biosystems
udtIsoPct114 = DefineIsotopeContribution(0, 1, 92.9F, 5.9F, 0.2F);
udtIsoPct115 = DefineIsotopeContribution(0, 2, 92.3F, 5.6F, 0.1F);
udtIsoPct116 = DefineIsotopeContribution(0, 3, 92.4F, 4.5F, 0.1F);
udtIsoPct117 = DefineIsotopeContribution(0.1F, 4, 92.3F, 3.5F, 0.1F);
}
else if (ITraq4PlexCorrectionFactorType == CorrectionFactorsiTRAQ4Plex.BroadInstitute)
{
// 4-plex ITraq, isotope contribution table
// Source percentages provided by Philipp Mertins at the Broad Institute ([email protected])
udtIsoPct114 = DefineIsotopeContribution(0, 0, 95.5F, 4.5F, 0);
udtIsoPct115 = DefineIsotopeContribution(0, 0.9F, 94.6F, 4.5F, 0);
udtIsoPct116 = DefineIsotopeContribution(0, 0.9F, 95.7F, 3.4F, 0);
udtIsoPct117 = DefineIsotopeContribution(0, 1.4F, 98.6F, 0, 0);
}
else
{
throw new ArgumentOutOfRangeException(nameof(ITraq4PlexCorrectionFactorType), "Unrecognized value for the iTRAQ 4 plex correction type");
}
// Goal is to generate either of these two matrices (depending on mITraq4PlexCorrectionFactorType):
// 0 1 2 3
// ----- ----- ----- -----
// 0 0.929 0.020 0 0
// 1 0.059 0.923 0.030 0.001
// 2 0.002 0.056 0.924 0.040
// 3 0 0.001 0.045 0.923
// 0 1 2 3
// ----- ----- ----- -----
// 0 0.955 0.009 0 0
// 1 0.045 0.946 0.009 0
// 2 0 0.045 0.957 0.014
// 3 0 0 0.034 0.986
mCoeffs = new double[maxIndex + 1, maxIndex + 1];
mCoeffs[0, 0] = udtIsoPct114.Zero;
mCoeffs[0, 1] = udtIsoPct115.Minus1;
mCoeffs[0, 2] = udtIsoPct116.Minus2;
mCoeffs[1, 0] = udtIsoPct114.Plus1;
mCoeffs[1, 1] = udtIsoPct115.Zero;
mCoeffs[1, 2] = udtIsoPct116.Minus1;
mCoeffs[1, 3] = udtIsoPct117.Minus2;
mCoeffs[2, 0] = udtIsoPct114.Plus2;
mCoeffs[2, 2] = udtIsoPct116.Zero;
mCoeffs[2, 1] = udtIsoPct115.Plus1;
mCoeffs[2, 3] = udtIsoPct117.Minus1;
mCoeffs[3, 1] = udtIsoPct115.Plus2;
mCoeffs[3, 2] = udtIsoPct116.Plus1;
mCoeffs[3, 3] = udtIsoPct117.Zero;
break;
case clsReporterIons.ReporterIonMassModeConstants.ITraqEightMZHighRes:
// 8-plex ITraq, isotope contribution table for High Res MS/MS
// Source percentages provided by Applied Biosystems
// Note there is a 2 Da jump between 119 and 121, which is why 7.44 and 0.87 are not included in mCoeffs()
udtIsoPct113 = DefineIsotopeContribution(0, 0, 92.89F, 6.89F, 0.22F);
udtIsoPct114 = DefineIsotopeContribution(0, 0.94F, 93.01F, 5.9F, 0.16F);
udtIsoPct115 = DefineIsotopeContribution(0, 1.88F, 93.12F, 4.9F, 0.1F);
udtIsoPct116 = DefineIsotopeContribution(0, 2.82F, 93.21F, 3.9F, 0.07F);
udtIsoPct117 = DefineIsotopeContribution(0.06F, 3.77F, 93.29F, 2.88F, 0);
udtIsoPct118 = DefineIsotopeContribution(0.09F, 4.71F, 93.32F, 1.88F, 0);
udtIsoPct119 = DefineIsotopeContribution(0.14F, 5.66F, 93.34F, 0.87F, 0);
udtIsoPct121 = DefineIsotopeContribution(0.27F, 7.44F, 92.11F, 0.18F, 0);
// Goal is to generate this matrix:
// 0 1 2 3 4 5 6 7
// ------ ------ ------ ------ ------ ------ ------ ------
// 0 0.9289 0.0094 0 0 0 0 0 0
// 1 0.0689 0.9301 0.0188 0 0 0 0 0
// 2 0.0022 0.0590 0.9312 0.0282 0.0006 0 0 0
// 3 0 0.0016 0.0490 0.9321 0.0377 0.0009 0 0
// 4 0 0 0.0010 0.0390 0.9329 0.0471 0.0014 0
// 5 0 0 0 0.0007 0.0288 0.9332 0.0566 0
// 6 0 0 0 0 0 0.0188 0.9334 0.0027
// 7 0 0 0 0 0 0 0 0.9211
mCoeffs = new double[maxIndex + 1, maxIndex + 1];
mCoeffs[0, 0] = udtIsoPct113.Zero;
mCoeffs[0, 1] = udtIsoPct114.Minus1;
mCoeffs[0, 2] = udtIsoPct115.Minus2;
mCoeffs[1, 0] = udtIsoPct113.Plus1;
mCoeffs[1, 1] = udtIsoPct114.Zero;
mCoeffs[1, 2] = udtIsoPct115.Minus1;
mCoeffs[1, 3] = udtIsoPct116.Minus2;
mCoeffs[2, 0] = udtIsoPct113.Plus2;
mCoeffs[2, 1] = udtIsoPct114.Plus1;
mCoeffs[2, 2] = udtIsoPct115.Zero;
mCoeffs[2, 3] = udtIsoPct116.Minus1;
mCoeffs[2, 4] = udtIsoPct117.Minus2;
mCoeffs[3, 1] = udtIsoPct114.Plus2;
mCoeffs[3, 2] = udtIsoPct115.Plus1;
mCoeffs[3, 3] = udtIsoPct116.Zero;
mCoeffs[3, 4] = udtIsoPct117.Minus1;
mCoeffs[3, 5] = udtIsoPct118.Minus2;
mCoeffs[4, 2] = udtIsoPct115.Plus2;
mCoeffs[4, 3] = udtIsoPct116.Plus1;
mCoeffs[4, 4] = udtIsoPct117.Zero;
mCoeffs[4, 5] = udtIsoPct118.Minus1;
mCoeffs[4, 6] = udtIsoPct119.Minus2;
mCoeffs[5, 3] = udtIsoPct116.Plus2;
mCoeffs[5, 4] = udtIsoPct117.Plus1;
mCoeffs[5, 5] = udtIsoPct118.Zero;
mCoeffs[5, 6] = udtIsoPct119.Minus1;
mCoeffs[5, 7] = 0;
mCoeffs[6, 4] = udtIsoPct117.Plus2;
mCoeffs[6, 5] = udtIsoPct118.Plus1;
mCoeffs[6, 6] = udtIsoPct119.Zero;
mCoeffs[6, 7] = udtIsoPct121.Minus2;
mCoeffs[7, 5] = 0; // udtIsoPct118.Plus2
mCoeffs[7, 7] = udtIsoPct121.Zero;
break;
case clsReporterIons.ReporterIonMassModeConstants.ITraqEightMZLowRes:
// 8-plex ITraq, isotope contribution table for Low Res MS/MS
// ReSharper disable CommentTypo
// Source percentages come from page 664 in:
// Vaudel, M., Sickmann, A., and L. Martens. "Peptide and protein quantification: A map of the minefield",
// Proteomics 2010, 10, 650-670.
// ReSharper restore CommentTypo
udtIsoPct113 = DefineIsotopeContribution(0, 0, 92.89F, 6.89F, 0.22F);
udtIsoPct114 = DefineIsotopeContribution(0, 0.94F, 93.01F, 5.9F, 0.16F);
udtIsoPct115 = DefineIsotopeContribution(0, 1.88F, 93.12F, 4.9F, 0.1F);
udtIsoPct116 = DefineIsotopeContribution(0, 2.82F, 93.21F, 3.9F, 0.07F);
udtIsoPct117 = DefineIsotopeContribution(0.06F, 3.77F, 93.29F, 2.88F, 0);
udtIsoPct118 = DefineIsotopeContribution(0.09F, 4.71F, 93.32F, 1.88F, 0);
udtIsoPct119 = DefineIsotopeContribution(0.14F, 5.66F, 93.34F, 0.87F, 0);
udtIsoPct120 = DefineIsotopeContribution(0, 0, 91.01F, 8.62F, 0);
udtIsoPct121 = DefineIsotopeContribution(0.27F, 7.44F, 92.11F, 0.18F, 0);
// Goal is to generate this expanded matrix, which takes Phenylalanine into account
// 0 1 2 3 4 5 6 7 8
// ------ ------ ------ ------ ------ ------ ------ ------ ------
// 0 0.9289 0.0094 0 0 0 0 0 0 0
// 1 0.0689 0.9301 0.0188 0 0 0 0 0 0
// 2 0.0022 0.0590 0.9312 0.0282 0.0006 0 0 0 0
// 3 0 0.0016 0.0490 0.9321 0.0377 0.0009 0 0 0
// 4 0 0 0.0010 0.0390 0.9329 0.0471 0.0014 0 0
// 5 0 0 0 0.0007 0.0288 0.9332 0.0566 0 0
// 6 0 0 0 0 0 0.0188 0.9334 0 0.0027
// 7 0 0 0 0 0 0 0.8700 0.9101 0.0744
// 8 0 0 0 0 0 0 0 0.0862 0.9211
mCoeffs = new double[maxIndex + 1, maxIndex + 1];
mCoeffs[0, 0] = udtIsoPct113.Zero;
mCoeffs[0, 1] = udtIsoPct114.Minus1;
mCoeffs[0, 2] = udtIsoPct115.Minus2;
mCoeffs[1, 0] = udtIsoPct113.Plus1;
mCoeffs[1, 1] = udtIsoPct114.Zero;
mCoeffs[1, 2] = udtIsoPct115.Minus1;
mCoeffs[1, 3] = udtIsoPct116.Minus2;
mCoeffs[2, 0] = udtIsoPct113.Plus2;
mCoeffs[2, 1] = udtIsoPct114.Plus1;
mCoeffs[2, 2] = udtIsoPct115.Zero;
mCoeffs[2, 3] = udtIsoPct116.Minus1;
mCoeffs[2, 4] = udtIsoPct117.Minus2;
mCoeffs[3, 1] = udtIsoPct114.Plus2;
mCoeffs[3, 2] = udtIsoPct115.Plus1;
mCoeffs[3, 3] = udtIsoPct116.Zero;
mCoeffs[3, 4] = udtIsoPct117.Minus1;
mCoeffs[3, 5] = udtIsoPct118.Minus2;
mCoeffs[4, 2] = udtIsoPct115.Plus2;
mCoeffs[4, 3] = udtIsoPct116.Plus1;
mCoeffs[4, 4] = udtIsoPct117.Zero;
mCoeffs[4, 5] = udtIsoPct118.Minus1;
mCoeffs[4, 6] = udtIsoPct119.Minus2;
mCoeffs[5, 3] = udtIsoPct116.Plus2;
mCoeffs[5, 4] = udtIsoPct117.Plus1;
mCoeffs[5, 5] = udtIsoPct118.Zero;
mCoeffs[5, 6] = udtIsoPct119.Minus1;
mCoeffs[5, 7] = 0;
mCoeffs[6, 4] = udtIsoPct117.Plus2;
mCoeffs[6, 5] = udtIsoPct118.Plus1;
mCoeffs[6, 6] = udtIsoPct119.Zero;
mCoeffs[6, 7] = 0;
mCoeffs[6, 8] = udtIsoPct121.Minus2;
mCoeffs[7, 5] = 0;
mCoeffs[7, 6] = udtIsoPct119.Plus1;
mCoeffs[7, 7] = udtIsoPct120.Zero;
mCoeffs[7, 8] = udtIsoPct121.Minus1;
mCoeffs[8, 6] = udtIsoPct119.Plus2;
mCoeffs[8, 7] = udtIsoPct120.Plus1;
mCoeffs[8, 8] = udtIsoPct121.Zero;
break;
case clsReporterIons.ReporterIonMassModeConstants.TMTTenMZ:
case clsReporterIons.ReporterIonMassModeConstants.TMTElevenMZ:
// 10-plex TMT and 11-plex TMT, isotope contribution table for High Res MS/MS
// Source percentages provided by Thermo
// TMT10plex lot RG234623
// TMT11plex lot SD250515
// udtIsoPct126 = DefineIsotopeContribution(0, 0, 95.1, 4.9, 0)
// udtIsoPct127N = DefineIsotopeContribution(0, 0.2, 94, 5.8, 0)
// udtIsoPct127C = DefineIsotopeContribution(0, 0.3, 94.9, 4.8, 0)
// udtIsoPct128N = DefineIsotopeContribution(0, 0.3, 96.1, 3.6, 0)
// udtIsoPct128C = DefineIsotopeContribution(0, 0.6, 95.5, 3.9, 0)
// udtIsoPct129N = DefineIsotopeContribution(0, 0.8, 96.2, 3, 0)
// udtIsoPct129C = DefineIsotopeContribution(0, 1.3, 95.8, 2.9, 0)
// udtIsoPct130N = DefineIsotopeContribution(0, 1.4, 93, 2.3, 3.3)
// udtIsoPct130C = DefineIsotopeContribution(0, 1.7, 96.1, 2.2, 0)
// udtIsoPct131N = DefineIsotopeContribution(0.2, 2, 95.6, 2.2, 0)
// udtIsoPct131C = DefineIsotopeContribution(0, 2.6, 94.5, 2.9, 0)
// TMT10plex lot A37725
// TMT11plex lot TB265130
// udtIsoPct126 = DefineIsotopeContribution(0, 0, 92.081, 7.551, 0.368)
// udtIsoPct127N = DefineIsotopeContribution(0, 0.093, 92.593, 7.315, 0)
// udtIsoPct127C = DefineIsotopeContribution(0, 0.468, 93.633, 5.899, 0)
// udtIsoPct128N = DefineIsotopeContribution(0, 0.658, 93.985, 5.357, 0)
// udtIsoPct128C = DefineIsotopeContribution(0.186, 1.484, 92.764, 5.566, 0)
// udtIsoPct129N = DefineIsotopeContribution(0, 2.326, 93.023, 4.651, 0)
// udtIsoPct129C = DefineIsotopeContribution(0, 2.158, 93.809, 4.034, 0)
// udtIsoPct130N = DefineIsotopeContribution(0, 2.533, 93.809, 3.659, 0)
// udtIsoPct130C = DefineIsotopeContribution(0, 1.628, 95.785, 2.586, 0)
// udtIsoPct131N = DefineIsotopeContribution(0, 3.625, 92.937, 3.439, 0)
// udtIsoPct131C = DefineIsotopeContribution(0, 3.471, 93.809, 2.72, 0)
// TMT10plex lot SG252258
// TMT11plex lot T4259309
udtIsoPct126 = DefineIsotopeContribution(0, 0, 100, 7.2F, 0.2F);
udtIsoPct127N = DefineIsotopeContribution(0, 0.4F, 100, 7.3F, 0.2F);
udtIsoPct127C = DefineIsotopeContribution(0, 0.5F, 100, 6.3F, 0);
udtIsoPct128N = DefineIsotopeContribution(0, 0.7F, 100, 5.7F, 0);
udtIsoPct128C = DefineIsotopeContribution(0, 1.4F, 100, 5.1F, 0);
udtIsoPct129N = DefineIsotopeContribution(0, 2.5F, 100, 5, 0);
udtIsoPct129C = DefineIsotopeContribution(0, 2.3F, 100, 4.3F, 0);
udtIsoPct130N = DefineIsotopeContribution(0, 2.7F, 100, 3.9F, 0);
udtIsoPct130C = DefineIsotopeContribution(0.4F, 2.9F, 100, 3.3F, 0);
udtIsoPct131N = DefineIsotopeContribution(0, 3.4F, 100, 3.3F, 0);
udtIsoPct131C = DefineIsotopeContribution(0, 3.7F, 100, 2.9F, 0);
// Goal is to generate this matrix (11-plex will not have the final row or final column)
// 0 1 2 3 4 5 6 7 8 9 10
// ------ ------ ------ ------ ------ ------ ------ ------ ------ ------ ------
// 0 0.9260 0 0.0050 0 0 0 0 0 0 0 0
// 1 0 0.9210 0 0.0070 0 0 0 0 0 0 0
// 2 0.0720 0 0.9320 0 0.0140 0 0 0 0 0 0
// 3 0 0.0730 0 0.9360 0 0.0250 0 0 0 0 0
// 4 0.0020 0 0.0630 0 0.9350 0 0.0230 0 0.0040 0 0
// 5 0 0.0020 0 0.0570 0 0.9250 0 0.0270 0 0 0
// 6 0 0 0 0 0.0510 0 0.9340 0 0.0290 0 0
// 7 0 0 0 0 0 0.0500 0 0.9340 0 0.0340 0
// 8 0 0 0 0 0 0 0.0430 0 0.9340 0 0.0370
// 9 0 0 0 0 0 0 0 0.0390 0 0.9330 0
// 10 0 0 0 0 0 0 0 0 0.0330 0 0.9340
//
mCoeffs = new double[maxIndex + 1, maxIndex + 1];
mCoeffs[0, 0] = udtIsoPct126.Zero;
mCoeffs[0, 1] = 0;
mCoeffs[0, 2] = udtIsoPct127C.Minus1;
mCoeffs[0, 3] = 0;
mCoeffs[0, 4] = udtIsoPct128C.Minus2;
mCoeffs[1, 0] = 0;
mCoeffs[1, 1] = udtIsoPct127N.Zero;
mCoeffs[1, 2] = 0;
mCoeffs[1, 3] = udtIsoPct128N.Minus1;
mCoeffs[1, 4] = 0;
mCoeffs[1, 5] = udtIsoPct129N.Minus2;
mCoeffs[2, 0] = udtIsoPct126.Plus1;
mCoeffs[2, 1] = 0;
mCoeffs[2, 2] = udtIsoPct127C.Zero;
mCoeffs[2, 3] = 0;
mCoeffs[2, 4] = udtIsoPct128C.Minus1;
mCoeffs[2, 5] = 0;
mCoeffs[2, 6] = udtIsoPct129C.Minus2;
mCoeffs[3, 0] = 0;
mCoeffs[3, 1] = udtIsoPct127N.Plus1;
mCoeffs[3, 2] = 0;
mCoeffs[3, 3] = udtIsoPct128N.Zero;
mCoeffs[3, 4] = 0;
mCoeffs[3, 5] = udtIsoPct129N.Minus1;
mCoeffs[3, 6] = 0;
mCoeffs[3, 7] = udtIsoPct130N.Minus2;
mCoeffs[4, 0] = udtIsoPct126.Plus2;
mCoeffs[4, 1] = 0;
mCoeffs[4, 2] = udtIsoPct127C.Plus1;
mCoeffs[4, 3] = 0;
mCoeffs[4, 4] = udtIsoPct128C.Zero;
mCoeffs[4, 5] = 0;
mCoeffs[4, 6] = udtIsoPct129C.Minus1;
mCoeffs[4, 7] = 0;
mCoeffs[4, 8] = udtIsoPct130C.Minus2;
mCoeffs[5, 1] = udtIsoPct127N.Plus2;
mCoeffs[5, 2] = 0;
mCoeffs[5, 3] = udtIsoPct128N.Plus1;
mCoeffs[5, 4] = 0;
mCoeffs[5, 5] = udtIsoPct129N.Zero;
mCoeffs[5, 6] = 0;
mCoeffs[5, 7] = udtIsoPct130N.Minus1;
mCoeffs[5, 8] = 0;
mCoeffs[5, 9] = udtIsoPct131N.Minus2;
mCoeffs[6, 2] = udtIsoPct127C.Plus2;
mCoeffs[6, 3] = 0;
mCoeffs[6, 4] = udtIsoPct128C.Plus1;
mCoeffs[6, 5] = 0;
mCoeffs[6, 6] = udtIsoPct129C.Zero;
mCoeffs[6, 7] = 0;
mCoeffs[6, 8] = udtIsoPct130C.Minus1;
mCoeffs[7, 3] = udtIsoPct128N.Plus2;
mCoeffs[7, 4] = 0;
mCoeffs[7, 5] = udtIsoPct129N.Plus1;
mCoeffs[7, 6] = 0;
mCoeffs[7, 7] = udtIsoPct130N.Zero;
mCoeffs[7, 8] = 0;
mCoeffs[7, 9] = udtIsoPct131N.Minus1;
mCoeffs[8, 4] = udtIsoPct128C.Plus2;
mCoeffs[8, 5] = 0;
mCoeffs[8, 6] = udtIsoPct129C.Plus1;
mCoeffs[8, 7] = 0;
mCoeffs[8, 8] = udtIsoPct130C.Zero;
mCoeffs[8, 9] = 0;
if (maxIndex >= 10)
{
mCoeffs[8, 10] = udtIsoPct131C.Minus1;
}
mCoeffs[9, 5] = udtIsoPct129N.Plus2;
mCoeffs[9, 6] = 0;
mCoeffs[9, 7] = udtIsoPct130N.Plus1;
mCoeffs[9, 8] = 0;
mCoeffs[9, 9] = udtIsoPct131N.Zero;
if (maxIndex >= 10)
{
mCoeffs[10, 6] = udtIsoPct129C.Plus2;
mCoeffs[10, 7] = 0;
mCoeffs[10, 8] = udtIsoPct130C.Plus1;
mCoeffs[10, 9] = 0;
mCoeffs[10, 10] = udtIsoPct131C.Zero;
}
break;
case clsReporterIons.ReporterIonMassModeConstants.TMTSixteenMZ:
// 16-plex TMT, isotope contribution table for High Res MS/MS
// Source percentages provided by Thermo
// TMTpro lot UH290428
udtIsoPct126 = DefineIsotopeContribution(0, 0, 100, 7.73F, 0.22F);
udtIsoPct127N = DefineIsotopeContribution(0, 0, 100, 7.46F, 0.22F);
udtIsoPct127C = DefineIsotopeContribution(0, 0.71F, 100, 6.62F, 0.16F);
udtIsoPct128N = DefineIsotopeContribution(0, 0.75F, 100, 6.67F, 0.16F);
udtIsoPct128C = DefineIsotopeContribution(0.06F, 1.34F, 100, 5.31F, 0.11F);
udtIsoPct129N = DefineIsotopeContribution(0.01F, 1.29F, 100, 5.48F, 0.1F);
udtIsoPct129C = DefineIsotopeContribution(0.26F, 2.34F, 100, 4.87F, 0.08F);
udtIsoPct130N = DefineIsotopeContribution(0.39F, 2.36F, 100, 4.57F, 0.07F);
udtIsoPct130C = DefineIsotopeContribution(0.05F, 2.67F, 100, 3.85F, 0.15F);
udtIsoPct131N = DefineIsotopeContribution(0.05F, 2.71F, 100, 3.73F, 0.04F);
udtIsoPct131C = DefineIsotopeContribution(0.09F, 3.69F, 100, 2.77F, 0.01F);
udtIsoPct132N = DefineIsotopeContribution(0.09F, 2.51F, 100, 2.76F, 0.01F);
udtIsoPct132C = DefineIsotopeContribution(0.1F, 4.11F, 100, 1.63F, 0);
udtIsoPct133N = DefineIsotopeContribution(0.09F, 3.09F, 100, 1.58F, 0);
udtIsoPct133C = DefineIsotopeContribution(0.36F, 4.63F, 100, 0.88F, 0);
udtIsoPct134N = DefineIsotopeContribution(0.38F, 4.82F, 100, 0.86F, 0);
// Goal is to generate a 16x16 matrix
// 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
// -- ------ ------ ------ ------ ------ ------ ------ ------ ------ ------ ------ ------ ------ ------ ------ ------
// 0 0.9205 0 0.0071 0 0.0006 0 0 0 0 0 0 0 0 0 0 0
// 1 0 0.9232 0 0.0075 0 0.0001 0 0 0 0 0 0 0 0 0 0
// 2 0.0773 0 0.9251 0 0.0134 0 0.0026 0 0 0 0 0 0 0 0 0
// 3 0 0.0746 0 0.9242 0 0.0129 0 0.0039 0 0 0 0 0 0 0 0
// 4 0.0022 0 0.0662 0 0.9318 0 0.0234 0 0.0005 0 0 0 0 0 0 0
// 5 0 0.0022 0 0.0667 0 0.9312 0 0.0236 0 0.0005 0 0 0 0 0 0
// 6 0 0 0.0016 0 0.0531 0 0.9245 0 0.0267 0 0.0009 0 0 0 0 0
// 7 0 0 0 0.0016 0 0.0548 0 0.9261 0 0.0271 0 0.0009 0 0 0 0
// 8 0 0 0 0 0.0011 0 0.0487 0 0.9328 0 0.0369 0 0.0010 0 0 0
// 9 0 0 0 0 0 0.0010 0 0.0457 0 0.9347 0 0.0251 0 0.0009 0 0
// 10 0 0 0 0 0 0 0.0008 0 0.0385 0 0.9344 0 0.0411 0 0.0036 0
// 11 0 0 0 0 0 0 0 0.0007 0 0.0373 0 0.9463 0 0.0309 0 0.0038
// 12 0 0 0 0 0 0 0 0 0.0015 0 0.0277 0 0.9416 0 0.0463 0
// 13 0 0 0 0 0 0 0 0 0 0.0004 0 0.0276 0 0.9524 0 0.0482
// 14 0 0 0 0 0 0 0 0 0 0 0.0001 0 0.0163 0 0.9413 0
// 15 0 0 0 0 0 0 0 0 0 0 0 0.0001 0 0.0158 0 0.9394
mCoeffs = new double[maxIndex + 1, maxIndex + 1];
mCoeffs[0, 0] = udtIsoPct126.Zero;
mCoeffs[0, 1] = 0;
mCoeffs[0, 2] = udtIsoPct127C.Minus1;
mCoeffs[0, 3] = 0;
mCoeffs[0, 4] = udtIsoPct128C.Minus2;
mCoeffs[1, 0] = 0;
mCoeffs[1, 1] = udtIsoPct127N.Zero;
mCoeffs[1, 2] = 0;
mCoeffs[1, 3] = udtIsoPct128N.Minus1;
mCoeffs[1, 4] = 0;
mCoeffs[1, 5] = udtIsoPct129N.Minus2;
mCoeffs[2, 0] = udtIsoPct126.Plus1;
mCoeffs[2, 1] = 0;
mCoeffs[2, 2] = udtIsoPct127C.Zero;
mCoeffs[2, 3] = 0;
mCoeffs[2, 4] = udtIsoPct128C.Minus1;
mCoeffs[2, 5] = 0;
mCoeffs[2, 6] = udtIsoPct129C.Minus2;
mCoeffs[3, 0] = 0;
mCoeffs[3, 1] = udtIsoPct127N.Plus1;
mCoeffs[3, 2] = 0;
mCoeffs[3, 3] = udtIsoPct128N.Zero;
mCoeffs[3, 4] = 0;
mCoeffs[3, 5] = udtIsoPct129N.Minus1;
mCoeffs[3, 6] = 0;
mCoeffs[3, 7] = udtIsoPct130N.Minus2;
mCoeffs[4, 0] = udtIsoPct126.Plus2;
mCoeffs[4, 1] = 0;
mCoeffs[4, 2] = udtIsoPct127C.Plus1;
mCoeffs[4, 3] = 0;
mCoeffs[4, 4] = udtIsoPct128C.Zero;
mCoeffs[4, 5] = 0;
mCoeffs[4, 6] = udtIsoPct129C.Minus1;
mCoeffs[4, 7] = 0;
mCoeffs[4, 8] = udtIsoPct130C.Minus2;
mCoeffs[5, 1] = udtIsoPct127N.Plus2;
mCoeffs[5, 2] = 0;
mCoeffs[5, 3] = udtIsoPct128N.Plus1;
mCoeffs[5, 4] = 0;
mCoeffs[5, 5] = udtIsoPct129N.Zero;
mCoeffs[5, 6] = 0;
mCoeffs[5, 7] = udtIsoPct130N.Minus1;
mCoeffs[5, 8] = 0;
mCoeffs[5, 9] = udtIsoPct131N.Minus2;
mCoeffs[6, 2] = udtIsoPct127C.Plus2;
mCoeffs[6, 3] = 0;
mCoeffs[6, 4] = udtIsoPct128C.Plus1;
mCoeffs[6, 5] = 0;
mCoeffs[6, 6] = udtIsoPct129C.Zero;
mCoeffs[6, 7] = 0;
mCoeffs[6, 8] = udtIsoPct130C.Minus1;
mCoeffs[6, 9] = 0;
mCoeffs[6, 10] = udtIsoPct131C.Minus2;
mCoeffs[7, 3] = udtIsoPct128N.Plus2;
mCoeffs[7, 4] = 0;
mCoeffs[7, 5] = udtIsoPct129N.Plus1;
mCoeffs[7, 6] = 0;
mCoeffs[7, 7] = udtIsoPct130N.Zero;
mCoeffs[7, 8] = 0;
mCoeffs[7, 9] = udtIsoPct131N.Minus1;
mCoeffs[7, 10] = 0;
mCoeffs[7, 11] = udtIsoPct132N.Minus2;
mCoeffs[8, 4] = udtIsoPct128C.Plus2;
mCoeffs[8, 5] = 0;
mCoeffs[8, 6] = udtIsoPct129C.Plus1;
mCoeffs[8, 7] = 0;
mCoeffs[8, 8] = udtIsoPct130C.Zero;
mCoeffs[8, 9] = 0;
mCoeffs[8, 10] = udtIsoPct131C.Minus1;
mCoeffs[8, 11] = 0;
mCoeffs[8, 12] = udtIsoPct132C.Minus2;
mCoeffs[9, 5] = udtIsoPct129N.Plus2;
mCoeffs[9, 6] = 0;
mCoeffs[9, 7] = udtIsoPct130N.Plus1;
mCoeffs[9, 8] = 0;
mCoeffs[9, 9] = udtIsoPct131N.Zero;
mCoeffs[9, 10] = 0;
mCoeffs[9, 11] = udtIsoPct132N.Minus1;
mCoeffs[9, 12] = 0;
mCoeffs[9, 13] = udtIsoPct133N.Minus2;
mCoeffs[10, 6] = udtIsoPct129C.Plus2;
mCoeffs[10, 7] = 0;
mCoeffs[10, 8] = udtIsoPct130C.Plus1;
mCoeffs[10, 9] = 0;
mCoeffs[10, 10] = udtIsoPct131C.Zero;
mCoeffs[10, 11] = 0;
mCoeffs[10, 12] = udtIsoPct132C.Minus1;
mCoeffs[10, 13] = 0;
mCoeffs[10, 14] = udtIsoPct133C.Minus2;
mCoeffs[11, 7] = udtIsoPct130N.Plus2;
mCoeffs[11, 8] = 0;
mCoeffs[11, 9] = udtIsoPct131N.Plus1;
mCoeffs[11, 10] = 0;
mCoeffs[11, 11] = udtIsoPct132N.Zero;
mCoeffs[11, 12] = 0;
mCoeffs[11, 13] = udtIsoPct133N.Minus1;
mCoeffs[11, 14] = 0;
mCoeffs[11, 15] = udtIsoPct134N.Minus2;
mCoeffs[12, 8] = udtIsoPct130C.Plus2;
mCoeffs[12, 9] = 0;
mCoeffs[12, 10] = udtIsoPct131C.Plus1;
mCoeffs[12, 11] = 0;
mCoeffs[12, 12] = udtIsoPct132C.Zero;
mCoeffs[12, 13] = 0;
mCoeffs[12, 14] = udtIsoPct133C.Minus1;
mCoeffs[13, 9] = udtIsoPct131N.Plus2;
mCoeffs[13, 10] = 0;
mCoeffs[13, 11] = udtIsoPct132N.Plus1;
mCoeffs[13, 12] = 0;
mCoeffs[13, 13] = udtIsoPct133N.Zero;
mCoeffs[13, 14] = 0;
mCoeffs[13, 15] = udtIsoPct134N.Minus1;
mCoeffs[14, 10] = udtIsoPct131C.Plus2;
mCoeffs[14, 11] = 0;
mCoeffs[14, 12] = udtIsoPct132C.Plus1;
mCoeffs[14, 13] = 0;
mCoeffs[14, 14] = udtIsoPct133C.Zero;
mCoeffs[15, 11] = udtIsoPct132N.Plus2;
mCoeffs[15, 12] = 0;
mCoeffs[15, 13] = udtIsoPct133N.Plus1;
mCoeffs[15, 14] = 0;
mCoeffs[15, 15] = udtIsoPct134N.Zero;
break;
default:
throw new Exception("Invalid reporter ion mode in IntensityCorrection.InitializeCoefficients");
}
// Now divide all of the weights by 100
for (var i = 0; i <= maxIndex; i++)
{
for (var j = 0; j <= maxIndex; j++)
{
mCoeffs[i, j] /= 100.0;
}
}
if (debugShowMatrixTable)
{
// Print out the matrix
Console.WriteLine();
Console.WriteLine("Reporter Ion Correction Matrix; mode = " + ReporterIonMode);
for (var i = 0; i <= maxIndex; i++)
{
if (i == 0)
{
// Header line
Console.Write(" ");
for (var j = 0; j <= maxIndex; j++)
{
if (j < 10)
{
Console.Write(" " + j + " ");
}
else
{
Console.Write(" " + j + " ");
}
}
Console.WriteLine();
Console.Write(" ");
for (var k = 0; k <= maxIndex; k++)
{
Console.Write(" ------ ");
}
Console.WriteLine();
}
string indexSpacer;
if (i < 10)
indexSpacer = " ";
else
indexSpacer = " ";
Console.Write(" " + i + indexSpacer);
for (var j = 0; j <= maxIndex; j++)
{
if (Math.Abs(mCoeffs[i, j]) < float.Epsilon)
{
Console.Write(" 0 ");
}
else
{
Console.Write(" " + mCoeffs[i, j].ToString("0.0000") + " ");
}
}
Console.WriteLine();
}
Console.WriteLine();
}
}
/// <summary>
/// Given a set of isotope correction values
/// </summary>
/// <param name="minus2">Value between 0 and 100, but typically close to 0</param>
/// <param name="minus1">Value between 0 and 100, but typically close to 0</param>
/// <param name="zero">Value between 0 and 100, but typically close to 98; if this is 0 or 100, it is auto-computed</param>
/// <param name="plus1">Value between 0 and 100, but typically close to 0</param>
/// <param name="plus2">Value between 0 and 100, but typically close to 0</param>
/// <remarks>The values should sum to 100; however, if zero (aka the Monoisotopic Peak) is 0, its value will be auto-computed</remarks>
private IsotopeContributionType DefineIsotopeContribution(
float minus2,
float minus1,
float zero,
float plus1,
float plus2)
{
IsotopeContributionType udtIsotopePct;
if (Math.Abs(zero) < float.Epsilon ||
zero < 0 ||
minus2 + minus1 + plus1 + plus2 > 0 && Math.Abs(zero - 100) < float.Epsilon)
{
// Auto-compute the monoisotopic abundance
zero = 100 - minus2 - minus1 - plus1 - plus2;
}
var sum = minus2 + minus1 + zero + plus1 + plus2;
if (Math.Abs(100 - sum) > 0.05)
{
throw new Exception(string.Format("Parameters for DefineIsotopeContribution should add up to 100; current sum is {0:F1}", sum));
}
udtIsotopePct.Minus2 = minus2;
udtIsotopePct.Minus1 = minus1;
udtIsotopePct.Zero = zero;
udtIsotopePct.Plus1 = plus1;
udtIsotopePct.Plus2 = plus2;
return udtIsotopePct;
}
}
}