public bool Run_TdMzCal(InputFile raw_file, List <TopDownHit> topdown_hits)
{
all_topdown_hits = topdown_hits.Where(h => h.score > 0).ToList();
//need to reset m/z in case same td hits used for multiple calibration raw files...
Parallel.ForEach(all_topdown_hits, h => h.mz = h.reported_mass.ToMz(h.charge));
high_scoring_topdown_hits = all_topdown_hits.Where(h => h.score >= 40).ToList();
this.raw_file = raw_file;
if (high_scoring_topdown_hits.Count < 5)
{
return(false);
}
myMsDataFile = Path.GetExtension(raw_file.complete_path) == ".raw" ?
ThermoStaticData.LoadAllStaticData(raw_file.complete_path) :
null;
if (myMsDataFile == null)
{
myMsDataFile = Mzml.LoadAllStaticData(raw_file.complete_path);
}
if (myMsDataFile == null)
{
return(false);
}
DataPointAquisitionResults dataPointAcquisitionResult = GetDataPoints();
if (dataPointAcquisitionResult.Ms1List.Count < 10)
{
return(false);
}
var myMs1DataPoints = new List <(double[] xValues, double yValue)>();
for (int i = 0; i < dataPointAcquisitionResult.Ms1List.Count; i++)
{
//x values
var explanatoryVariables = new double[4];
explanatoryVariables[0] = dataPointAcquisitionResult.Ms1List[i].mz;
explanatoryVariables[1] = dataPointAcquisitionResult.Ms1List[i].retentionTime;
explanatoryVariables[2] = dataPointAcquisitionResult.Ms1List[i].logTotalIonCurrent;
explanatoryVariables[3] = dataPointAcquisitionResult.Ms1List[i].logInjectionTime;
//yvalue
double mzError = dataPointAcquisitionResult.Ms1List[i].massError;
myMs1DataPoints.Add((explanatoryVariables, mzError));
}
var ms1Model = GetRandomForestModel(myMs1DataPoints);
CalibrateHitsAndComponents(ms1Model);
if (Sweet.lollipop.calibrate_raw_files)
{
MzmlMethods.CreateAndWriteMyMzmlWithCalibratedSpectra(myMsDataFile, raw_file.directory + "\\" + raw_file.filename + "_calibrated.mzML", false);
}
return(true);
}
public bool Run_TdMzCal(InputFile raw_file, List <SpectrumMatch> topdown_hits)
{
all_topdown_hits = topdown_hits.Where(h => h.score > 0).ToList();
//need to reset m/z in case same td hits used for multiple calibration raw files...
Parallel.ForEach(all_topdown_hits, h => h.mz = h.reported_mass.ToMz(h.charge));
high_scoring_topdown_hits = all_topdown_hits.Where(h => h.score >= 40).ToList();
this.raw_file = raw_file;
if (high_scoring_topdown_hits.Count < 5)
{
return(false);
}
myMsDataFile = Path.GetExtension(raw_file.complete_path) == ".raw" ?
ThermoStaticData.LoadAllStaticData(raw_file.complete_path) :
null;
if (myMsDataFile == null)
{
myMsDataFile = Mzml.LoadAllStaticData(raw_file.complete_path);
}
if (myMsDataFile == null)
{
return(false);
}
DataPointAquisitionResults dataPointAcquisitionResult = GetDataPoints();
if (dataPointAcquisitionResult.Ms1List.Count < 10)
{
return(false);
}
if (Sweet.lollipop.mass_calibration)
{
var myMs1DataPoints = new List <(double[] xValues, double yValue)>();
for (int i = 0; i < dataPointAcquisitionResult.Ms1List.Count; i++)
{
//x values
var explanatoryVariables = new double[4];
explanatoryVariables[0] = dataPointAcquisitionResult.Ms1List[i].mz;
explanatoryVariables[1] = dataPointAcquisitionResult.Ms1List[i].retentionTime;
explanatoryVariables[2] = dataPointAcquisitionResult.Ms1List[i].logTotalIonCurrent;
explanatoryVariables[3] = dataPointAcquisitionResult.Ms1List[i].logInjectionTime;
//yvalue
double mzError = dataPointAcquisitionResult.Ms1List[i].massError;
myMs1DataPoints.Add((explanatoryVariables, mzError));
}
var ms1Model = GetRandomForestModel(myMs1DataPoints);
CalibrateHitsAndComponents(ms1Model);
if (Sweet.lollipop.calibrate_raw_files)
{
MzmlMethods.CreateAndWriteMyMzmlWithCalibratedSpectra(myMsDataFile,
raw_file.directory + "\\" + raw_file.filename + "_calibrated.mzML", false);
}
}
if (Sweet.lollipop.retention_time_calibration)
{
var myMs1DataPoints = new List <(double[] xValues, double yValue)>();
List <SpectrumMatch> firstElutingTopDownHit = new List <SpectrumMatch>();
List <string> PFRs = high_scoring_topdown_hits.Select(h => h.pfr_accession).Distinct().ToList();
foreach (var PFR in PFRs)
{
var firstHitWithPFR = high_scoring_topdown_hits
.Where(h => h.pfr_accession == PFR).OrderBy(h => h.ms2_retention_time).First();
firstElutingTopDownHit.Add(firstHitWithPFR);
}
for (int i = 0; i < dataPointAcquisitionResult.Ms1List.Count; i++)
{
if (firstElutingTopDownHit.Contains(dataPointAcquisitionResult.Ms1List[i].identification))
{
//x values
var explanatoryVariables = new double[1];
explanatoryVariables[0] = dataPointAcquisitionResult.Ms1List[i].retentionTime;
//yvalue
double RTError = dataPointAcquisitionResult.Ms1List[i].RTError;
myMs1DataPoints.Add((explanatoryVariables, RTError));
}
}
if (myMs1DataPoints.Count < 10)
{
return(false);
}
var ms1Model = GetRandomForestModel(myMs1DataPoints);
foreach (Component c in Sweet.lollipop.calibration_components.Where(h => h.input_file.lt_condition == raw_file.lt_condition && h.input_file.biological_replicate == raw_file.biological_replicate && h.input_file.fraction == raw_file.fraction && h.input_file.technical_replicate == raw_file.technical_replicate))
{
c.rt_apex = c.rt_apex - ms1Model.Predict(new double[] { c.rt_apex });
}
}
return(true);
}
private DataPointAquisitionResults GetDataPoints()
{
DataPointAquisitionResults res = new DataPointAquisitionResults()
{
Ms1List = new List <LabeledMs1DataPoint>()
};
// Set of peaks, identified by m/z and retention time. If a peak is in here, it means it has been a part of an accepted identification, and should be rejected
var peaksAddedFromMS1HashSet = new HashSet <Tuple <double, int> >();
foreach (SpectrumMatch identification in high_scoring_topdown_hits.OrderByDescending(h => h.score).ThenBy(h => h.pscore).ThenBy(h => h.reported_mass))
{
int scanNum = myMsDataFile.GetClosestOneBasedSpectrumNumber(identification.ms2_retention_time);
List <int> scanNumbers = new List <int>()
{
scanNum
};
int proteinCharge = identification.charge;
Component matching_component = null;
if (identification.filename != raw_file.filename) //if calibrating across files find component with matching mass and retention time
{
//NOTE: only looking at components from same raw file... looking for components corresponding to td hits from any files w/ same br, fraction, condition however.
//look around theoretical mass of topdown hit identified proteoforms - 10 ppm and 5 minutes same br, tr, fraction, condition (same file!)
//if neucode labled, look for the light component mass (loaded in...)
List <Component> potential_matches = Sweet.lollipop.calibration_components.
Where(c => c.input_file.lt_condition == raw_file.lt_condition &&
c.input_file.biological_replicate == raw_file.biological_replicate &&
c.input_file.fraction == raw_file.fraction &&
c.input_file.technical_replicate == raw_file.technical_replicate).ToList();
if (potential_matches.Count > 0)
{
matching_component = potential_matches.Where(c =>
Math.Abs(c.charge_states.OrderByDescending(s => s.intensity).First().mz_centroid.ToMass(c.charge_states.OrderByDescending(s => s.intensity).First().charge_count) - identification.theoretical_mass) * 1e6 / c.charge_states.OrderByDescending(s => s.intensity).First().mz_centroid.ToMass(c.charge_states.OrderByDescending(s => s.intensity).First().charge_count) < Sweet.lollipop.cali_mass_tolerance &&
Math.Abs(c.rt_apex - identification.ms1_scan.RetentionTime) < Sweet.lollipop.cali_rt_tolerance).OrderBy(c => Math.Abs(c.charge_states.OrderByDescending(s => s.intensity).First().mz_centroid.ToMass(c.charge_states.OrderByDescending(s => s.intensity).First().charge_count) - identification.theoretical_mass)).FirstOrDefault();
}
else
{
matching_component = null;
}
if (matching_component == null)
{
continue;
}
scanNumbers.Clear();
//get scan numbers using retention time (if raw file is spliced, scan numbers change)
double rt = matching_component.min_rt;
while (Math.Round(rt, 2) <= Math.Round(matching_component.max_rt, 2))
{
int scanNumber = myMsDataFile.GetClosestOneBasedSpectrumNumber(rt);
scanNumbers.Add(scanNumber);
rt = myMsDataFile.GetOneBasedScan(scanNumber + 1).RetentionTime;
}
proteinCharge = matching_component.charge_states.OrderByDescending(c => c.intensity).First().charge_count;
if (matching_component.charge_states.Count == 1)
{
proteinCharge = identification.charge;
}
}
var formula = identification.GetChemicalFormula();
if (formula == null)
{
continue;
}
// Calculate isotopic distribution of the full peptide
var dist = IsotopicDistribution.GetDistribution(formula, 0.1, 0.001);
double[] masses = dist.Masses.ToArray();
double[] intensities = dist.Intensities.ToArray();
Array.Sort(intensities, masses, Comparer <double> .Create((x, y) => y.CompareTo(x)));
List <int> scansAdded = new List <int>();
foreach (int scanNumber in scanNumbers)
{
res.Ms1List.AddRange(SearchMS1Spectra(masses, intensities, scanNumber, -1, scansAdded, peaksAddedFromMS1HashSet, proteinCharge, identification));
res.Ms1List.AddRange(SearchMS1Spectra(masses, intensities, scanNumber, 1, scansAdded, peaksAddedFromMS1HashSet, proteinCharge, identification));
}
}
return(res);
}