/// <summary>
/// The extent of the isolation window in m/z above the isolation window target m/z.
/// The lower and upper offsets may be asymmetric about the target m/z. [PSI:MS]
/// </summary>
/// <param name="etype"></param>
/// <param name="offset"></param>
/// <returns></returns>
public static IParamEdit MS_IsolationWindowUpperOffset(
this IParamEdit etype, double offset)
{
if (offset < 0)
{
throw new ArgumentOutOfRangeException("offset");
}
return(etype.SetCvParam("MS:1000829").SetValue(offset).MS_Mz());
}
/// <summary>
/// Stages of ms achieved in a multi stage mass spectrometry experiment. [PSI:MS]
/// </summary>
/// <param name="etype"></param>
/// <returns></returns>
public static IParamEdit MS_MsLevel(
this IParamEdit etype, int level)
{
if (level < 1)
{
throw new ArgumentOutOfRangeException("level");
}
return(etype.SetCvParam("MS:1000511").SetValue(level).NoUnit());
}
/// <summary>
/// The primary or reference m/z about which the isolation window is defined. [PSI:MS]
/// </summary>
/// <param name="etype"></param>
/// <param name="mz"></param>
/// <returns></returns>
public static IParamEdit MS_IsolationWindowTargetMz(
this IParamEdit etype, double mz)
{
if (mz < 0)
{
throw new ArgumentOutOfRangeException("mz");
}
return(etype.SetCvParam("MS:1000827").SetValue(mz).MS_Mz());
}
/// <summary>
/// Energy for an ion experiencing collision with a stationary gas particle resulting in dissociation of the ion. [PSI:MS]
/// </summary>
/// <param name="etype"></param>
/// <param name="ce"></param>
/// <returns></returns>
public static IParamEdit MS_CollisionEnergy(
this IParamEdit etype, double ce)
{
if (ce < 0)
{
throw new ArgumentOutOfRangeException("ce");
}
return(etype.SetCvParam("MS:1000045").SetValue(ce).UO_Electronvolt());
}
/// <summary>
/// Mass-to-charge ratio of a precursor ion selected for fragmentation. [PSI:PI]
/// </summary>
/// <param name="etype"></param>
/// <param name="mz"></param>
/// <returns></returns>
public static IParamEdit MS_SelectedIonMz(
this IParamEdit etype, double mz)
{
if (mz < 0)
{
throw new ArgumentOutOfRangeException("mz");
}
return(etype.SetCvParam("MS:1002234").SetValue(mz).MS_Mz());
}
private static SWATHIndexerItem CreateItem(MassSpectrum ms)
{
if (ms.BeginParamEdit().Get_MS_Level().GetInt32() != 2)
{
return(null);
}
if (ms.Precursors.Count < 1 ||
ms.Precursors[0].SelectedIons.Count < 1 ||
ms.Scans.Count < 1)
{
return(null);
}
IValueConverter rt = ms.Scans[0].BeginParamEdit().Get_MS_ScanStartTime();
IParamEdit isoWin = ms.Precursors[0].IsolationWindow.BeginParamEdit();
IValueConverter mz = isoWin.Get_MS_IsolationWindowTargetMz();
IValueConverter mzLow = isoWin.Get_MS_IsolationWindowLowerOffset();
IValueConverter mzHigh = isoWin.Get_MS_IsolationWindowUpperOffset();
if (rt.HasValue() &&
mz.HasValue() &&
mzLow.HasValue() &&
mzHigh.HasValue())
{
double mzValue = mz.GetDouble();
return(new SWATHIndexerItem()
{
Mz = mz.GetDouble(),
MzStart = SaveSubtract(mzValue, mzLow.GetDouble()),
MzEnd = SaveAdd(mzValue, mzHigh.GetDouble()),
Rt = rt.GetDouble(),
SpectrumID = ms.ID
});
}
else
{
return(null);
}
}
/// <summary>
/// Andromeda is a peptide search engine. [MS:PI]
/// </summary>
/// <param name="etype"></param>
/// <returns></returns>
public static IParamEdit MS_Andromeda(
this IParamEdit etype)
{
return(etype.SetCvParam("MS:1002337").NoValue().NoUnit());
}
/// <summary>
/// The time that an analyzer started a scan, relative to the start of the MS run. [PSI:MS]
/// </summary>
public static IValueConverter Get_MS_ScanStartTime(this IParamEdit etype)
{
return(etype.GetCvParam("MS:1000016"));
}
/// <summary>
/// The theoretical mass of the molecule (e.g. the peptide sequence and its modifications). [MS:PI]
/// </summary>
/// <param name="etype"></param>
/// <param name="mass"></param>
/// <returns></returns>
public static IParamEdit MS_TheoreticalMass(
this IParamEdit etype, double mass)
{
return(etype.SetCvParam("MS:1001117").SetValue(mass).UO_Dalton());
}
/// <summary>
/// Compression using MS-Numpress positive integer compression. [https://github.com/fickludd/ms-numpress]
/// </summary>
/// <param name="etype"></param>
/// <returns></returns>
public static IParamEdit MS_MSNumpressPositiveIntegerCompression(
this IParamEdit etype)
{
return(etype.SetCvParam("MS:1002313").NoValue().NoUnit());
}
/// <summary>
/// The time that an analyzer started a scan, relative to the start of the MS run. [PSI:MS]
/// </summary>
/// <param name="etype"></param>
/// <param name="value"></param>
/// <returns></returns>
public static IHasUnit MS_ScanStartTime(
this IParamEdit etype, double value)
{
return(etype.SetCvParam("MS:1000016").SetValue(value));
}
/// <summary>
/// The data type PEP (posterior error probability) produced by MaxQuant. [MS:MS]
/// </summary>
/// <param name="etype"></param>
/// <param name="pep"></param>
/// <returns></returns>
public static IParamEdit MS_MaxQuantPEP(
this IParamEdit etype, double pep)
{
return(etype.SetCvParam("MS:1001901").SetValue(pep).NoUnit());
}
public static bool Is_MS_32BitInteger(
this IParamEdit etype)
{
return(etype.HasCvParam("MS:1000519"));
}
/// <summary>
/// The data type feature intensity produced by MaxQuant. [MS:MS]
/// </summary>
/// <param name="etype"></param>
/// <param name="pep"></param>
/// <returns></returns>
public static IParamEdit MS_MaxQuantFeatureIntensity(
this IParamEdit etype, double intensity)
{
return(etype.SetCvParam("MS:1001903").SetValue(intensity).NoUnit());
}
public static IParamEdit MS_ThermoRawFormat(
this IParamEdit etype)
{
return(etype.SetCvParam("MS:1000563").NoValue().NoUnit());
}
/// <summary>
/// 32-bit precision little-endian floating point conforming to IEEE-754. [PSI:MS]
/// </summary>
/// <param name="etype"></param>
/// <returns></returns>
public static IParamEdit MS_32BitFloat(
this IParamEdit etype)
{
return(etype.SetCvParam("MS:1000521").NoValue().NoUnit());
}
/// <summary>
/// The extent of the isolation window in m/z above the isolation window target m/z.
/// The lower and upper offsets may be asymmetric about the target m/z. [PSI:MS]
/// </summary>
public static IValueConverter Get_MS_IsolationWindowUpperOffset(
this IParamEdit etype)
{
return(etype.GetCvParam("MS:1000829"));
}
public static IParamEdit MS_SampleBatch(
this IParamEdit etype, string value)
{
return(etype.SetCvParam("MS:1000053").SetValue(value).NoUnit());
}
/// <summary>
/// The primary or reference m/z about which the isolation window is defined. [PSI:MS]
/// </summary>
public static IValueConverter Get_MS_IsolationWindowTargetMz(
this IParamEdit etype)
{
return(etype.GetCvParam("MS:1000827"));
}
public static bool Is_MS_32BitFloat(
this IParamEdit etype)
{
return(etype.HasCvParam("MS:1000521"));
}
/// <summary>
/// The probability based score of the Andromeda search engine. [MS:PI]
/// </summary>
/// <param name="etype"></param>
/// <param name="score"></param>
/// <returns></returns>
public static IParamEdit MS_AndromedaScore(
this IParamEdit etype, double score)
{
return(etype.SetCvParam("MS:1002338").SetValue(score).NoUnit());
}
/// <summary>
/// Compression using MS-Numpress short logged float compression. [https://github.com/fickludd/ms-numpress]
/// </summary>
/// <param name="etype"></param>
/// <returns></returns>
public static IParamEdit MS_MSNumpressShortLoggedFloatCompression(
this IParamEdit etype)
{
return(etype.SetCvParam("MS:1002314").NoValue().NoUnit());
}
/// <summary>
/// MaxQuant is a quantitative proteomics software package designed for analyzing large mass spectrometric data sets.
/// It is specifically aimed at high resolution MS data. [MS:MS]
/// </summary>
/// <param name="etype"></param>
/// <returns></returns>
public static IParamEdit MS_MaxQuant(
this IParamEdit etype)
{
return(etype.SetCvParam("MS:1001583").NoValue().NoUnit());
}
public static IHasUnit MS_SampleConcentration(
this IParamEdit etype, double value)
{
return(etype.SetCvParam("MS:1000006").SetValue(value));
}
public static IHasUnit MS_SampleMass(
this IParamEdit etype, double value)
{
return(etype.SetCvParam("MS:1000004").SetValue(value));
}
/// <summary>
/// Signed 32-bit little-endian integer. [PSI:MS]
/// </summary>
/// <param name="etype"></param>
/// <returns></returns>
public static IParamEdit MS_32BitInteger(
this IParamEdit etype)
{
return(etype.SetCvParam("MS:1000519").NoValue().NoUnit());
}
public static IParamEdit MS_GenericExperimentalCondition(
this IParamEdit etype, string value)
{
return(etype.SetCvParam("MS:1001814").SetValue(value).NoUnit());
}
/// <summary>
/// Mass-to-charge ratio of a precursor ion selected for fragmentation. [PSI:PI]
/// </summary>
public static IValueConverter Get_MS_SelectedIonMz(
this IParamEdit etype)
{
return(etype.GetCvParam("MS:1002234"));
}
public static IParamEdit MS_ABIWIFFFormat(
this IParamEdit etype)
{
return(etype.SetCvParam("MS:1000562").NoValue().NoUnit());
}
/// <summary>
/// The charge state of the ion, single or multiple and positive or negatively charged. [PSI:MS]
/// </summary>
/// <param name="etype"></param>
/// <param name="state"></param>
/// <returns></returns>
public static IParamEdit MS_ChargeState(
this IParamEdit etype, int state)
{
return(etype.SetCvParam("MS:1000041").SetValue(state).NoUnit());
}
