public void GetCalibratedMass1()
{
//see https://jira.pnnl.gov/jira/browse/OMCS-870
var testFile =
@"\\protoapps\DataPkgs\Public\2013\743_Mycobacterium_tuberculosis_Cys_and_Ser_ABP\IQ_Analysis\Testing\LNA_A_Stat_Sample_SC_28_LNA_ExpA_Expo_Stat_SeattleBioMed_15Feb13_Cougar_12-12-36.raw";
var run = new RunFactory().CreateRun(testFile);
var calibrationData = new ViperMassCalibrationData();
calibrationData.MassError = 4.8;
var massAlignmentInfo = new MassAlignmentInfoLcmsWarp();
massAlignmentInfo.SetMassAlignmentData(calibrationData);
run.MassAlignmentInfo = massAlignmentInfo;
var observedMZ = 440.5887078;
var theorMZ = 440.5858315;
var calibratedMZ = run.GetAlignedMZ(observedMZ);
Assert.AreEqual(440.5866m, (decimal)Math.Round(calibratedMZ, 4));
var ppmDiffBefore = (observedMZ - theorMZ) / theorMZ * 1e6;
var ppmDiffAfter = (calibratedMZ - theorMZ) / theorMZ * 1e6;
Console.WriteLine("input m/z= " + observedMZ);
Console.WriteLine("calibrated m/z= " + calibratedMZ);
Console.WriteLine("ppmDiffBeforeCalibration= " + ppmDiffBefore);
Console.WriteLine("ppmDiffAftereCalibration= " + ppmDiffAfter);
var theorMZToLookForInRawData = run.GetTargetMZAligned(theorMZ);
var ppmDiffTheor = (theorMZToLookForInRawData - theorMZ) / theorMZ * 1e6;
Console.WriteLine();
Console.WriteLine("Theor m/z = " + theorMZ);
Console.WriteLine("Theor m/z to look for = " + theorMZToLookForInRawData);
Console.WriteLine("ppmDiff = " + ppmDiffTheor);
Assert.AreEqual(4.8m, (decimal)Math.Round(ppmDiffTheor, 1));
}
