public void DetermineMRMScanType(string filterText, MRMScanTypeConstants expectedResult)
{
var mrmScanType = XRawFileIO.DetermineMRMScanType(filterText);
Console.WriteLine(filterText + " " + mrmScanType);
Assert.AreEqual(expectedResult, mrmScanType);
}
/// <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();
}
}
/// <summary>
/// Examines filterText to validate that it is a supported MS1 scan type (MS, SIM, or MRMQMS, or SRM scan)
/// </summary>
/// <param name="filterText"></param>
/// <param name="msLevel"></param>
/// <param name="simScan">True if mrmScanType is SIM or MRMQMS</param>
/// <param name="mrmScanType"></param>
/// <param name="zoomScan"></param>
/// <returns>True if filterText contains a known MS scan type</returns>
/// <remarks>Returns false for MSn scans (like ms2 or ms3)</remarks>
public static bool ValidateMSScan(
string filterText,
out int msLevel,
out bool simScan,
out MRMScanTypeConstants mrmScanType,
out bool zoomScan)
{
simScan = false;
mrmScanType = MRMScanTypeConstants.NotMRM;
zoomScan = false;
var ms1Tags = new List<string> {
FULL_MS_TEXT,
MS_ONLY_C_TEXT,
MS_ONLY_P_TEXT,
MS_ONLY_P_NSI_TEXT,
FULL_PR_TEXT,
FULL_LOCK_MS_TEXT
};
var zoomTags = new List<string> {
MS_ONLY_Z_TEXT,
MS_ONLY_PZ_TEXT,
MS_ONLY_DZ_TEXT
};
if (ContainsAny(filterText, ms1Tags, 1))
{
// This is a Full MS scan
msLevel = 1;
return true;
}
if (ContainsAny(filterText, zoomTags, 1))
{
msLevel = 1;
zoomScan = true;
return true;
}
if (ContainsText(filterText, MS_ONLY_PZ_MS2_TEXT, 1))
{
// Technically, this should have MSLevel = 2, but that would cause a bunch of problems elsewhere in MASIC
// Thus, we'll pretend it's MS1
msLevel = 1;
zoomScan = true;
return true;
}
mrmScanType = DetermineMRMScanType(filterText);
switch (mrmScanType)
{
case MRMScanTypeConstants.SIM:
// Selected ion monitoring, which is MS1 of a narrow m/z range
msLevel = 1;
simScan = true;
return true;
case MRMScanTypeConstants.MRMQMS:
// Multiple SIM ranges in a single scan
msLevel = 1;
simScan = true;
return true;
case MRMScanTypeConstants.SRM:
msLevel = 2;
return true;
case MRMScanTypeConstants.FullNL:
msLevel = 2;
return true;
default:
string mzText;
ExtractMSLevel(filterText, out msLevel, out mzText);
return false;
}
}
public void ValidateMSScan(
string filterText,
bool expectedIsValidMS1orSIM,
int expectedMSLevel,
bool expectedIsSIMScan,
MRMScanTypeConstants expectedMRMScanType,
bool expectedIsZoomScan)
{
int msLevel;
bool isSIMScan;
MRMScanTypeConstants mrmScanType;
bool zoomScan;
var isValid = XRawFileIO.ValidateMSScan(filterText, out msLevel, out isSIMScan, out mrmScanType, out zoomScan);
Console.WriteLine(filterText + " -- ms" + msLevel + "; SIM=" + isSIMScan + "; MRMScanType=" + mrmScanType);
Assert.AreEqual(expectedIsValidMS1orSIM, isValid, "Mismatch for IsValidMS1orSIM");
Assert.AreEqual(expectedMSLevel, msLevel, "MSLevel mismatch");
Assert.AreEqual(expectedIsSIMScan, isSIMScan, "SIMScan mismatch");
Assert.AreEqual(expectedMRMScanType, mrmScanType, "MRMScanType mismatch");
Assert.AreEqual(expectedIsZoomScan, zoomScan, "ZoomScan mismatch");
}
