public static MRMInfo InitializeMRMInfo()
{
var udtMRMInfo = new MRMInfo();
udtMRMInfo.Clear();
return(udtMRMInfo);
}
public static MRMInfo InitializeMRMInfo()
{
var mrmInfo = new MRMInfo();
mrmInfo.Clear();
return(mrmInfo);
}
/// <summary>
/// Duplicate the MRM info
/// </summary>
/// <param name="source"></param>
/// <param name="target"></param>
public static void DuplicateMRMInfo(MRMInfo source, out MRMInfo target)
{
target = new MRMInfo();
target.Clear();
foreach (var item in source.MRMMassList)
{
target.MRMMassList.Add(item);
}
}
/// <summary>
/// Duplicate the MRM info
/// </summary>
/// <param name="udtSource"></param>
/// <param name="udtTarget"></param>
public static void DuplicateMRMInfo(MRMInfo udtSource, out MRMInfo udtTarget)
{
udtTarget = new MRMInfo();
udtTarget.Clear();
foreach (var item in udtSource.MRMMassList)
{
udtTarget.MRMMassList.Add(item);
}
}
public static void InitializeMRMInfo(out MRMInfo mrmInfo, int initialMassCountCapacity)
{
mrmInfo = InitializeMRMInfo();
}
public static void InitializeMRMInfo(out MRMInfo udtMRMInfo, int intInitialMassCountCapacity)
{
udtMRMInfo = InitializeMRMInfo();
}
public static MRMInfo InitializeMRMInfo()
{
var udtMRMInfo = new MRMInfo();
udtMRMInfo.Clear();
return udtMRMInfo;
}
/// <summary>
/// Duplicate the MRM info
/// </summary>
/// <param name="udtSource"></param>
/// <param name="udtTarget"></param>
public static void DuplicateMRMInfo(MRMInfo udtSource, out MRMInfo udtTarget)
{
udtTarget = new MRMInfo();
udtTarget.Clear();
foreach (var item in udtSource.MRMMassList)
{
udtTarget.MRMMassList.Add(item);
}
}
/// <summary>
/// Parse out the MRM_QMS or SRM mass info from filterText
/// </summary>
/// <param name="filterText"></param>
/// <param name="mrmScanType"></param>
/// <param name="mrmInfo">Output: MRM info class</param>
/// <remarks>We do not parse mass information out for Full Neutral Loss scans</remarks>
public static void ExtractMRMMasses(string filterText, MRMScanTypeConstants mrmScanType, out MRMInfo mrmInfo)
{
// Parse out the MRM_QMS or SRM mass info from filterText
// It should be of the form
// SIM: p NSI SIM ms [330.00-380.00]
// or
// MRM_Q1MS_TEXT: p NSI Q1MS [179.652-184.582, 505.778-510.708, 994.968-999.898]
// or
// MRM_Q3MS_TEXT: p NSI Q3MS [150.070-1500.000]
// or
// MRM_SRM_TEXT: c NSI SRM ms2 [email protected] [397.209-392.211, 579.289-579.291]
// Note: we do not parse mass information out for Full Neutral Loss scans
// MRM_FullNL_TEXT: c NSI Full cnl 162.053 [300.000-1200.000]
mrmInfo = new MRMInfo();
if (string.IsNullOrWhiteSpace(filterText))
{
return;
}
if (!(mrmScanType == MRMScanTypeConstants.SIM |
mrmScanType == MRMScanTypeConstants.MRMQMS |
mrmScanType == MRMScanTypeConstants.SRM))
{
// Unsupported MRM type
return;
}
// Parse out the text between the square brackets
var reMatch = mMassList.Match(filterText);
if (!reMatch.Success)
{
return;
}
reMatch = mMassRanges.Match(reMatch.Value);
while (reMatch.Success)
{
try
{
// Note that group 0 is the full mass range (two mass values, separated by a dash)
// Group 1 is the first mass value
// Group 2 is the second mass value
var mrmMassRange = new udtMRMMassRangeType
{
StartMass = double.Parse(reMatch.Groups["StartMass"].Value),
EndMass = double.Parse(reMatch.Groups["EndMass"].Value)
};
var centralMass = mrmMassRange.StartMass + (mrmMassRange.EndMass - mrmMassRange.StartMass) / 2;
mrmMassRange.CentralMass = Math.Round(centralMass, 6);
mrmInfo.MRMMassList.Add(mrmMassRange);
}
catch (Exception)
{
// Error parsing out the mass values; skip this group
}
reMatch = reMatch.NextMatch();
}
}
public bool GetScanInfo(int scan, out clsScanInfo scanInfo)
{
// Check for the scan in the cache
if (mCachedScanInfo.TryGetValue(scan, out scanInfo))
{
return true;
}
if (scan < mFileInfo.ScanStart)
{
scan = mFileInfo.ScanStart;
}
else if (scan > mFileInfo.ScanEnd)
{
scan = mFileInfo.ScanEnd;
}
scanInfo = new clsScanInfo(scan);
try
{
if (mXRawFile == null)
return false;
// Make sure the MS controller is selected
if (!SetMSController())
return false;
// Initialize the values that will be populated using GetScanHeaderInfoForScanNum()
scanInfo.NumPeaks = 0;
scanInfo.TotalIonCurrent = 0;
scanInfo.SIMScan = false;
scanInfo.MRMScanType = MRMScanTypeConstants.NotMRM;
scanInfo.ZoomScan = false;
scanInfo.CollisionMode = string.Empty;
scanInfo.FilterText = string.Empty;
scanInfo.IonMode = IonModeConstants.Unknown;
var numPeaks = 0;
double retentionTime = 0;
double lowMass = 0;
double highMass = 0;
double totalIonCurrent = 0;
double basePeakMZ = 0;
double basePeakIntensity = 0;
var numChannels = 0;
double frequency = 0;
var booleanValue = 0;
var errorCode = 0;
mXRawFile.GetScanHeaderInfoForScanNum(
scan, ref numPeaks, ref retentionTime, ref lowMass, ref highMass,
ref totalIonCurrent, ref basePeakMZ, ref basePeakIntensity, ref numChannels, booleanValue, ref frequency);
scanInfo.NumPeaks = numPeaks;
scanInfo.RetentionTime = retentionTime;
scanInfo.LowMass = lowMass;
scanInfo.HighMass = highMass;
scanInfo.TotalIonCurrent = totalIonCurrent;
scanInfo.BasePeakMZ = basePeakMZ;
scanInfo.BasePeakIntensity = basePeakIntensity;
scanInfo.NumChannels = numChannels;
scanInfo.Frequency = frequency;
mXRawFile.IsError(ref errorCode);
// Unfortunately, .IsError() always returns 0, even if an error occurred
if (errorCode != 0)
{
CacheScanInfo(scan, scanInfo);
return false;
}
scanInfo.UniformTime = Convert.ToBoolean(booleanValue);
booleanValue = 0;
mXRawFile.IsCentroidScanForScanNum(scan, ref booleanValue);
scanInfo.IsCentroided = Convert.ToBoolean(booleanValue);
var arrayCount = 0;
object objLabels = null;
object objValues = null;
try
{
if (!mCorruptMemoryEncountered)
{
// Retrieve the additional parameters for this scan (including Scan Event)
mXRawFile.GetTrailerExtraForScanNum(scan, ref objLabels, ref objValues, ref arrayCount);
}
}
catch (AccessViolationException ex)
{
var msg = "Warning: Exception calling mXRawFile.GetTrailerExtraForScanNum for scan " + scan + ": " + ex.Message;
RaiseWarningMessage(msg);
arrayCount = 0;
}
catch (Exception ex)
{
var msg = "Warning: Exception calling mXRawFile.GetTrailerExtraForScanNum for scan " + scan + ": " + ex.Message;
RaiseWarningMessage(msg);
arrayCount = 0;
if (ex.Message.ToLower().Contains("memory is corrupt"))
{
mCorruptMemoryEncountered = true;
}
}
scanInfo.EventNumber = 1;
if (arrayCount > 0 && objLabels != null && objValues != null)
{
var scanEventNames =
((IEnumerable)objLabels).Cast<object>()
.Select(x => x.ToString())
.ToArray();
var scanEventValues =
((IEnumerable)objValues).Cast<object>()
.Select(x => x.ToString())
.ToArray();
scanInfo.StoreScanEvents(scanEventNames, scanEventValues);
// Look for the entry in strLabels named "Scan Event:"
// Entries for the LCQ are:
// Wideband Activation
// Micro Scan Count
// Ion Injection Time (ms)
// Scan Segment
// Scan Event
// Elapsed Scan Time (sec)
// API Source CID Energy
// Resolution
// Average Scan by Inst
// BackGd Subtracted by Inst
// Charge State
foreach (var scanEvent in from item in scanInfo.ScanEvents where item.Key.ToLower().StartsWith("scan event") select item)
{
try
{
scanInfo.EventNumber = Convert.ToInt32(scanEvent.Value);
}
catch (Exception)
{
// Ignore errors here
}
break;
}
}
// Lookup the filter text for this scan
// Parse out the parent ion m/z for fragmentation scans
// Must set filterText to Nothing prior to calling .GetFilterForScanNum()
string filterText = null;
mXRawFile.GetFilterForScanNum(scan, ref filterText);
scanInfo.FilterText = string.Copy(filterText);
scanInfo.IsFTMS = ScanIsFTMS(filterText);
if (string.IsNullOrWhiteSpace(scanInfo.FilterText))
scanInfo.FilterText = string.Empty;
if (scanInfo.EventNumber <= 1)
{
int msLevel;
// XRaw periodically mislabels a scan as .EventNumber = 1 when it's really an MS/MS scan; check for this
string mzText;
if (ExtractMSLevel(scanInfo.FilterText, out msLevel, out mzText))
{
scanInfo.EventNumber = msLevel;
}
}
if (scanInfo.EventNumber > 1)
{
// MS/MS data
scanInfo.MSLevel = 2;
if (string.IsNullOrWhiteSpace(scanInfo.FilterText))
{
// FilterText is empty; this indicates a problem with the .Raw file
// This is rare, but does happen (see scans 2 and 3 in QC_Shew_08_03_pt5_1_MAXPRO_27Oct08_Raptor_08-01-01.raw)
// We'll set the Parent Ion to 0 m/z and the collision mode to CID
scanInfo.ParentIonMZ = 0;
scanInfo.CollisionMode = "cid";
if (scanInfo.ActivationType == ActivationTypeConstants.Unknown)
{
scanInfo.ActivationType = ActivationTypeConstants.CID;
}
scanInfo.MRMScanType = MRMScanTypeConstants.NotMRM;
}
else
{
double parentIonMz;
int msLevel;
string collisionMode;
// Parse out the parent ion and collision energy from .FilterText
if (ExtractParentIonMZFromFilterText(scanInfo.FilterText, out parentIonMz, out msLevel, out collisionMode))
{
scanInfo.ParentIonMZ = parentIonMz;
scanInfo.CollisionMode = collisionMode;
if (msLevel > 2)
{
scanInfo.MSLevel = msLevel;
}
// Check whether this is an SRM MS2 scan
scanInfo.MRMScanType = DetermineMRMScanType(scanInfo.FilterText);
}
else
{
// Could not find "Full ms2" in .FilterText
// XRaw periodically mislabels a scan as .EventNumber > 1 when it's really an MS scan; check for this
bool simScan;
MRMScanTypeConstants eMRMScanType;
bool zoomScan;
if (ValidateMSScan(scanInfo.FilterText, out msLevel, out simScan, out eMRMScanType, out zoomScan))
{
// Yes, scan is an MS, SIM, or MRMQMS, or SRM scan
scanInfo.MSLevel = msLevel;
scanInfo.SIMScan = simScan;
scanInfo.MRMScanType = eMRMScanType;
scanInfo.ZoomScan = zoomScan;
}
else
{
// Unknown format for .FilterText; return an error
RaiseErrorMessage("Unknown format for Scan Filter: " + scanInfo.FilterText);
return false;
}
}
}
}
else
{
// MS1 data
// Make sure .FilterText contains one of the known MS1, SIM or MRM tags
if (scanInfo.FilterText == string.Empty)
{
// FilterText is empty; this indicates a problem with the .Raw file
// This is rare, but does happen (see scans 2 and 3 in QC_Shew_08_03_pt5_1_MAXPRO_27Oct08_Raptor_08-01-01.raw)
scanInfo.MSLevel = 1;
scanInfo.SIMScan = false;
scanInfo.MRMScanType = MRMScanTypeConstants.NotMRM;
}
else
{
int msLevel;
bool simScan;
MRMScanTypeConstants eMRMScanType;
bool zoomScan;
if (ValidateMSScan(scanInfo.FilterText, out msLevel, out simScan, out eMRMScanType, out zoomScan))
{
// Yes, scan is an MS, SIM, or MRMQMS, or SRM scan
scanInfo.MSLevel = msLevel;
scanInfo.SIMScan = simScan;
scanInfo.MRMScanType = eMRMScanType;
scanInfo.ZoomScan = zoomScan;
}
else
{
// Unknown format for .FilterText; return an error
RaiseErrorMessage("Unknown format for Scan Filter: " + scanInfo.FilterText);
return false;
}
}
}
scanInfo.IonMode = DetermineIonizationMode(scanInfo.FilterText);
// Now that we know MSLevel we can lookup the activation type (aka activation method)
scanInfo.ActivationType = GetActivationType(scan, scanInfo.MSLevel);
MRMInfo newMRMInfo;
if (scanInfo.MRMScanType != MRMScanTypeConstants.NotMRM)
{
// Parse out the MRM_QMS or SRM information for this scan
ExtractMRMMasses(scanInfo.FilterText, scanInfo.MRMScanType, out newMRMInfo);
}
else
{
newMRMInfo = new MRMInfo();
}
scanInfo.MRMInfo = newMRMInfo;
// Retrieve the Status Log for this scan using the following
// The Status Log includes numerous instrument parameters, including voltages, temperatures, pressures, turbo pump speeds, etc.
arrayCount = 0;
objLabels = null;
objValues = null;
try
{
if (!mCorruptMemoryEncountered)
{
double statusLogRT = 0;
mXRawFile.GetStatusLogForScanNum(scan, statusLogRT, ref objLabels, ref objValues, ref arrayCount);
}
}
catch (AccessViolationException ex)
{
var msg = "Warning: Exception calling mXRawFile.GetStatusLogForScanNum for scan " + scan + ": " + ex.Message;
RaiseWarningMessage(msg);
arrayCount = 0;
}
catch (Exception ex)
{
var msg = "Warning: Exception calling mXRawFile.GetStatusLogForScanNum for scan " + scan + ": " + ex.Message;
RaiseWarningMessage(msg);
arrayCount = 0;
if (ex.Message.ToLower().Contains("memory is corrupt"))
{
mCorruptMemoryEncountered = true;
}
}
if (arrayCount > 0)
{
var logNames =
((IEnumerable)objLabels).Cast<object>()
.Select(x => x.ToString())
.ToArray();
var logValues =
((IEnumerable)objValues).Cast<object>()
.Select(x => x.ToString())
.ToArray();
scanInfo.StoreStatusLog(logNames, logValues);
}
}
catch (Exception ex)
{
var msg = "Error: Exception in GetScanInfo: " + ex.Message;
RaiseWarningMessage(msg);
CacheScanInfo(scan, scanInfo);
return false;
}
CacheScanInfo(scan, scanInfo);
return true;
}
