public void TestGetScanCountsByScanType(
string dotDFolderName,
int scanStart,
int scanEnd,
int expectedMS1,
int expectedMS2,
int expectedTotalScanCount)
{
var dataFolder = GetBrukerDataFolder(dotDFolderName);
using (var reader = new MSDataFileReader(dataFolder.FullName))
{
Console.WriteLine("Parsing scan headers for {0}", dataFolder.Name);
var scanCount = reader.SpectrumCount;
Console.WriteLine("Total scans: {0}", scanCount);
Assert.AreEqual(expectedTotalScanCount, scanCount, "Total scan count mismatch");
Console.WriteLine();
var scanNumberToIndexMap = reader.GetScanToIndexMapping();
var scanCountMS1 = 0;
var scanCountMS2 = 0;
foreach (var scan in scanNumberToIndexMap.Where(x => x.Key >= scanStart && x.Key <= scanEnd))
{
// var scanNumber = scan.Key;
var spectrumIndex = scan.Value;
var spectrum = reader.GetSpectrum(spectrumIndex, false);
if (spectrum.Level > 1)
{
scanCountMS2++;
}
else
{
scanCountMS1++;
}
}
Console.WriteLine("scanCountMS1={0}", scanCountMS1);
Console.WriteLine("scanCountMS2={0}", scanCountMS2);
Assert.AreEqual(expectedMS1, scanCountMS1, "MS1 scan count mismatch");
Assert.AreEqual(expectedMS2, scanCountMS2, "MS2 scan count mismatch");
}
}
public void TestGetScanData(string dotDFolderName, int scanStart, int scanEnd)
{
var expectedData = new Dictionary <string, Dictionary <int, string> >();
// Keys in this dictionary are the scan number of data being retrieved
var file1Data = new Dictionary <int, string>
{
{ 5, "5 39775 39775 982.741 0.0E+0 1410.843 8.7E+4" },
{ 6, "6 39775 39775 982.741 0.0E+0 1410.843 9.1E+4" },
{ 7, "7 39775 39775 982.741 0.0E+0 1410.843 8.7E+4" },
{ 8, "8 39775 39775 982.741 0.0E+0 1410.843 4.5E+4" },
{ 9, "9 39775 39775 982.741 0.0E+0 1410.843 1.4E+5" }
};
expectedData.Add("Humira_100fmol_20121026_hi_res_9_01_716", file1Data);
var file2Data = new Dictionary <int, string>
{
{ 1, "1 7615807 7615807 110.561 3.8E+4 202.468 4.2E+5" }
};
expectedData.Add("Blank-2_05May16_Leopard_Infuse_1_01_7976", file2Data);
var dataFolder = GetBrukerDataFolder(dotDFolderName);
using (var reader = new MSDataFileReader(dataFolder.FullName))
{
Console.WriteLine("Scan data for {0}", dataFolder.Name);
Console.WriteLine("{0} {1,-8} {2,-8} {3,-8} {4,-8} {5,-8} {6}",
"Scan", "MzCount", "IntCount",
"FirstMz", "FirstInt", "MidMz", "MidInt");
var scanNumberToIndexMap = reader.GetScanToIndexMapping();
foreach (var scan in scanNumberToIndexMap.Where(x => x.Key >= scanStart && x.Key <= scanEnd))
{
var scanNumber = scan.Key;
var spectrumIndex = scan.Value;
var spectrum = reader.GetSpectrum(spectrumIndex, true);
var dataPointsRead = spectrum.Mzs.Length;
Assert.IsTrue(dataPointsRead > 0, "GetScanData returned 0 for scan {0}", scanNumber);
var midPoint = (int)(spectrum.Intensities.Length / 2f);
var scanSummary =
string.Format(
"{0} {1,-8} {2,-8} {3,-8:0.000} {4,-8:0.0E+0} {5,-8:0.000} {6:0.0E+0}",
scanNumber,
spectrum.Mzs.Length, spectrum.Intensities.Length,
spectrum.Mzs[0], spectrum.Intensities[0],
spectrum.Mzs[midPoint], spectrum.Intensities[midPoint]);
Console.WriteLine(scanSummary);
if (!expectedData.TryGetValue(Path.GetFileNameWithoutExtension(dataFolder.Name), out var expectedDataThisFile))
{
Assert.Fail("Dataset {0} not found in dictionary expectedData", dataFolder.Name);
}
if (expectedDataThisFile.TryGetValue(scanNumber, out var expectedDataDetails))
{
Assert.AreEqual(expectedDataDetails, scanSummary,
"Scan details mismatch, scan " + scanNumber);
}
}
}
}
public void TestCorruptDataHandling(
string dotDFolderName,
int scanStart,
int scanEnd,
int expectedMS1,
int expectedMS2)
{
var dataFolder = GetBrukerDataFolder(dotDFolderName);
try
{
using (var reader = new MSDataFileReader(dataFolder.FullName))
{
var scanCount = reader.SpectrumCount;
Console.WriteLine("Scan count for {0}: {1}", dataFolder.Name, scanCount);
if (expectedMS1 + expectedMS2 == 0)
{
Assert.IsTrue(scanCount == 0, "ScanCount is non-zero, while we expected it to be 0");
}
else
{
Assert.IsTrue(scanCount > 0, "ScanCount is zero, while we expected it to be > 0");
}
var scanNumberToIndexMap = reader.GetScanToIndexMapping();
var scanCountMS1 = 0;
var scanCountMS2 = 0;
foreach (var scan in scanNumberToIndexMap.Where(x => x.Key >= scanStart && x.Key <= scanEnd))
{
var scanNumber = scan.Key;
var spectrumIndex = scan.Value;
try
{
var spectrum = reader.GetSpectrum(spectrumIndex, true);
var cvScanInfo = reader.GetSpectrumScanInfo(spectrumIndex);
Assert.IsTrue(cvScanInfo != null, "GetSpectrumScanInfo returned a null object for scan {0}", scanNumber);
if (spectrum.Level > 1)
{
scanCountMS2++;
}
else
{
scanCountMS1++;
}
var dataPointCount = spectrum.Mzs.Length;
Assert.IsTrue(dataPointCount > 0, "Data point count is 0 for scan {0}", scanNumber);
Assert.IsTrue(spectrum.Mzs.Length > 0, "m/z data is empty for scan {0}", scanNumber);
Assert.IsTrue(spectrum.Intensities.Length > 0, "Intensity data is empty for scan {0}", scanNumber);
Assert.IsTrue(spectrum.Mzs.Length == spectrum.Intensities.Length, "Array length mismatch for m/z and intensity data for scan {0}", scanNumber);
}
catch (Exception ex)
{
Console.WriteLine("Exception reading scan {0}: {1}", scanNumber, ex.Message);
Assert.Fail("Exception reading scan {0}", scanNumber);
}
}
Console.WriteLine("scanCountMS1={0}", scanCountMS1);
Console.WriteLine("scanCountMS2={0}", scanCountMS2);
Assert.AreEqual(expectedMS1, scanCountMS1, "MS1 scan count mismatch");
Assert.AreEqual(expectedMS2, scanCountMS2, "MS2 scan count mismatch");
}
}
catch (Exception ex)
{
if (expectedMS1 + expectedMS2 == 0)
{
Console.WriteLine("Error opening .D folder (this was expected):\n{0}", ex.Message);
}
else
{
var msg = string.Format("Exception opening .D folder {0}:\n{1}", dotDFolderName, ex.Message);
Console.WriteLine(msg);
Assert.Fail(msg);
}
}
}
public void TestGetScanInfo(string dotDFolderName, int scanStart, int scanEnd, int expectedMS1, int expectedMS2)
{
var expectedData = new Dictionary <string, Dictionary <int, string> >();
// Keys in this dictionary are the scan number whose metadata is being retrieved
var file1Data = new Dictionary <int, string>
{
// Scan MSLevel NumPeaks RetentionTime ScanStartTime DriftTimeMsec LowMass HighMass TotalIonCurrent BasePeakMZ BasePeakIntensity ParentIonMZ
{ 1, "1 1 7794096 0.59 35.34 0 92 1300 7.1E+9 0.000 5.5E+8 0.00 positive False 696.00" },
{ 2, "2 1 7794096 1.10 66.27 0 92 1300 7.2E+9 0.000 5.6E+8 0.00 positive False 696.00" },
{ 3, "3 1 7794096 1.62 97.18 0 92 1300 7.2E+9 0.000 5.5E+8 0.00 positive False 696.00" },
{ 4, "4 1 7794096 2.14 128.17 0 92 1300 7.1E+9 0.000 5.3E+8 0.00 positive False 696.00" },
{ 5, "5 1 7794096 2.65 159.12 0 92 1300 7.1E+9 0.000 5.4E+8 0.00 positive False 696.00" }
};
expectedData.Add("2016_04_12_Background_000001", file1Data);
var file2Data = new Dictionary <int, string>
{
{ 1, "1 1 7615807 3.58 214.92 0 111 1200 3.6E+10 0.000 3.1E+9 0.00 negative False 655.50" }
};
expectedData.Add("Blank-2_05May16_Leopard_Infuse_1_01_7976", file2Data);
var file3Data = new Dictionary <int, string>
{
{ 15, "15 1 39775 2.38 142.89 0 983 984 0.0E+0 0.000 0.0E+0 0.00 positive False 983.50" },
{ 16, "16 1 39775 2.53 152.06 0 983 984 0.0E+0 0.000 0.0E+0 0.00 positive False 983.50" },
{ 17, "17 1 39775 2.69 161.24 0 983 984 0.0E+0 0.000 0.0E+0 0.00 positive False 983.50" },
{ 18, "18 1 39775 2.84 170.41 0 983 984 0.0E+0 0.000 0.0E+0 0.00 positive False 983.50" },
{ 19, "19 1 39775 2.99 179.58 0 983 984 0.0E+0 0.000 0.0E+0 0.00 positive False 983.50" },
{ 20, "20 1 39775 3.15 188.76 0 983 984 0.0E+0 0.000 0.0E+0 0.00 positive False 983.50" }
};
expectedData.Add("Humira_100fmol_20121026_hi_res_9_01_716", file3Data);
var file4Data = new Dictionary <int, string>
{
{ 1, "1 2 8214787 2.20 131.89 0 207 10000 6.0E+8 0.000 1.3E+7 1600.00 cid negative False 1600.00" }
};
expectedData.Add("MZ20160603PPS_edta_000004", file4Data);
var dataFolder = GetBrukerDataFolder(dotDFolderName);
using (var reader = new MSDataFileReader(dataFolder.FullName))
{
Console.WriteLine("Scan info for {0}", dataFolder.Name);
Console.WriteLine("{0} {1} {2} {3} {4} {5} {6} {7} {8} {9} {10} {11} {12} {13} {14} {15}",
"Scan", "MSLevel",
"NumPeaks", "RetentionTime",
"ScanStartTime",
"DriftTimeMsec",
"LowMass", "HighMass", "TotalIonCurrent",
"BasePeakMZ", "BasePeakIntensity",
"ParentIonMZ", "ActivationType",
"IonMode", "IsCentroided",
"IsolationMZ");
var scanNumberToIndexMap = reader.GetScanToIndexMapping();
var scanCountMS1 = 0;
var scanCountMS2 = 0;
foreach (var scan in scanNumberToIndexMap.Where(x => x.Key >= scanStart && x.Key <= scanEnd))
{
var scanNumber = scan.Key;
var spectrumIndex = scan.Value;
var spectrum = reader.GetSpectrum(spectrumIndex, true);
var spectrumParams = reader.GetSpectrumCVParamData(spectrumIndex);
var cvScanInfo = reader.GetSpectrumScanInfo(spectrumIndex);
Assert.IsTrue(spectrum != null, "GetSpectrum returned a null object for scan " + scanNumber);
var totalIonCurrent = cvParamUtilities.GetCvParamValueDbl(spectrumParams, cvParamUtilities.CVIDs.MS_TIC);
var basePeakMZ = cvParamUtilities.GetCvParamValueDbl(spectrumParams, cvParamUtilities.CVIDs.MS_base_peak_m_z);
var basePeakIntensity = cvParamUtilities.GetCvParamValueDbl(spectrumParams, cvParamUtilities.CVIDs.MS_base_peak_intensity);
double isolationMZ = 0;
double parentIonMZ = 0;
var activationType = string.Empty;
if (spectrum.Precursors.Length > 0)
{
var precursor = spectrum.Precursors[0];
isolationMZ = precursor.IsolationMz.GetValueOrDefault();
parentIonMZ = precursor.PrecursorMz.GetValueOrDefault();
if (precursor.ActivationTypes != null)
{
activationType = string.Join(", ", precursor.ActivationTypes);
}
}
GetScanMetadata(cvScanInfo, out var scanStartTime, out var lowMass, out var highMass);
var retentionTime = cvParamUtilities.CheckNull(spectrum.RetentionTime);
var numPeaks = spectrum.Mzs.Length;
var ionMode = spectrum.NegativeCharge ? "negative" : "positive";
var scanSummary =
string.Format(
"{0} {1} {2,5} {3,6:0.00} {4,6:0.00} {5:0} {6,3:0} {7,5:0} {8,6:0.0E+0} {9,8:0.000} {10,6:0.0E+0} {11,8:0.00} {12,-8} {13} {14,-5} {15,8:0.00}",
scanNumber, spectrum.Level,
numPeaks, retentionTime, scanStartTime,
cvParamUtilities.CheckNull(spectrum.DriftTimeMsec),
lowMass, highMass,
totalIonCurrent,
basePeakMZ, basePeakIntensity, parentIonMZ,
activationType,
ionMode, spectrum.Centroided, isolationMZ);
Console.WriteLine(scanSummary);
if (spectrum.Level > 1)
{
scanCountMS2++;
}
else
{
scanCountMS1++;
}
if (!expectedData.TryGetValue(Path.GetFileNameWithoutExtension(dataFolder.Name), out var expectedDataThisFile))
{
Assert.Fail("Dataset {0} not found in dictionary expectedData", dataFolder.Name);
}
if (expectedDataThisFile.TryGetValue(scanNumber, out var expectedScanSummary))
{
Assert.AreEqual(expectedScanSummary, scanSummary,
"Scan summary mismatch, scan " + scanNumber);
}
var expectedNativeId = string.Format("scan={0}", scanNumber);
Assert.AreEqual(spectrum.NativeId, expectedNativeId, "NativeId is not in the expected format for scan {0}", scanNumber);
}
Console.WriteLine("scanCountMS1={0}", scanCountMS1);
Console.WriteLine("scanCountMS2={0}", scanCountMS2);
Assert.AreEqual(expectedMS1, scanCountMS1, "MS1 scan count mismatch");
Assert.AreEqual(expectedMS2, scanCountMS2, "MS2 scan count mismatch");
}
}
