protected bool IsValid(SapMatchedCount smc)
{
if (smc.MS3Matched.Count < options.MinimumMatchedMS3SpectrumCount)
{
return(false);
}
if (smc.MS3Matched.All(l => l < options.MinimumMatchedMS3IonCount))
{
return(false);
}
return(true);
}
protected static void OutputIntervalResult(StreamWriter sw, MS2Item query, MS2Item libms2, SapMatchedCount ms3match)
{
sw.WriteLine("{0}\t{1}\t{2}\t{3}\t{4}\t{5}\t{6}\t{7}\t{8}\t{9}\t{10}\t{11}",
query.GetFileScans(),
query.Precursor,
query.Charge,
libms2.Precursor,
ms3match.PrecursorMatched.ConvertAll(m => m.ToString()).Merge(";"),
ms3match.MS3Matched.ConvertAll(m => m.ToString()).Merge(";"),
(query.Precursor - libms2.Precursor) * query.Charge,
libms2.GetFileScans(),
libms2.Peptide,
libms2.Score,
libms2.ExpectValue,
libms2.Proteins);
}
protected void CheckTerminalLoss(List <SapPredicted> predicted, MS2Item query, MS2Item libms2, SapMatchedCount ms3match)
{
foreach (var nl in libms2.TerminalLoss)
{
if (nl.Precursor >= query.MinPrecursorMz && nl.Precursor <= query.MaxPrecursorMz)
{
var curp = new SapPredicted()
{
Ms2 = query,
LibMs2 = libms2,
Matched = ms3match,
Target = new TargetVariant()
{
Source = PeptideUtils.GetPureSequence(libms2.Peptide),
Target = new HashSet <string>(new[] { nl.Sequence }),
DeltaMass = (nl.Precursor - libms2.Precursor) * libms2.Charge,
TargetType = nl.IsNterminal ? VariantType.NTerminalLoss : VariantType.CTerminalLoss
}
};
predicted.Add(curp);
}
}
}
protected void CheckTerminalExtension(List <SapPredicted> predicted, MS2Item query, MS2Item libms2, SapMatchedCount ms3match)
{
var bNterminalValid = libms2.Peptide.StartsWith("-");
var bCterminalValid = libms2.Peptide.EndsWith("-");
if (bNterminalValid || bCterminalValid)
{
foreach (var ne in options.ExtensionDeltaMassList)
{
var neMz = libms2.Precursor + ne.DeltaMass / libms2.Charge;
if (neMz >= query.MinPrecursorMz && neMz <= query.MaxPrecursorMz)
{
var seq = PeptideUtils.GetPureSequence(libms2.Peptide);
if (bNterminalValid)
{
predicted.Add(new SapPredicted()
{
Ms2 = query,
LibMs2 = libms2,
Matched = ms3match,
Target = new TargetVariant()
{
Source = PeptideUtils.GetPureSequence(libms2.Peptide),
Target = new HashSet <string>(from t in ne.Target select t + seq),
DeltaMass = ne.DeltaMass,
TargetType = VariantType.NTerminalExtension
}
});
}
if (bCterminalValid)
{
predicted.Add(new SapPredicted()
{
Ms2 = query,
LibMs2 = libms2,
Matched = ms3match,
Target = new TargetVariant()
{
Source = PeptideUtils.GetPureSequence(libms2.Peptide),
Target = new HashSet <string>(from t in ne.Target select seq + t),
DeltaMass = ne.DeltaMass,
TargetType = VariantType.CTerminalExtension
}
});
}
}
}
}
}
protected void CheckSAP(List <SapPredicted> predicted, MS2Item query, MS2Item libms2, SapMatchedCount ms3match)
{
foreach (var aa in libms2.AminoacidCompsition)
{
var lst = options.SubstitutionDeltaMassMap[aa];
//the list has been ordered by deltamass
foreach (var ts in lst)
{
var targetMz = libms2.Precursor + ts.DeltaMass / query.Charge;
if (targetMz < query.MinPrecursorMz)
{
continue;
}
if (targetMz > query.MaxPrecursorMz)
{
break;
}
var curp = new SapPredicted()
{
Ms2 = query,
LibMs2 = libms2,
Matched = ms3match,
Target = new TargetVariant()
{
Source = ts.Source,
Target = ts.Target,
DeltaMass = ts.DeltaMass,
TargetType = ts.TargetType
}
};
predicted.Add(curp);
}
}
}
