Skip to content

Commit

Permalink
Change delta mass to true instead of peak apex
Browse files Browse the repository at this point in the history
  • Loading branch information
@danielgeiszler
danielgeiszler committed May 9, 2024
1 parent 09a97a6 commit 3b9d8a7
Show file tree
Hide file tree
Showing 2 changed files with 28 additions and 16 deletions.
32 changes: 17 additions & 15 deletions src/edu/umich/andykong/ptmshepherd/iterativelocalization/IterativeLocalizer.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -173,8 +173,8 @@ private void fitMatchedIonDistribution() throws Exception {
//ArrayList<Float> decoySitePepFrags = DownstreamPepFragGenerator.calculatePeptideFragments(
// decoyPep, this.ionTypes, mutationSite, 1);
// Generate target and decoy fragments
ArrayList<Float> sitePepFrags = targetPep.calculatePeptideFragments(this.ionTypes, 2);
ArrayList<Float> decoySitePepFrags = decoyPep.calculatePeptideFragments(this.ionTypes, 2);
ArrayList<Float> sitePepFrags = targetPep.calculatePeptideFragments(this.ionTypes, 1);
ArrayList<Float> decoySitePepFrags = decoyPep.calculatePeptideFragments(this.ionTypes, 1);

// Score over all possible sites
/**
Expand Down Expand Up @@ -318,9 +318,9 @@ private void calculateLocalizationProbabilities() throws Exception {
dMassApex = dMass;
else
continue;
} else {
dMassApex = dMass; // Using real dmass prevents bad peakpicking from distorting loc
}
else
dMassApex = (float) this.peaks[0][cBin]; // TODO which ones to use?

// Ignore zero bin, unless on the last pass and writing results TODO: set up custom bounds?
if ((zbL <= dMass) && (dMass <= zbR)) {
Expand Down Expand Up @@ -360,14 +360,14 @@ private void calculateLocalizationProbabilities() throws Exception {
}
}

//if (specName.equals("02330a_GC1_3990_03_PTM_TrainKit_Rmod_Dimethyl_asymm_200fmol_3xHCD_R1.15210.15210")) {
// this.debugFlag = true;
//}
if (specName.equals("02330a_GH3_3991_13_PTM_TrainKit_Pmod_Hydroxyproline_200fmol_3xHCD_R1.07708.07708")) {
this.debugFlag = true;
}

// Calculate site-specific localization probabilities
float[] mods = psm.getModsAsArray();
boolean[] allowedPoses = parseAllowedPositions(pep, this.allowedAAs, mods);
double[] siteProbs = localizePsm(psm, spec, pep, mods, dMassApex, cBin, allowedPoses); // TODO check whether raw, theoretical, or peakapex is better
double[] siteProbs = localizePsm(psm, spec, pep, mods, dMassApex, cBin, allowedPoses, false); // TODO check whether raw, theoretical, or peakapex is better

// Update prior probabilities
if (!finalPass)
Expand All @@ -387,7 +387,7 @@ private void calculateLocalizationProbabilities() throws Exception {
boolean[] decoyAllowedPoses = parseAllowedPositions(decoyPep.pepSeq,
this.allowedAAs, decoyPep.mods);
double[] decoySiteProbs = localizePsm(psm, spec, decoyPep.pepSeq, decoyPep.mods, dMassApex,
cBin, decoyAllowedPoses);
cBin, decoyAllowedPoses, true);
double decoyMaxProb = findMaxLocalizationProbability(decoySiteProbs);
String decoyMaxProbAA = findMaxLocalizationProbabilitySite(decoySiteProbs, decoyPep.pepSeq);
strMaxProbsDecoy.add(maxProbToString(decoyMaxProb, decoyMaxProbAA));
Expand Down Expand Up @@ -879,7 +879,7 @@ boolean isDecoyAA(char aa) {
* @param allowedPoses array of allowed positions based on peptide sequence localization restrictions TODO add mods
* @return double[] of localization probabilities
*/
private double[] localizePsm (PSMFile.PSM psm, Spectrum spec, String pep, float[] mods, float dMass, int cBin, boolean[] allowedPoses) {
private double[] localizePsm (PSMFile.PSM psm, Spectrum spec, String pep, float[] mods, float dMass, int cBin, boolean[] allowedPoses, boolean isDecoy) {
double[] sitePriorProbs;
double[] siteLikelihoods = new double[pep.length()];
double marginalProb = 0.0;
Expand All @@ -895,12 +895,13 @@ private double[] localizePsm (PSMFile.PSM psm, Spectrum spec, String pep, float[
// There are no ions that can differentiate termini and terminal AAs, so the likelihood for each terminus
// is equal to the proximal AA
// Check to see if the likelihood has already been computed. If it has, grab it. If not, compute it.
if (this.localizationLikelihoodMap.containsKey(psm.getSpec())) {
if (this.localizationLikelihoodMap.containsKey(psm.getSpec()) && !isDecoy) {
siteLikelihoods = this.localizationLikelihoodMap.get(psm.getSpec()).getMod().getSiteLikelihoods();
} else {
//siteLikelihoods = computePoissonBinomialLikelihood(pep, mods, dMass, allowedPoses, spec);
siteLikelihoods = computeLikelihoods(pep, mods, dMass, allowedPoses, spec);
this.localizationLikelihoodMap.put(psm.getSpec(), new LocalizationLikelihood(dMass, siteLikelihoods));
if (!isDecoy)
this.localizationLikelihoodMap.put(psm.getSpec(), new LocalizationLikelihood(dMass, siteLikelihoods));
}

// Compute marginal probability for peptide Sum_{k=0}^{{L_i}+1} P(Pep_{ik})*P(Spec_i|Pep_{ik})
Expand Down Expand Up @@ -997,9 +998,10 @@ private double[] computePoissonBinomialLikelihood(String pep, float[] mods, floa
// Map matched ion intensities to MatchedIonDistribution, negative intensities will be returned as -1
double[] matchedIonProbabilities = this.matchedIonDist.calcIonProbabilities(matchedIonIntensities, matchedIonMassErrors);
if (debugFlag) {
System.out.println("Matched ions");
System.out.println("Start");
System.out.println(pep);
System.out.println("Position " + (i + 1));;
System.out.println("Matched ions");
System.out.println(Arrays.toString(matchedIonIntensities));
System.out.println(Arrays.toString(matchedIonProbabilities));
System.out.println("Matched ions done");
Expand Down Expand Up @@ -1075,7 +1077,7 @@ private double[] computeLikelihoods(String pep, float[] mods, float dMass, boole
if (!allowedPoses[i])
continue;
mods[i] += dMass;
ArrayList<Float> sitePepFrags = Peptide.calculatePeptideFragments(pep, mods, this.ionTypes, 2);
ArrayList<Float> sitePepFrags = Peptide.calculatePeptideFragments(pep, mods, this.ionTypes, 1);
// Find matched ion intensities. Matched ions will have positive intensities, unmatched ions will have negative
float[][] matchedIons = findMatchedIons(sitePepFrags, reducedMzs, reducedInts);
float[] matchedIonIntensities = matchedIons[0];
Expand Down Expand Up @@ -1190,7 +1192,7 @@ private double computeLikelihood(ArrayList<Float> pepFrags, float[] peakMzs, flo

public float[][] getReducedIons(Spectrum spec, Peptide pep, float dMass) {
// First calculate the set of shifted and unshifted ions
ArrayList<Float> pepFrags = pep.calculatePeptideFragments(this.ionTypes, 2);
ArrayList<Float> pepFrags = pep.calculatePeptideFragments(this.ionTypes, 1);
ArrayList<Float> shiftedPepFrags = new ArrayList<>(pepFrags.size());
for (Float frag : pepFrags)
shiftedPepFrags.add(frag + dMass);
Expand Down
12 changes: 11 additions & 1 deletion test/utils/PeptideTest.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,7 @@

import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import java.util.Random;

import static org.junit.jupiter.api.Assertions.*;
Expand Down Expand Up @@ -36,7 +37,7 @@ void generateDecoy() {
@Test
void calculatePeptideFragments() {
String seq = "PEPT";
float[] mods = new float[]{0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f};
float[] mods = new float[]{0.0f, 0.0f, 0.0f, 0.0f};
Peptide pep = new Peptide(seq, mods);

ArrayList<Float> sitePepFrags = pep.calculatePeptideFragments("b", 1);
Expand All @@ -51,5 +52,14 @@ void calculatePeptideFragments() {
for (int i = 0; i < expectedFrags.size(); i++) {
assertEquals(expectedFrags.get(i), sitePepFrags.get(i), 0.0001, "Mismatch at index " + i);
}

seq = "PASGAGAGAGAGKR";
mods = new float[]{114.0448f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f};
pep = new Peptide(seq, mods);

sitePepFrags = pep.calculatePeptideFragments("b", 1);

System.out.println(sitePepFrags.toString());

}
}

0 comments on commit 3b9d8a7

Please sign in to comment.