private IEnumerable <SpectrumFilterPair> FindFilterPairs(IsolationWindowFilter isoWin,
FullScanAcquisitionMethod acquisitionMethod, bool ignoreIsolationScheme = false)
{
if (!isoWin.IsolationMz.HasValue)
{
return(new SpectrumFilterPair[0]); // empty
}
// Return cached value from dictionary if we've seen this target previously.
var isoWinKey = isoWin;
IList <SpectrumFilterPair> filterPairsCached;
if (_filterPairDictionary.TryGetValue(isoWinKey, out filterPairsCached))
{
return(filterPairsCached);
}
var filterPairs = new List <SpectrumFilterPair>();
if (acquisitionMethod == FullScanAcquisitionMethod.DIA)
{
var isoTargMz = isoWin.IsolationMz;
double?isoTargWidth = isoWin.IsolationWidth;
if (!ignoreIsolationScheme)
{
CalcDiaIsolationValues(ref isoTargMz, ref isoTargWidth);
}
if (isoTargWidth.HasValue)
{
// For multiple case, find the first possible value, and iterate until
// no longer matching or the end of the array is encountered
int iFilter = IndexOfFilter(isoTargMz, isoTargWidth.Value);
if (iFilter != -1)
{
while (iFilter < _filterMzValues.Length && CompareMz(isoTargMz,
_filterMzValues[iFilter].Q1, isoTargWidth.Value) == 0)
{
filterPairs.Add(_filterMzValues[iFilter++]);
}
}
}
}
else
{
// For single (Targeted) case, review all possible matches for the one closest to the
// desired precursor m/z value.
// per "Issue 263: Too strict about choosing only one precursor for every MS/MS scan in Targeted MS/MS",
// if more than one match at this m/z value return a list
double minMzDelta = double.MaxValue;
double mzDeltaEpsilon = Math.Min(_instrument.MzMatchTolerance, .0001);
// Isolation width for single is based on the instrument m/z match tolerance
var isoTargMz = isoWin.IsolationMz;
var isoWinSingle = new IsolationWindowFilter(isoTargMz, _instrument.MzMatchTolerance * 2);
foreach (var filterPair in FindFilterPairs(isoWinSingle, FullScanAcquisitionMethod.DIA, true))
{
double mzDelta = Math.Abs(isoTargMz - filterPair.Q1);
if (mzDelta < minMzDelta) // new best match
{
minMzDelta = mzDelta;
// are any existing matches no longer within epsilion of new best match?
for (int n = filterPairs.Count; n-- > 0;)
{
if ((Math.Abs(isoTargMz - filterPairs[n].Q1) - minMzDelta) > mzDeltaEpsilon)
{
filterPairs.RemoveAt(n); // no longer a match by our new standard
}
}
filterPairs.Add(filterPair);
}
else if ((mzDelta - minMzDelta) <= mzDeltaEpsilon)
{
filterPairs.Add(filterPair); // not the best, but close to it
}
}
}
_filterPairDictionary[isoWinKey] = filterPairs;
return(filterPairs);
}
private bool Equals(IsolationWindowFilter other)
{
return(other.IsolationMz.Equals(IsolationMz) &&
other.IsolationWidth.Equals(IsolationWidth));
}
private static bool IsSimIsolation(IsolationWindowFilter isoWin)
{
return(isoWin.IsolationMz.HasValue && isoWin.IsolationWidth.HasValue &&
// TODO: Introduce a variable cut-off in the document settings
isoWin.IsolationWidth.Value < 200);
}
private IEnumerable<SpectrumFilterPair> FindFilterPairs(IsolationWindowFilter isoWin,
FullScanAcquisitionMethod acquisitionMethod, bool ignoreIsolationScheme = false)
{
if (!isoWin.IsolationMz.HasValue)
return new SpectrumFilterPair[0]; // empty
// Return cached value from dictionary if we've seen this target previously.
var isoWinKey = isoWin;
IList<SpectrumFilterPair> filterPairsCached;
if (_filterPairDictionary.TryGetValue(isoWinKey, out filterPairsCached))
{
return filterPairsCached;
}
var filterPairs = new List<SpectrumFilterPair>();
if (acquisitionMethod == FullScanAcquisitionMethod.DIA)
{
double isoTargMz = isoWin.IsolationMz.Value;
double? isoTargWidth = isoWin.IsolationWidth;
if (!ignoreIsolationScheme)
{
CalcDiaIsolationValues(ref isoTargMz, ref isoTargWidth);
}
if (isoTargWidth.HasValue)
{
// For multiple case, find the first possible value, and iterate until
// no longer matching or the end of the array is encountered
int iFilter = IndexOfFilter(isoTargMz, isoTargWidth.Value);
if (iFilter != -1)
{
while (iFilter < _filterMzValues.Length && CompareMz(isoTargMz,
_filterMzValues[iFilter].Q1, isoTargWidth.Value) == 0)
filterPairs.Add(_filterMzValues[iFilter++]);
}
}
}
else
{
// For single (Targeted) case, review all possible matches for the one closest to the
// desired precursor m/z value.
// per "Issue 263: Too strict about choosing only one precursor for every MS/MS scan in Targeted MS/MS",
// if more than one match at this m/z value return a list
double minMzDelta = double.MaxValue;
double mzDeltaEpsilon = Math.Min(_instrument.MzMatchTolerance, .0001);
// Isolation width for single is based on the instrument m/z match tolerance
double isoTargMz = isoWin.IsolationMz.Value;
var isoWinSingle = new IsolationWindowFilter(isoTargMz, _instrument.MzMatchTolerance * 2);
foreach (var filterPair in FindFilterPairs(isoWinSingle, FullScanAcquisitionMethod.DIA, true))
{
double mzDelta = Math.Abs(isoTargMz - filterPair.Q1);
if (mzDelta < minMzDelta) // new best match
{
minMzDelta = mzDelta;
// are any existing matches no longer within epsilion of new best match?
for (int n = filterPairs.Count; n-- > 0; )
{
if ((Math.Abs(isoTargMz - filterPairs[n].Q1) - minMzDelta) > mzDeltaEpsilon)
{
filterPairs.RemoveAt(n); // no longer a match by our new standard
}
}
filterPairs.Add(filterPair);
}
else if ((mzDelta - minMzDelta) <= mzDeltaEpsilon)
{
filterPairs.Add(filterPair); // not the best, but close to it
}
}
}
_filterPairDictionary[isoWinKey] = filterPairs;
return filterPairs;
}
private static bool IsSimIsolation(IsolationWindowFilter isoWin)
{
return isoWin.IsolationMz.HasValue && isoWin.IsolationWidth.HasValue &&
// TODO: Introduce a variable cut-off in the document settings
isoWin.IsolationWidth.Value < 200;
}
private bool Equals(IsolationWindowFilter other)
{
return other.IsolationMz.Equals(IsolationMz) &&
other.IsolationWidth.Equals(IsolationWidth);
}
