/// <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="fastAFile">The FileInfo object for the FASTA file containg all protein sequences you want to search.</param>
/// <param name="featureFile">The FileInfo object for the LC-IMS-MS features file, created by the LC-IMS-MS Feature Finder. (email [email protected] for more info)</param>
/// <param name="peaksFile">The FileInfo object for the Isotopic Peaks file, created by DeconTools. (email [email protected] for more info)</param>
/// <returns>An enumerable of CrossLinkResult objects.</returns>
public static IList<CrossLinkResult> Execute(CrossLinkSettings settings, FileInfo fastAFile, FileInfo featureFile, FileInfo peaksFile)
{
IEnumerable<ISequence> sequenceEnumerable;
List<LcImsMsFeature> featureList;
List<IsotopicPeak> peakEnumerable;
Console.WriteLine();
try
{
// Read in FASTA File
var fastAParser = new FastAParser(fastAFile.FullName);
sequenceEnumerable = fastAParser.Parse();
Console.WriteLine("FASTA file: " + GetRelativePath(fastAFile.FullName));
}
catch (Exception ex)
{
Console.WriteLine("Error reading the FASTA file: " + ex.Message);
throw;
}
try
{
// Read in LC-IMS-MS Features
featureList = LcImsMsFeatureReader.ReadFile(featureFile);
Console.WriteLine("Features file: " + GetRelativePath(featureFile.FullName));
}
catch (Exception ex)
{
Console.WriteLine("Error reading the LCMSFeatures file: " + ex.Message);
throw;
}
try
{
// Read in Isotopic Peaks (not Isotopic Profile)
peakEnumerable = IsotopicPeakReader.ReadFile(peaksFile);
Console.WriteLine("Peaks file: " + GetRelativePath(peaksFile.FullName));
}
catch (Exception ex)
{
Console.WriteLine("Error reading the Isotopic Peaks file: " + ex.Message);
throw;
}
// Now call the executor that expects the opbjects instead of the file locations
return Execute(settings, sequenceEnumerable, featureList, peakEnumerable);
}
static int Main(string[] args)
{
try
{
// Handles a bug in .NET console applications
var handle = Process.GetCurrentProcess().MainWindowHandle;
SetConsoleMode(handle, ENABLE_EXTENDED_FLAGS);
// Get the version number
var assembly = Assembly.GetExecutingAssembly();
var assemblyVersion = assembly.GetName().Version.ToString();
Console.WriteLine("CrossLinkingIMS Console Application Version " + assemblyVersion);
var commandLineUtil = new CommandLineUtil(caseSensitiveSwitchNames: false);
// Make sure we have parameters. If not, then show the user the proper syntax
var doParametersExist = commandLineUtil.ParseCommandLine();
if (!doParametersExist)
{
ShowSyntax();
return -1;
}
// Get the Feature File Location
string featureFileLocation;
if (!commandLineUtil.RetrieveValueForParameter("f", out featureFileLocation))
{
Console.WriteLine("-f switch is missing");
ShowSyntax();
return -2;
}
if (!FileExists(featureFileLocation))
{
return -4;
}
var featureFile = new FileInfo(featureFileLocation);
// Get the Peaks File Location
string peaksFileLocation;
if (!commandLineUtil.RetrieveValueForParameter("p", out peaksFileLocation))
{
Console.WriteLine("-p switch is missing");
ShowSyntax();
return -2;
}
if (!FileExists(peaksFileLocation))
{
return -4;
}
var peaksFile = new FileInfo(peaksFileLocation);
// Get the FastA File Location
string fastAFileLocation;
if (!commandLineUtil.RetrieveValueForParameter("fasta", out fastAFileLocation))
{
Console.WriteLine("-fasta switch is missing");
ShowSyntax();
return -2;
}
if (!FileExists(fastAFileLocation))
{
return -4;
}
var fastAFile = new FileInfo(fastAFileLocation);
// Get the PPM Mass Tolerance
string massToleranceString;
if (!commandLineUtil.RetrieveValueForParameter("ppm", out massToleranceString))
{
Console.WriteLine("-ppm switch is missing");
ShowSyntax();
return -2;
}
var massTolerance = double.Parse(massToleranceString);
// Get the Max Missed Cleavages
string maxMissedCleavagesString;
commandLineUtil.RetrieveValueForParameter("c", out maxMissedCleavagesString);
if (string.IsNullOrEmpty(maxMissedCleavagesString))
maxMissedCleavagesString = "1";
var maxMissedCleavages = int.Parse(maxMissedCleavagesString);
// Get the Partially Tryptic Flag
string trypticString;
commandLineUtil.RetrieveValueForParameter("t", out trypticString);
string staticDeltaMassString;
var staticDeltaMass = 0.0;
if (commandLineUtil.RetrieveValueForParameter("static", out staticDeltaMassString))
{
double.TryParse(staticDeltaMassString, out staticDeltaMass);
}
var useC13 = true;
var useN15 = true;
if (commandLineUtil.IsParameterPresent("c13off"))
useC13 = false;
if (commandLineUtil.IsParameterPresent("n15off"))
useN15 = false;
if (!(useC13 || useN15) && Math.Abs(staticDeltaMass) < float.Epsilon)
{
Console.WriteLine("If you use both -C13off and -N15off, you must use -Static:MassDiff to specify a static mass difference");
Thread.Sleep(1500);
return -3;
}
var settings = new CrossLinkSettings(massTolerance, maxMissedCleavages, trypticString, useC13, useN15, staticDeltaMass);
// Get the Output File Location
string outputFileLocation;
if (!commandLineUtil.RetrieveValueForParameter("o", out outputFileLocation))
{
if (featureFile.DirectoryName != null && featureFile.DirectoryName == peaksFile.DirectoryName)
outputFileLocation = Path.Combine(featureFile.DirectoryName, "crossLinkResults.csv");
else
outputFileLocation = "crossLinkResults.csv";
}
// Run the cross-linking application
Console.WriteLine("Executing...");
var crossLinkResults = CrossLinkingImsController.Execute(settings, fastAFile, featureFile, peaksFile);
var outputFileInfo = new FileInfo(outputFileLocation);
// Output the results
Console.WriteLine("Outputting " + crossLinkResults.Count().ToString("#,##0") + " results to \n" + outputFileInfo.FullName);
CrossLinkUtil.OutputCrossLinkResults(crossLinkResults, outputFileInfo);
return 0;
}
catch (Exception ex)
{
Console.WriteLine();
Console.WriteLine("=========================================");
Console.WriteLine("Error: " + ex.Message);
Console.WriteLine(ex.StackTrace);
Console.WriteLine("=========================================");
Thread.Sleep(2000);
return -10;
}
}
/// <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;
}