public override PrositRTInput.PrositPeptideInput CreatePrositInputRow(SrmSettings settings, PeptideDocNodeWrapper skylineInput,
out PrositException exception)
{
var sequence = PrositHelpers.EncodeSequence(settings, (PeptideDocNode)skylineInput, IsotopeLabelType.light, out exception);
if (sequence == null)
{
return(null);
}
return(new PrositRTInput.PrositPeptideInput(sequence));
}
public override PrositIntensityInput.PrositPrecursorInput CreatePrositInputRow(SrmSettings settings, PeptidePrecursorNCE skylineInput, out PrositException exception)
{
var peptideSequence = PrositHelpers.EncodeSequence(settings, skylineInput.NodePep, IsotopeLabelType.light, out exception);
if (peptideSequence == null) // equivalently, exception != null
{
return(null);
}
var precursorCharge = PrositHelpers.OneHotEncode(skylineInput.NodeGroup.PrecursorCharge - 1, PrositConstants.PRECURSOR_CHARGES);
return(new PrositIntensityInput.PrositPrecursorInput(peptideSequence, precursorCharge, skylineInput.NCE.Value / 100.0f));
}
/// <summary> /// Construct Prosit input given Skyline input. Note that /// this function does not throw any exceptions but uses the exception out /// parameter to speed up constructing large amounts of inputs. /// </summary> /// <param name="settings">Settings to use for construction</param> /// <param name="skylineInput">The input at the Skyline level (for example docnodes)</param> /// <param name="exception">Exception that occured during the creating Process</param> /// <returns>The input at the Prosit level</returns> public abstract TPrositInputRow CreatePrositInputRow(SrmSettings settings, TSkylineInputRow skylineInput, out PrositException exception);
/// <summary>
/// Sequences are passed to Prosit as an array of indices mapping into an array
/// of amino acids (with modifications). Actually throwing exceptions in this method
/// slows down constructing inputs (for larger data sets with unknown mods (and aa's)significantly,
/// which is why PrositExceptions (only) are set as an output parameter and null is returned.
/// </summary>
public static int[] EncodeSequence(SrmSettings settings, ISequenceContainer peptide, IsotopeLabelType label, out PrositException exception)
{
if (!peptide.Target.IsProteomic)
{
throw new PrositSmallMoleculeException(peptide.ModifiedTarget);
}
var sequence = peptide.Target.Sequence;
if (sequence.Length > PrositConstants.PEPTIDE_SEQ_LEN)
{
exception = new PrositPeptideTooLongException(peptide.ModifiedTarget);
return(null);
}
var modifiedSequence = ModifiedSequence.GetModifiedSequence(settings, peptide, label);
var result = new int[PrositConstants.PEPTIDE_SEQ_LEN];
for (var i = 0; i < sequence.Length; ++i)
{
if (!PrositConstants.AMINO_ACIDS.TryGetValue(sequence[i], out var prositAA))
{
exception = new PrositUnsupportedAminoAcidException(peptide.ModifiedTarget, i);
return(null);
}
var mods = modifiedSequence.ExplicitMods.Where(m => m.IndexAA == i).ToArray();
foreach (var mod in mods)
{
if (mod.MonoisotopicMass == 0.0)
{
continue;
}
var staticMod = UniMod.FindMatchingStaticMod(mod.StaticMod, true) ?? mod.StaticMod;
if (!PrositConstants.MODIFICATIONS.TryGetValue(staticMod.Name, out var prositAAMod))
{
exception = new PrositUnsupportedModificationException(peptide.ModifiedTarget,
mod.StaticMod,
mod.IndexAA);
return(null);
}
result[i] = prositAAMod.PrositIndex;
break;
}
if (result[i] == 0)
{
// Not modified
result[i] = prositAA.PrositIndex;
}
}
exception = null;
return(result);
}
