/// <summary>
/// This only constructor for CrossLinkResult requires the CrossLink, LC-IMS-MS Feature, and LC Scan.
/// The Mass Shift Results are added later on.
/// </summary>
/// <param name="crossLink"></param>
/// <param name="lcImsMsFeature"></param>
/// <param name="scanLc"></param>
public CrossLinkResult(CrossLink crossLink, LcImsMsFeature lcImsMsFeature, int scanLc)
{
this.CrossLink = crossLink;
this.LcImsMsFeature = lcImsMsFeature;
this.ScanLc = scanLc;
this.MassShiftResults = new MassShiftResult();
}
/// <summary>
/// This only constructor for CrossLinkResult requires the CrossLink, LC-IMS-MS Feature, and LC Scan.
/// The Mass Shift Results are added later on.
/// </summary>
/// <param name="crossLink"></param>
/// <param name="lcImsMsFeature"></param>
/// <param name="scanLc"></param>
public CrossLinkResult(CrossLink crossLink, LcImsMsFeature lcImsMsFeature, int scanLc)
{
this.CrossLink = crossLink;
this.LcImsMsFeature = lcImsMsFeature;
this.ScanLc = scanLc;
this.MassShiftResults = new MassShiftResult();
}
/// <summary>
/// Parses a single line of the input file and returns a single LC-IMS-MS Feature.
/// </summary>
/// <param name="line">The line to read, as a string.</param>
/// <param name="columnMapping">The column mapping for the input file.</param>
/// <returns>A single LcImsMsFeature object created by using the information from the parsed line.</returns>
private static LcImsMsFeature ParseLine(string line, IDictionary <string, int> columnMapping)
{
string[] columns = line.Split('\t');
LcImsMsFeature lcImsMsFeature = new LcImsMsFeature();
if (columnMapping.ContainsKey(FEATURE_INDEX))
{
lcImsMsFeature.FeatureId = int.Parse(columns[columnMapping[FEATURE_INDEX]]);
}
if (columnMapping.ContainsKey(MONOISOTOPIC_MASS))
{
lcImsMsFeature.MassMonoisotopic = double.Parse(columns[columnMapping[MONOISOTOPIC_MASS]]);
}
if (columnMapping.ContainsKey(LC_SCAN_START))
{
lcImsMsFeature.ScanLcStart = int.Parse(columns[columnMapping[LC_SCAN_START]]);
}
if (columnMapping.ContainsKey(LC_SCAN_END))
{
lcImsMsFeature.ScanLcEnd = int.Parse(columns[columnMapping[LC_SCAN_END]]);
}
if (columnMapping.ContainsKey(LC_SCAN_REP))
{
lcImsMsFeature.ScanLcRep = int.Parse(columns[columnMapping[LC_SCAN_REP]]);
}
// Need to subtract 1 because the isos file reports the IMS Scan as 1-based and the peaks file reports it as 0-based. Need to get Slysz to fix that.
if (columnMapping.ContainsKey(IMS_SCAN_REP))
{
lcImsMsFeature.ScanImsRep = int.Parse(columns[columnMapping[IMS_SCAN_REP]]) - 1;
}
if (columnMapping.ContainsKey(CHARGE_STATE))
{
lcImsMsFeature.ChargeState = int.Parse(columns[columnMapping[CHARGE_STATE]]);
}
if (columnMapping.ContainsKey(DRIFT_TIME))
{
lcImsMsFeature.DriftTime = double.Parse(columns[columnMapping[DRIFT_TIME]]);
}
if (columnMapping.ContainsKey(ABUNDANCE))
{
lcImsMsFeature.Abundance = double.Parse(columns[columnMapping[ABUNDANCE]]);
}
if (columnMapping.ContainsKey(MONOISOTOPIC_MASS) && columnMapping.ContainsKey(CHARGE_STATE))
{
double mz = (lcImsMsFeature.MassMonoisotopic / lcImsMsFeature.ChargeState) + GeneralConstants.MASS_OF_PROTON;
lcImsMsFeature.MzMonoisotopic = mz;
}
return(lcImsMsFeature);
}
/// <summary>
/// Reads an LC-IMS-MS Feature file and returns the list of LC-IMS-MS Features.
/// </summary>
/// <param name="featureFile">The FileInfo object for the file to be read.</param>
/// <returns>A List of LcImsMsFeature objects read in from the file.</returns>
public static List <LcImsMsFeature> ReadFile(FileInfo featureFile)
{
List <LcImsMsFeature> featureList = new List <LcImsMsFeature>();
using (TextReader textReader = new StreamReader(featureFile.FullName))
{
string columnHeaders = textReader.ReadLine();
Dictionary <string, int> columnMapping = CreateColumnMapping(columnHeaders);
string line = "";
while ((line = textReader.ReadLine()) != null)
{
LcImsMsFeature feature = ParseLine(line, columnMapping);
featureList.Add(feature);
}
}
return(featureList);
}
/// <summary>
/// Executes the cross-link search for LC-IMS-TOF data.
/// </summary>
/// <param name="settings">Settings object to control parameters for cross-linking.</param>
/// <param name="proteinSequenceEnumerable">IEnumerable of protein sequences, as a .NET Bio ISequence object.</param>
/// <param name="featureList">List of LC-IMS-MS Features, as LcImsMsFeature.</param>
/// <param name="peakList">List of Isotopic Peaks, as IsotopicPeak.</param>
/// <returns>An enumerable of CrossLinkResult objects.</returns>
public static IList <CrossLinkResult> Execute(
CrossLinkSettings settings,
IEnumerable <ISequence> proteinSequenceEnumerable,
List <LcImsMsFeature> featureList,
List <IsotopicPeak> peakList)
{
var massToleranceBase = settings.MassTolerance;
var maxMissedCleavages = settings.MaxMissedCleavages;
var digestionRule = settings.TrypticType;
CrossLinkUtil.StaticDeltaMass = settings.StaticDeltaMass;
CrossLinkUtil.UseC13 = settings.UseC13;
CrossLinkUtil.UseN15 = settings.UseN15;
Console.WriteLine();
Console.WriteLine("Mass Tolerance: " + massToleranceBase + " ppm");
Console.WriteLine("Max missed cleavages: " + maxMissedCleavages);
Console.WriteLine("Digestion rule: " + settings.TrypticType);
Console.WriteLine("Delta mass uses C13: " + settings.UseC13);
Console.WriteLine("Delta mass uses N15: " + settings.UseN15);
Console.WriteLine("Static delta mass addon: " + settings.StaticDeltaMass + " Da");
// Used for finding Isotopic Profiles in the data
var msFeatureFinder = new BasicTFF();
var crossLinkList = new List <CrossLink>();
var lastProgress = DateTime.UtcNow;
var proteinsProcessed = 0;
// Create CrossLink objects from all of the protein sequences
foreach (var proteinSequence in proteinSequenceEnumerable)
{
var proteinSequenceString = new string(proteinSequence.Select((a => (char)a)).ToArray());
var proteinId = proteinSequence.ID;
// Get a List of Peptides from the Protein Sequence
var peptideList = SequenceUtil.DigestProtein(proteinSequenceString, digestionRule, maxMissedCleavages);
// Find all possible cross links from the peptide list
var crossLinkEnumerable = CrossLinkUtil.GenerateTheoreticalCrossLinks(peptideList, proteinSequenceString, proteinId);
crossLinkList.AddRange(crossLinkEnumerable);
proteinsProcessed++;
if (DateTime.UtcNow.Subtract(lastProgress).TotalSeconds >= 15)
{
lastProgress = DateTime.UtcNow;
Console.WriteLine("Creating cross linked peptide list; " + proteinsProcessed + " proteins processed");
}
}
Console.WriteLine("Sorting cross-linked peptides");
// Sort the CrossLinks by mass so that the results are ordered in a friendly way
IEnumerable <CrossLink> orderedCrossLinkEnumerable = crossLinkList.OrderBy(x => x.Mass);
// Sort Feature by mass so we can use binary search
featureList = featureList.OrderBy(x => x.MassMonoisotopic).ToList();
// Set up a Feature Comparer and Peak Comparer to use for binary search later on
var featureComparer = new AnonymousComparer <LcImsMsFeature>((x, y) => x.MassMonoisotopic.CompareTo(y.MassMonoisotopic));
var peakComparer = new AnonymousComparer <IsotopicPeak>((x, y) => x.ScanLc != y.ScanLc ? x.ScanLc.CompareTo(y.ScanLc) : x.ScanIms != y.ScanIms ? x.ScanIms.CompareTo(y.ScanIms) : x.Mz.CompareTo(y.Mz));
// Sort the Isotopic Peaks by LC Scan, IMS Scan, and m/z to set them up for binary search later on
peakList.Sort(peakComparer);
var crossLinkResultList = new List <CrossLinkResult>();
var totalCandidatePeptides = crossLinkList.Count;
Console.WriteLine("Searching isotopic data vs. " + totalCandidatePeptides.ToString("#,##0") + " candidate cross-linked peptides");
lastProgress = DateTime.UtcNow;
var crosslinkCandidatesProcessed = 0;
// Search the data for the existence of cross-links
foreach (var crossLink in orderedCrossLinkEnumerable)
{
// Calculate mass tolerance to use for binary search
var massTolerance = massToleranceBase * crossLink.Mass / GeneralConstants.PPM_DIVISOR;
var lowFeature = new LcImsMsFeature {
MassMonoisotopic = crossLink.Mass - massTolerance
};
var highFeature = new LcImsMsFeature {
MassMonoisotopic = crossLink.Mass + massTolerance
};
var lowFeaturePosition = featureList.BinarySearch(lowFeature, featureComparer);
var highFeaturePosition = featureList.BinarySearch(highFeature, featureComparer);
lowFeaturePosition = lowFeaturePosition < 0 ? ~lowFeaturePosition : lowFeaturePosition;
highFeaturePosition = highFeaturePosition < 0 ? ~highFeaturePosition : highFeaturePosition;
// Iterate over all LC-IMS-MS Features that match the Unmodified cross-link mass
for (var i = lowFeaturePosition; i < highFeaturePosition; i++)
{
var feature = featureList[i];
// Search for a mass shift in each of the LC Scans the unmodified cross-link mass was found
for (var currentScanLc = feature.ScanLcStart; currentScanLc <= feature.ScanLcEnd; currentScanLc++)
{
var crossLinkResult = new CrossLinkResult(crossLink, feature, currentScanLc);
var candidatePeaks = PeakUtil.FindCandidatePeaks(peakList, feature.MzMonoisotopic, currentScanLc, feature.ScanImsRep);
var massShiftList = crossLink.MassShiftList;
var shiftedMassList = new List <double>();
// Calculate the shifted mass values that we want to search for
switch (massShiftList.Count)
{
case 1:
{
var firstNewMass = feature.MassMonoisotopic + massShiftList[0];
shiftedMassList.Add(firstNewMass);
}
break;
case 2:
{
var firstNewMass = feature.MassMonoisotopic + massShiftList[0];
var secondNewMass = feature.MassMonoisotopic + massShiftList[1];
var thirdNewMass = feature.MassMonoisotopic + massShiftList[0] + massShiftList[1];
shiftedMassList.Add(firstNewMass);
shiftedMassList.Add(secondNewMass);
shiftedMassList.Add(thirdNewMass);
}
break;
}
// Search for shifted mass values in Isotopic Peaks
foreach (var shiftedMass in shiftedMassList)
{
var shiftedMz = (shiftedMass / feature.ChargeState) + GeneralConstants.MASS_OF_PROTON;
// Create theoretical Isotopic Peaks that will later form a theoretical Isotopic Profile
var theoreticalPeakList = new List <MSPeak> {
new MSPeak {
XValue = shiftedMz, Height = 1
}
};
for (double k = 1; k < 4; k++)
{
theoreticalPeakList.Add(new MSPeak {
XValue = shiftedMz + (k * 1.003 / feature.ChargeState), Height = (float)(1.0 - (k / 4))
});
theoreticalPeakList.Add(new MSPeak {
XValue = shiftedMz - (k * 1.003 / feature.ChargeState), Height = (float)(1.0 - (k / 4))
});
}
// Sort peaks by m/z
var sortPeaksQuery = from peak in theoreticalPeakList
orderby peak.XValue
select peak;
// Create a theoretical Isotopic Profile for DeconTools to search for
var isotopicProfile = new IsotopicProfile
{
MonoIsotopicMass = shiftedMass,
MonoPeakMZ = shiftedMz,
ChargeState = feature.ChargeState,
Peaklist = sortPeaksQuery.ToList()
};
// Search for the theoretical Isotopic Profile
var foundProfile = msFeatureFinder.FindMSFeature(candidatePeaks, isotopicProfile, massToleranceBase, false);
/*
* It is possible that the set mono pass of the previous theoretical distribution was the right-most peak of the actual distribution
* If so, we should be able to shift the theoretical distribution over to the left and find the actual distribution
*/
if (foundProfile == null)
{
foreach (var msPeak in sortPeaksQuery)
{
msPeak.XValue -= (1.003 / feature.ChargeState);
}
isotopicProfile = new IsotopicProfile
{
MonoIsotopicMass = shiftedMass - 1.003,
MonoPeakMZ = shiftedMz - (1.003 / feature.ChargeState),
ChargeState = feature.ChargeState,
Peaklist = sortPeaksQuery.ToList()
};
foundProfile = msFeatureFinder.FindMSFeature(candidatePeaks, isotopicProfile, massToleranceBase, false);
}
// Add to results, even if we did not find it.
var didFindProfile = foundProfile != null;
crossLinkResult.MassShiftResults.KvpList.Add(new KeyValuePair <double, bool>(shiftedMass, didFindProfile));
}
crossLinkResultList.Add(crossLinkResult);
}
}
crosslinkCandidatesProcessed++;
if (DateTime.UtcNow.Subtract(lastProgress).TotalSeconds >= 10)
{
lastProgress = DateTime.UtcNow;
var percentComplete = crosslinkCandidatesProcessed / (double)totalCandidatePeptides * 100;
Console.WriteLine("Searching isotopic data; " + percentComplete.ToString("0.0") + "% complete");
}
}
return(crossLinkResultList);
}
