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clsReporterIons.cs
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clsReporterIons.cs
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using System;
using System.Collections.Generic;
namespace MASIC
{
/// <summary>
/// Container for reporter ions to find
/// </summary>
public class clsReporterIons
{
// ReSharper disable CommentTypo
// Ignore Spelling: acet, acetylated, Acetylation, Alfaro, Amine, Carboxylic, Chengdong, Da, Du, Fracking
// Ignore Spelling: Galnaz, immonium, Lys, Merkley, Nakayasu, plex, Xu
// ReSharper restore CommentTypo
/// <summary>
/// Default reporter ion tolerance, in Da
/// </summary>
public const double REPORTER_ION_TOLERANCE_DA_DEFAULT = 0.5;
/// <summary>
/// Default minimum allowed reporter ion tolerance, in Da
/// </summary>
public const double REPORTER_ION_TOLERANCE_DA_MINIMUM = 0.001;
/// <summary>
/// Default reporter ion tolerance for 8-plex iTRAQ
/// </summary>
public const double REPORTER_ION_TOLERANCE_DA_DEFAULT_ITRAQ8_HIGH_RES = 0.015;
/// <summary>
/// Default reporter ion tolerance for 6-plex TMT reporter ions
/// </summary>
public const double REPORTER_ION_TOLERANCE_DA_DEFAULT_TMT6 = 0.015;
/// <summary>
/// Default reporter ion tolerance for 10-plex TMT reporter ions (also applies to 11-plex ans 16-plex TMT)
/// </summary>
public const double REPORTER_ION_TOLERANCE_DA_DEFAULT_TMT10 = 0.015;
/// <summary>
/// Reporter ion mass modes
/// </summary>
public enum ReporterIonMassModeConstants
{
/// <summary>
/// Custom / none
/// </summary>
CustomOrNone = 0,
/// <summary>
/// 4-plex iTRAQ
/// </summary>
ITraqFourMZ = 1,
/// <summary>
/// 3-plex iTRAQ
/// </summary>
ITraqETDThreeMZ = 2,
/// <summary>
/// 2-plex TMT
/// </summary>
TMTTwoMZ = 3,
/// <summary>
/// 6-plex TMT
/// </summary>
TMTSixMZ = 4,
/// <summary>
/// 8-plex iTRAQ
/// </summary>
/// <remarks>
/// This version of 8-plex iTraq should be used when the reporter ion search tolerance is +/-0.03 Da or smaller
/// </remarks>
ITraqEightMZHighRes = 5,
/// <summary>
/// 8-plex iTRAQ
/// </summary>
/// <remarks>
/// This version of 8-plex iTraq will account for immonium loss from phenylalanine
/// </remarks>
ITraqEightMZLowRes = 6,
/// <summary>
/// PC Galnaz fragments
/// </summary>
PCGalnaz = 7,
/// <summary>
/// Heme-C fragments
/// </summary>
HemeCFragment = 8,
/// <summary>
/// Lys acet fragments
/// </summary>
LycAcetFragment = 9,
/// <summary>
/// 10-plex TMT
/// </summary>
/// <remarks>
/// Several of the reporter ion masses are just 49 ppm apart, thus you must use a very tight tolerance of +/-0.003 Da
/// </remarks>
TMTTenMZ = 10,
/// <summary>
/// O-GlcNAc fragments
/// </summary>
OGlcNAc = 11,
/// <summary>
/// Fracking amine fragments
/// </summary>
FrackingAmine20160217 = 12,
/// <summary>
/// FSFA carbonyl fragments
/// </summary>
FSFACustomCarbonyl = 13,
/// <summary>
/// FSFA carboxylic fragments
/// </summary>
FSFACustomCarboxylic = 14,
/// <summary>
/// FSFA hydroxyl fragments
/// </summary>
FSFACustomHydroxyl = 15,
/// <summary>
/// 11-plex TMT
/// </summary>
/// <remarks>
/// Several of the reporter ion masses are just 49 ppm apart, thus you must use a very tight tolerance of +/-0.003 Da
/// </remarks>
TMTElevenMZ = 16,
/// <summary>
/// Acetylation fragments
/// </summary>
Acetylation = 17,
/// <summary>
/// 16-plex TMT
/// </summary>
/// <remarks>
/// Several of the reporter ion masses are just 49 ppm apart, thus you must use a very tight tolerance of +/-0.003 Da
/// </remarks>
TMTSixteenMZ = 18,
/// <summary>
/// Native O-GlcNAc fragments
/// </summary>
NativeOGlcNAc = 19
}
private double mReporterIonToleranceDaDefault;
private ReporterIonMassModeConstants mReporterIonMassMode;
/// <summary>
/// When ReporterIonStatsEnabled = True, MZIntensityFilterIgnoreRangeStart and MZIntensityFilterIgnoreRangeEnd
/// will be populated with the m/z range of the reporter ions being processed
/// </summary>
public double MZIntensityFilterIgnoreRangeStart { get; set; }
/// <summary>
/// When ReporterIonStatsEnabled = True, MZIntensityFilterIgnoreRangeStart and MZIntensityFilterIgnoreRangeEnd
/// will be populated with the m/z range of the reporter ions being processed
/// </summary>
public double MZIntensityFilterIgnoreRangeEnd { get; set; }
/// <summary>
/// List of reporter ions
/// </summary>
public List<clsReporterIonInfo> ReporterIonList { get; }
/// <summary>
/// When true, Look for Reporter Ions in the fragmentation spectra
/// </summary>
public bool ReporterIonStatsEnabled { get; set; }
/// <summary>
/// When true, correct the reporter ion intensities using the Reporter Ion Intensity Corrector class
/// </summary>
public bool ReporterIonApplyAbundanceCorrection { get; set; }
/// <summary>
/// Correction factor to use when the reporter ion mass mode is ITraqFourMZ
/// </summary>
public clsITraqIntensityCorrection.CorrectionFactorsiTRAQ4Plex ReporterIonITraq4PlexCorrectionFactorType { get; set; }
/// <summary>
/// This is ignored if mReporterIonApplyAbundanceCorrection is False
/// </summary>
public bool ReporterIonSaveUncorrectedIntensities { get; set; }
/// <summary>
/// Reporter ion mass mode
/// </summary>
public ReporterIonMassModeConstants ReporterIonMassMode
{
get => mReporterIonMassMode;
set => SetReporterIonMassMode(value);
}
/// <summary>
/// When true, observed m/z values of the reporter ions will be included in the _ReporterIons.txt file
/// </summary>
public bool ReporterIonSaveObservedMasses { get; set; }
/// <summary>
/// Default reporter ion tolerance, in Da
/// </summary>
public double ReporterIonToleranceDaDefault
{
get
{
if (mReporterIonToleranceDaDefault < double.Epsilon)
mReporterIonToleranceDaDefault = REPORTER_ION_TOLERANCE_DA_DEFAULT;
return mReporterIonToleranceDaDefault;
}
set
{
if (value < double.Epsilon)
value = REPORTER_ION_TOLERANCE_DA_DEFAULT;
mReporterIonToleranceDaDefault = value;
}
}
/// <summary>
/// Constructor
/// </summary>
public clsReporterIons()
{
ReporterIonList = new List<clsReporterIonInfo>();
InitializeReporterIonInfo();
}
/// <summary>
/// Get the default reporter ions, using the default reporter ion m/z tolerance (customized based on reporterIonMassMode)
/// </summary>
/// <param name="reporterIonMassMode"></param>
public static List<clsReporterIonInfo> GetDefaultReporterIons(ReporterIonMassModeConstants reporterIonMassMode)
{
return reporterIonMassMode switch
{
ReporterIonMassModeConstants.TMTSixMZ =>
GetDefaultReporterIons(reporterIonMassMode, REPORTER_ION_TOLERANCE_DA_DEFAULT_TMT6),
ReporterIonMassModeConstants.TMTTenMZ or ReporterIonMassModeConstants.TMTElevenMZ or ReporterIonMassModeConstants.TMTSixteenMZ =>
GetDefaultReporterIons(reporterIonMassMode, REPORTER_ION_TOLERANCE_DA_DEFAULT_TMT10),
ReporterIonMassModeConstants.ITraqEightMZHighRes =>
GetDefaultReporterIons(reporterIonMassMode, REPORTER_ION_TOLERANCE_DA_DEFAULT_ITRAQ8_HIGH_RES),
_ =>
GetDefaultReporterIons(reporterIonMassMode, REPORTER_ION_TOLERANCE_DA_DEFAULT)
};
}
/// <summary>
/// Get the reporter ion m/z values for the given reporter ion mass mode
/// </summary>
/// <param name="reporterIonMassMode"></param>
/// <param name="mzToleranceDa"></param>
public static List<clsReporterIonInfo> GetDefaultReporterIons(
ReporterIonMassModeConstants reporterIonMassMode,
double mzToleranceDa)
{
var reporterIons = new List<clsReporterIonInfo>(16); // largest count is 16
switch (reporterIonMassMode)
{
case ReporterIonMassModeConstants.ITraqFourMZ:
// ITRAQ, aka iTRAQ4
reporterIons.Add(new clsReporterIonInfo(114.1112));
reporterIons.Add(new clsReporterIonInfo(115.1083));
reporterIons.Add(new clsReporterIonInfo(116.1116));
reporterIons.Add(new clsReporterIonInfo(117.115));
break;
case ReporterIonMassModeConstants.ITraqETDThreeMZ:
// ITRAQ ETD tags
reporterIons.Add(new clsReporterIonInfo(101.107));
reporterIons.Add(new clsReporterIonInfo(102.104));
reporterIons.Add(new clsReporterIonInfo(104.1107));
break;
case ReporterIonMassModeConstants.TMTTwoMZ:
// TMT duplex Isobaric tags (from Thermo)
reporterIons.Add(new clsReporterIonInfo(126.1283));
reporterIons.Add(new clsReporterIonInfo(127.1316));
break;
case ReporterIonMassModeConstants.TMTSixMZ:
// TMT 6-plex Isobaric tags (from Thermo), aka TMT6
// These mass values are for HCD spectra; ETD spectra are exactly 12 Da lighter
// ' Old values:
reporterIons.Add(new clsReporterIonInfo(126.127725)); // 126.1283
reporterIons.Add(new clsReporterIonInfo(127.12476)); // 127.1316
reporterIons.Add(new clsReporterIonInfo(128.134433)); // 128.135
reporterIons.Add(new clsReporterIonInfo(129.131468)); // 129.1383
reporterIons.Add(new clsReporterIonInfo(130.141141)); // 130.1417
reporterIons.Add(new clsReporterIonInfo(131.138176)); // 131.1387
break;
case ReporterIonMassModeConstants.TMTTenMZ:
// TMT 10-plex Isobaric tags (from Thermo), aka TMT10
// These mass values are for HCD spectra; ETD spectra are exactly 12 Da lighter
// Several of the reporter ion masses are just 49 ppm apart, thus you must use a very tight tolerance of +/-0.003 Da (which is +/-23 ppm)
reporterIons.Add(new clsReporterIonInfo(126.127726));
reporterIons.Add(new clsReporterIonInfo(127.124761)); // 127N
reporterIons.Add(new clsReporterIonInfo(127.131081)); // 127C
reporterIons.Add(new clsReporterIonInfo(128.128116)); // 128N
reporterIons.Add(new clsReporterIonInfo(128.134436)); // 128C
reporterIons.Add(new clsReporterIonInfo(129.131471)); // 129N
reporterIons.Add(new clsReporterIonInfo(129.137790)); // 129C
reporterIons.Add(new clsReporterIonInfo(130.134825)); // 130N
reporterIons.Add(new clsReporterIonInfo(130.141145)); // 130C
reporterIons.Add(new clsReporterIonInfo(131.138180)); // 131N
break;
case ReporterIonMassModeConstants.TMTElevenMZ:
// TMT 11-plex Isobaric tags (from Thermo), aka TMT11
// These mass values are for HCD spectra; ETD spectra are exactly 12 Da lighter
// Several of the reporter ion masses are just 49 ppm apart, thus you must use a very tight tolerance of +/-0.003 Da (which is +/-23 ppm)
reporterIons.Add(new clsReporterIonInfo(126.127726)); //
reporterIons.Add(new clsReporterIonInfo(127.124761)); // 127N
reporterIons.Add(new clsReporterIonInfo(127.131081)); // 127C
reporterIons.Add(new clsReporterIonInfo(128.128116)); // 128N
reporterIons.Add(new clsReporterIonInfo(128.134436)); // 128C
reporterIons.Add(new clsReporterIonInfo(129.131471)); // 129N
reporterIons.Add(new clsReporterIonInfo(129.137790)); // 129C
reporterIons.Add(new clsReporterIonInfo(130.134825)); // 130N
reporterIons.Add(new clsReporterIonInfo(130.141145)); // 130C
reporterIons.Add(new clsReporterIonInfo(131.138180)); // 131N
reporterIons.Add(new clsReporterIonInfo(131.144499)); // 131C
break;
case ReporterIonMassModeConstants.TMTSixteenMZ:
// ReSharper disable once CommentTypo
// TMT 16-plex Isobaric tags (from Thermo), aka TMT16 or TMTpro
// Several of the reporter ion masses are just 49 ppm apart, thus you must use a very tight tolerance of +/-0.003 Da (which is +/-23 ppm)
reporterIons.Add(new clsReporterIonInfo(126.127726)); //
reporterIons.Add(new clsReporterIonInfo(127.124761)); // 127N
reporterIons.Add(new clsReporterIonInfo(127.131081)); // 127C
reporterIons.Add(new clsReporterIonInfo(128.128116)); // 128N
reporterIons.Add(new clsReporterIonInfo(128.134436)); // 128C
reporterIons.Add(new clsReporterIonInfo(129.131471)); // 129N
reporterIons.Add(new clsReporterIonInfo(129.13779)); // 129C
reporterIons.Add(new clsReporterIonInfo(130.134825)); // 130N
reporterIons.Add(new clsReporterIonInfo(130.141145)); // 130C
reporterIons.Add(new clsReporterIonInfo(131.13818)); // 131N
reporterIons.Add(new clsReporterIonInfo(131.144499)); // 131C
reporterIons.Add(new clsReporterIonInfo(132.141535)); // 132N
reporterIons.Add(new clsReporterIonInfo(132.147855)); // 132C
reporterIons.Add(new clsReporterIonInfo(133.14489)); // 133N
reporterIons.Add(new clsReporterIonInfo(133.15121)); // 133C
reporterIons.Add(new clsReporterIonInfo(134.148245)); // 134N
break;
case ReporterIonMassModeConstants.ITraqEightMZHighRes:
// ITRAQ eight-plex Isobaric tags (iTRAQ8), High-Res MS/MS
reporterIons.Add(new clsReporterIonInfo(113.107873));
reporterIons.Add(new clsReporterIonInfo(114.111228));
reporterIons.Add(new clsReporterIonInfo(115.108263));
reporterIons.Add(new clsReporterIonInfo(116.111618));
reporterIons.Add(new clsReporterIonInfo(117.114973));
reporterIons.Add(new clsReporterIonInfo(118.112008));
reporterIons.Add(new clsReporterIonInfo(119.115363));
reporterIons.Add(new clsReporterIonInfo(121.122072));
break;
case ReporterIonMassModeConstants.ITraqEightMZLowRes:
// ITRAQ eight-plex Isobaric tags (iTRAQ8), Low-Res MS/MS
reporterIons.Add(new clsReporterIonInfo(113.107873));
reporterIons.Add(new clsReporterIonInfo(114.111228));
reporterIons.Add(new clsReporterIonInfo(115.108263));
reporterIons.Add(new clsReporterIonInfo(116.111618));
reporterIons.Add(new clsReporterIonInfo(117.114973));
reporterIons.Add(new clsReporterIonInfo(118.112008));
reporterIons.Add(new clsReporterIonInfo(119.115363));
// This corresponds to immonium ion loss from Phenylalanine (147.06841 - 26.9871 since Immonium is CO minus H)
reporterIons.Add(new clsReporterIonInfo(120.08131, true));
reporterIons.Add(new clsReporterIonInfo(121.122072));
break;
case ReporterIonMassModeConstants.PCGalnaz:
// ReSharper disable CommentTypo
// Custom reporter ions for Josh Alfaro
reporterIons.Add(new clsReporterIonInfo(204.0871934)); // C8H14NO5
reporterIons.Add(new clsReporterIonInfo(300.130787)); // C11H18N5O5
reporterIons.Add(new clsReporterIonInfo(503.2101566)); // C19H31N6O10
break;
case ReporterIonMassModeConstants.HemeCFragment:
// Custom reporter ions for Eric Merkley
reporterIons.Add(new clsReporterIonInfo(616.1767));
reporterIons.Add(new clsReporterIonInfo(617.1845));
break;
case ReporterIonMassModeConstants.LycAcetFragment:
// Custom reporter ions for Ernesto Nakayasu
reporterIons.Add(new clsReporterIonInfo(126.09134));
reporterIons.Add(new clsReporterIonInfo(127.094695));
break;
case ReporterIonMassModeConstants.OGlcNAc:
// O-GlcNAc
reporterIons.Add(new clsReporterIonInfo(204.0872));
reporterIons.Add(new clsReporterIonInfo(300.13079));
reporterIons.Add(new clsReporterIonInfo(503.21017));
break;
case ReporterIonMassModeConstants.FrackingAmine20160217:
// Product ions associated with FrackingFluid_amine_1_02172016
reporterIons.Add(new clsReporterIonInfo(157.089));
reporterIons.Add(new clsReporterIonInfo(170.097));
reporterIons.Add(new clsReporterIonInfo(234.059));
break;
case ReporterIonMassModeConstants.FSFACustomCarbonyl:
// Custom product ions from Chengdong Xu
reporterIons.Add(new clsReporterIonInfo(171.104));
reporterIons.Add(new clsReporterIonInfo(236.074));
reporterIons.Add(new clsReporterIonInfo(257.088));
break;
case ReporterIonMassModeConstants.FSFACustomCarboxylic:
// Custom product ions from Chengdong Xu
reporterIons.Add(new clsReporterIonInfo(171.104));
reporterIons.Add(new clsReporterIonInfo(234.058));
reporterIons.Add(new clsReporterIonInfo(336.174));
break;
case ReporterIonMassModeConstants.FSFACustomHydroxyl:
// Custom product ions from Chengdong Xu
reporterIons.Add(new clsReporterIonInfo(151.063));
reporterIons.Add(new clsReporterIonInfo(166.087));
break;
// ReSharper restore CommentTypo
case ReporterIonMassModeConstants.Acetylation:
// Reporter ions for peptides with acetylated lysine residues
reporterIons.Add(new clsReporterIonInfo(126.09134));
reporterIons.Add(new clsReporterIonInfo(143.11789));
break;
case ReporterIonMassModeConstants.NativeOGlcNAc:
// Native O-GlcNAc
reporterIons.Add(new clsReporterIonInfo(126.055));
reporterIons.Add(new clsReporterIonInfo(138.055));
reporterIons.Add(new clsReporterIonInfo(144.065));
reporterIons.Add(new clsReporterIonInfo(168.066));
reporterIons.Add(new clsReporterIonInfo(186.076));
reporterIons.Add(new clsReporterIonInfo(204.087));
reporterIons.Add(new clsReporterIonInfo(366.14));
break;
default:
// Includes ReporterIonMassModeConstants.CustomOrNone
reporterIons.Clear();
break;
}
foreach (var reporterIon in reporterIons)
{
reporterIon.MZToleranceDa = mzToleranceDa;
}
return reporterIons;
}
/// <summary>
/// Get a description of the given reporter ion mode
/// </summary>
/// <param name="reporterIonMode"></param>
public static string GetReporterIonModeDescription(ReporterIonMassModeConstants reporterIonMode)
{
return reporterIonMode switch
{
ReporterIonMassModeConstants.CustomOrNone => "Custom/None",
ReporterIonMassModeConstants.ITraqFourMZ => "4-plex iTraq",
ReporterIonMassModeConstants.ITraqETDThreeMZ => "3-plex ETD iTraq",
ReporterIonMassModeConstants.TMTTwoMZ => "2-plex TMT",
ReporterIonMassModeConstants.TMTSixMZ => "6-plex TMT",
ReporterIonMassModeConstants.TMTTenMZ => "10-plex TMT",
ReporterIonMassModeConstants.TMTElevenMZ => "11-plex TMT",
// ReSharper disable once StringLiteralTypo
ReporterIonMassModeConstants.TMTSixteenMZ => "16-plex TMT (aka TMTpro)",
ReporterIonMassModeConstants.ITraqEightMZHighRes => "8-plex iTraq (High Res MS/MS)",
ReporterIonMassModeConstants.ITraqEightMZLowRes => "8-plex iTraq (Low Res MS/MS)",
ReporterIonMassModeConstants.PCGalnaz => "PCGalnaz (300.13 m/z and 503.21 m/z)",
ReporterIonMassModeConstants.HemeCFragment => "Heme C (616.18 m/z and 616.19 m/z)",
ReporterIonMassModeConstants.LycAcetFragment => "Lys Acet (126.091 m/z and 127.095 m/z)",
ReporterIonMassModeConstants.OGlcNAc => "O-GlcNAc (204.087, 300.13, and 503.21 m/z)",
ReporterIonMassModeConstants.NativeOGlcNAc => "Native O-GlcNAc (126.055, 138.055, 144.065, 168.066, 186.076, 204.087, and 366.14 m/z)",
ReporterIonMassModeConstants.FrackingAmine20160217 => "Fracking Amine 20160217 (157.089, 170.097, and 234.059 m/z)",
ReporterIonMassModeConstants.FSFACustomCarbonyl => "FSFA Custom Carbonyl (171.104, 236.074, 157.088 m/z)",
ReporterIonMassModeConstants.FSFACustomCarboxylic => "FSFA Custom Carboxylic (171.104, 234.058, 336.174 m/z)",
ReporterIonMassModeConstants.FSFACustomHydroxyl => "FSFA Custom Hydroxyl (151.063 and 166.087 m/z)",
ReporterIonMassModeConstants.Acetylation => "Acetylated K (126.091 and 143.118 m/z)",
_ => throw new ArgumentOutOfRangeException(nameof(reporterIonMode), reporterIonMode, null)
};
}
private void InitializeReporterIonInfo()
{
ReporterIonList.Clear();
SetReporterIonMassMode(ReporterIonMassModeConstants.CustomOrNone);
ReporterIonToleranceDaDefault = REPORTER_ION_TOLERANCE_DA_DEFAULT;
ReporterIonApplyAbundanceCorrection = true;
ReporterIonITraq4PlexCorrectionFactorType = clsITraqIntensityCorrection.CorrectionFactorsiTRAQ4Plex.ABSciex;
ReporterIonSaveObservedMasses = false;
ReporterIonSaveUncorrectedIntensities = false;
}
/// <summary>
/// Set the reporter ion mass mode
/// </summary>
/// <param name="reporterIonMassMode"></param>
public void SetReporterIonMassMode(ReporterIonMassModeConstants reporterIonMassMode)
{
if (reporterIonMassMode == ReporterIonMassModeConstants.ITraqEightMZHighRes)
{
SetReporterIonMassMode(reporterIonMassMode, REPORTER_ION_TOLERANCE_DA_DEFAULT_ITRAQ8_HIGH_RES);
}
else
{
SetReporterIonMassMode(reporterIonMassMode, REPORTER_ION_TOLERANCE_DA_DEFAULT);
}
}
/// <summary>
/// Set the reporter ion mass mode
/// </summary>
/// <param name="reporterIonMassMode"></param>
/// <param name="mzToleranceDa"></param>
public void SetReporterIonMassMode(
ReporterIonMassModeConstants reporterIonMassMode,
double mzToleranceDa)
{
// Note: If reporterIonMassMode = ReporterIonMassModeConstants.CustomOrNone then nothing is changed
if (reporterIonMassMode != ReporterIonMassModeConstants.CustomOrNone)
{
ReporterIonToleranceDaDefault = mzToleranceDa;
var reporterIonInfo = GetDefaultReporterIons(reporterIonMassMode, mzToleranceDa);
SetReporterIons(reporterIonInfo, false);
mReporterIonMassMode = reporterIonMassMode;
}
}
/// <summary>
/// Define reporter ions to search for
/// </summary>
/// <param name="reporterIons"></param>
/// <param name="customReporterIons"></param>
public void SetReporterIons(
List<clsReporterIonInfo> reporterIons,
bool customReporterIons)
{
ReporterIonList.Clear();
if (reporterIons == null || reporterIons.Count == 0)
{
return;
}
ReporterIonList.Capacity = reporterIons.Count;
foreach (var reporterIon in reporterIons)
{
if (reporterIon.MZToleranceDa < REPORTER_ION_TOLERANCE_DA_MINIMUM)
{
reporterIon.MZToleranceDa = REPORTER_ION_TOLERANCE_DA_MINIMUM;
}
ReporterIonList.Add(reporterIon);
}
if (customReporterIons)
{
mReporterIonMassMode = ReporterIonMassModeConstants.CustomOrNone;
}
}
/// <summary>
/// Define reporter ions to search for
/// </summary>
/// <param name="reporterIonMZList"></param>
/// <remarks>Will use REPORTER_ION_TOLERANCE_DA_DEFAULT for the search tolerance</remarks>
public void SetReporterIons(
double[] reporterIonMZList)
{
SetReporterIons(reporterIonMZList, REPORTER_ION_TOLERANCE_DA_DEFAULT);
}
/// <summary>
/// Define reporter ions to search for
/// </summary>
/// <param name="reporterIonMZList"></param>
/// <param name="mzToleranceDa">Search tolerance (half width)</param>
public void SetReporterIons(
double[] reporterIonMZList,
double mzToleranceDa)
{
SetReporterIons(reporterIonMZList, mzToleranceDa, true);
}
/// <summary>
/// Define reporter ions to search for
/// </summary>
/// <param name="reporterIonMZList"></param>
/// <param name="mzToleranceDa">Search tolerance (half width); must be 0.001 or larger</param>
/// <param name="customReporterIons">True if these are custom reporter ions</param>
/// <remarks>When customReportIons is true, sets mReporterIonMassMode to ReporterIonMassModeConstants.CustomOrNone</remarks>
public void SetReporterIons(
double[] reporterIonMZList,
double mzToleranceDa,
bool customReporterIons)
{
if (mzToleranceDa < REPORTER_ION_TOLERANCE_DA_MINIMUM)
{
mzToleranceDa = REPORTER_ION_TOLERANCE_DA_MINIMUM;
}
ReporterIonList.Clear();
if (reporterIonMZList == null || reporterIonMZList.Length == 0)
{
mReporterIonMassMode = ReporterIonMassModeConstants.CustomOrNone;
return;
}
foreach (var reporterIonMZ in reporterIonMZList)
{
var newReporterIon = new clsReporterIonInfo(reporterIonMZ)
{
MZToleranceDa = mzToleranceDa
};
ReporterIonList.Add(newReporterIon);
}
if (customReporterIons)
{
mReporterIonMassMode = ReporterIonMassModeConstants.CustomOrNone;
}
}
/// <summary>
/// Look at the m/z values in ReporterIonList to determine the minimum and maximum m/z values
/// Update MZIntensityFilterIgnoreRangeStart and MZIntensityFilterIgnoreRangeEnd to be
/// 2x .MZToleranceDa away from the minimum and maximum
/// </summary>
public void UpdateMZIntensityFilterIgnoreRange()
{
if (!ReporterIonStatsEnabled || ReporterIonList.Count == 0)
{
MZIntensityFilterIgnoreRangeStart = 0;
MZIntensityFilterIgnoreRangeEnd = 0;
return;
}
MZIntensityFilterIgnoreRangeStart = ReporterIonList[0].MZ - ReporterIonList[0].MZToleranceDa * 2;
MZIntensityFilterIgnoreRangeEnd = ReporterIonList[0].MZ + ReporterIonList[0].MZToleranceDa * 2;
foreach (var reporterIon in ReporterIonList)
{
var mzStart = reporterIon.MZ - reporterIon.MZToleranceDa * 2;
MZIntensityFilterIgnoreRangeStart = Math.Min(MZIntensityFilterIgnoreRangeStart, mzStart);
var mzEnd = reporterIon.MZ + reporterIon.MZToleranceDa * 2;
MZIntensityFilterIgnoreRangeEnd = Math.Max(MZIntensityFilterIgnoreRangeEnd, mzEnd);
}
}
}
}