public IEnumerable<ExtractedSpectrum> SrmSpectraFromMs1Scan(double? retentionTime,
IList<MsPrecursor> precursors, MsDataSpectrum[] spectra)
{
if (!EnabledMs || !retentionTime.HasValue || spectra == null)
yield break;
// All filter pairs have a shot at filtering the MS1 scans
bool isSimSpectra = spectra.Any(IsSimSpectrum);
foreach (var filterPair in FindMs1FilterPairs(precursors))
{
if (!filterPair.ContainsRetentionTime(retentionTime.Value))
continue;
var filteredSrmSpectrum = filterPair.FilterQ1SpectrumList(spectra, isSimSpectra);
if (filteredSrmSpectrum != null)
yield return filteredSrmSpectrum;
}
}
public IEnumerable<ExtractedSpectrum> Extract(double? retentionTime, MsDataSpectrum[] spectra)
{
if (!EnabledMsMs || !retentionTime.HasValue || !spectra.Any())
yield break;
var handlingType = _fullScan.IsolationScheme == null || _fullScan.IsolationScheme.SpecialHandling == null
? IsolationScheme.SpecialHandlingType.NONE
: _fullScan.IsolationScheme.SpecialHandling;
bool ignoreIso = handlingType == IsolationScheme.SpecialHandlingType.OVERLAP ||
handlingType == IsolationScheme.SpecialHandlingType.OVERLAP_MULTIPLEXED;
foreach (var isoWin in GetIsolationWindows(spectra[0].Precursors))
{
foreach (var filterPair in FindFilterPairs(isoWin, _acquisitionMethod, ignoreIso))
{
if (!filterPair.ContainsRetentionTime(retentionTime.Value))
continue;
var filteredSrmSpectrum = filterPair.FilterQ3SpectrumList(spectra, _isWatersMse && GetMseLevel() > 1);
if (filteredSrmSpectrum != null)
yield return filteredSrmSpectrum;
}
}
}