diff --git a/pom.xml b/pom.xml
index 526d891..7e5e490 100644
--- a/pom.xml
+++ b/pom.xml
@@ -6,7 +6,7 @@
 
     <groupId>org.example</groupId>
     <artifactId>MSBooster</artifactId>
-    <version>1.2.36</version>
+    <version>1.2.37</version>
 
     <properties>
         <maven.compiler.source>1.8</maven.compiler.source>
diff --git a/src/main/java/Features/CalibrationFigure.java b/src/main/java/Features/CalibrationFigure.java
index 426f94d..d7e83b0 100644
--- a/src/main/java/Features/CalibrationFigure.java
+++ b/src/main/java/Features/CalibrationFigure.java
@@ -33,6 +33,7 @@ public class CalibrationFigure {
     String charge;
     public CalibrationFigure() {}
 
+    //TODO: repeat but with single entries at a time, with different outFile names
     public void plotFigure(MzmlReader mzml, String outFile, float opacity,
                            HashMap<String, double[][]> massToData,
                            HashMap<String, Function1<Double, Double>> loessFunctions) throws IOException {
diff --git a/src/main/java/Features/LoessUtilities.java b/src/main/java/Features/LoessUtilities.java
index 7a2a6b7..3252243 100644
--- a/src/main/java/Features/LoessUtilities.java
+++ b/src/main/java/Features/LoessUtilities.java
@@ -71,8 +71,9 @@ private static int getPSMs(MzmlReader mzml,
 
     //utility for getBetas and LOESS
     //returns exp and pred RT arrays
-    public static HashMap<String, double[][]> getArrays(MzmlReader mzml, int regressionSize, String mode, int charge)
+    public static Object[] getArrays(MzmlReader mzml, int regressionSize, String mode, int charge)
             throws FileParsingException {
+        //returns HashMap<String, double[][]> for arrays, and HashMap<String, ArrayList<String>> for peptides
         ArrayList<Float> expValues = new ArrayList<>();
         ArrayList<Float> predValues = new ArrayList<>();
         ArrayList<Float> eScores = new ArrayList<>(); //for sorting
@@ -146,15 +147,18 @@ public static HashMap<String, double[][]> getArrays(MzmlReader mzml, int regress
             massesList.add("");
         }
 
+        HashMap<String, ArrayList<String>> peptideMap = new HashMap<>();
         for (String mass : massesList) {
             ArrayList<Float> thisExpValues = new ArrayList<>();
             ArrayList<Float> thisPredValues = new ArrayList<>();
             ArrayList<Float> thisEscores = new ArrayList<>();
+            ArrayList<String> finalPeptides = new ArrayList<>();
             //get PSMs specific to this mass
             if (mass.isEmpty()) {
                 thisExpValues = expValues;
                 thisPredValues = predValues;
                 thisEscores = eScores;
+                finalPeptides = peptides;
             } else if (mass.equals("others")) {
                 for (int i = 0; i < peptides.size(); i++) {
                     boolean peptideContains = false;
@@ -175,6 +179,7 @@ public static HashMap<String, double[][]> getArrays(MzmlReader mzml, int regress
                         thisExpValues.add(expValues.get(i));
                         thisPredValues.add(predValues.get(i));
                         thisEscores.add(eScores.get(i));
+                        finalPeptides.add(peptides.get(i));
                     }
                 }
             } else {
@@ -185,6 +190,7 @@ public static HashMap<String, double[][]> getArrays(MzmlReader mzml, int regress
                             thisExpValues.add(expValues.get(i));
                             thisPredValues.add(predValues.get(i));
                             thisEscores.add(eScores.get(i));
+                            finalPeptides.add(peptides.get(i));
                             break;
                         }
                     }
@@ -231,11 +237,14 @@ public static HashMap<String, double[][]> getArrays(MzmlReader mzml, int regress
                 int[] sortedIndices2 = Arrays.copyOfRange(sortedIndices, 0, regressionSize);
 
                 double[][] thisValues = new double[2][regressionSize];
+                ArrayList<String> newFinalPeptides = new ArrayList<>();
                 for (int i = 0; i < regressionSize; i++) {
                     int idx = sortedIndices2[i];
                     thisValues[0][i] = thisExpValues.get(idx);
                     thisValues[1][i] = thisPredValues.get(idx);
+                    newFinalPeptides.add(finalPeptides.get(idx));
                 }
+                finalPeptides = newFinalPeptides;
                 massToDataMap.put(mass, thisValues);
             } else {
                 if (mass.isEmpty()) {
@@ -248,7 +257,9 @@ public static HashMap<String, double[][]> getArrays(MzmlReader mzml, int regress
                 thisValues[1] = thisPredValues.stream().mapToDouble(i -> i).toArray();
                 massToDataMap.put(mass, thisValues);
             }
+
+            peptideMap.put(mass, finalPeptides);
         }
-        return massToDataMap;
+        return new Object[] {massToDataMap, peptideMap};
     }
 }
diff --git a/src/main/java/Features/MainClass.java b/src/main/java/Features/MainClass.java
index e26d5b4..1a47da9 100644
--- a/src/main/java/Features/MainClass.java
+++ b/src/main/java/Features/MainClass.java
@@ -41,7 +41,7 @@ public class MainClass {
     public static ScheduledThreadPoolExecutor executorService;
     public static void main(String[] args) throws Exception {
         Locale.setDefault(Locale.US);
-        printInfo("MSBooster v1.2.36");
+        printInfo("MSBooster v1.2.37");
 
         try {
             //accept command line inputs
diff --git a/src/main/java/Features/MzmlReader.java b/src/main/java/Features/MzmlReader.java
index 25b76b5..6f38dbb 100644
--- a/src/main/java/Features/MzmlReader.java
+++ b/src/main/java/Features/MzmlReader.java
@@ -65,6 +65,8 @@ public class MzmlReader {
     public ArrayList<HashMap<String, Function1<Double, Double>>> IMLOESS = new ArrayList<>();
     public HashMap<String, double[][]> expAndPredRTs;
     public HashMap<Integer, HashMap<String, double[][]>> expAndPredIMsHashMap = new HashMap<>();
+    public HashMap<String, ArrayList<String>> RTpeptides;
+    public HashMap<String, ArrayList<String>> IMpeptides = new HashMap<>();
     public List<Future> futureList = new ArrayList<>(Constants.numThreads);
 
     public MzmlReader(String filename) throws FileParsingException, ExecutionException, InterruptedException {
@@ -806,7 +808,9 @@ public void setLOESS(int regressionSize, String bandwidth, int robustIters, Stri
         }
 
         if (mode.equals("RT")) {
-            expAndPredRTs = LoessUtilities.getArrays(this, regressionSize, mode, 0);
+            Object[] arraysAndPeptides = LoessUtilities.getArrays(this, regressionSize, mode, 0);
+            expAndPredRTs = (HashMap<String, double[][]>) arraysAndPeptides[0];
+            RTpeptides = (HashMap<String, ArrayList<String>>) arraysAndPeptides[1];
 
             //repeat this process for each mass shift group
             for (String mass : masses) {
@@ -870,8 +874,18 @@ public void setLOESS(int regressionSize, String bandwidth, int robustIters, Stri
             }
         } else if (mode.equals("IM")) {
             for (int charge = 1; charge < IMFunctions.numCharges + 1; charge++) {
-                HashMap<String, double[][]> expAndPredIMs =
-                        LoessUtilities.getArrays(this, regressionSize, mode, charge);
+                Object[] arraysAndPeptides = LoessUtilities.getArrays(this, regressionSize, mode, charge);
+                HashMap<String, double[][]> expAndPredIMs = (HashMap<String, double[][]>) arraysAndPeptides[0];
+                HashMap<String, ArrayList<String>> peptideMap =
+                        (HashMap<String, ArrayList<String>>) arraysAndPeptides[1];
+                for (Map.Entry<String, ArrayList<String>> entry : peptideMap.entrySet()) {
+                    if (!IMpeptides.containsKey(entry.getKey())) {
+                        IMpeptides.put(entry.getKey(), new ArrayList<>());
+                    }
+                    ArrayList<String> peptides = IMpeptides.get(entry.getKey());
+                    peptides.addAll(entry.getValue());
+                    IMpeptides.put(entry.getKey(), peptides);
+                }
                 HashMap<String, Function1<Double, Double>> IMLOESSmap = new HashMap<>();
 
                 for (String mass : masses) {
diff --git a/src/main/java/Features/PercolatorFormatter.java b/src/main/java/Features/PercolatorFormatter.java
index 2e9a9f7..0f5f63c 100644
--- a/src/main/java/Features/PercolatorFormatter.java
+++ b/src/main/java/Features/PercolatorFormatter.java
@@ -23,10 +23,13 @@
 import com.google.common.collect.Range;
 import com.google.common.collect.RangeMap;
 import com.google.common.collect.TreeRangeMap;
+import kotlin.jvm.functions.Function1;
 import org.apache.commons.lang3.ArrayUtils;
 import umich.ms.fileio.exceptions.FileParsingException;
 
+import java.io.BufferedWriter;
 import java.io.File;
+import java.io.FileWriter;
 import java.io.IOException;
 import java.sql.SQLException;
 import java.util.*;
@@ -518,8 +521,45 @@ public static void editPin(PinMzmlMatcher pmMatcher, String[] features, String o
                         }
                     }
                     if (plot) {
-                        new RTCalibrationFigure(mzml, pinFiles[i].getCanonicalPath(), 0.2f,
+                        CalibrationFigure cf = new RTCalibrationFigure(mzml, pinFiles[i].getCanonicalPath(), 0.2f,
                                 mzml.expAndPredRTs, mzml.RTLOESS);
+
+                        //individual figures by mass
+                        //separate figures
+                        for (String mass : mzml.expAndPredRTs.keySet()) {
+                            if (!mass.isEmpty()) {
+                                HashMap<String, double[][]> miniMassToData = new HashMap<>();
+                                miniMassToData.put(mass, mzml.expAndPredRTs.get(mass));
+                                HashMap<String, Function1<Double, Double>> miniLoessFunctions = new HashMap<>();
+                                miniLoessFunctions.put(mass, mzml.RTLOESS.get(mass));
+                                new RTCalibrationFigure(mzml,
+                                        pinFiles[i].getCanonicalPath().substring(0,
+                                                pinFiles[i].getCanonicalPath().length() - 4) + "_" + mass + ".pin",
+                                        0.2f, miniMassToData, miniLoessFunctions);
+                            }
+                        }
+
+                        //write peptides used
+                        File f = new File(pinFiles[i].getCanonicalPath());
+                        String calibrationPeptideFilePathBase =
+                                f.getParent() + File.separator + "MSBooster_plots" + File.separator + cf.folderString +
+                                File.separator + f.getName().substring(0, f.getName().length() - 4) +
+                                "_RTcalibrationPeptides";
+                        for (Map.Entry<String, ArrayList<String>> entry : mzml.RTpeptides.entrySet()) {
+                            String calibrationPeptideFilePath = calibrationPeptideFilePathBase;
+                            if (!entry.getKey().isEmpty()) {
+                                calibrationPeptideFilePath += "_" + entry.getKey();
+                            }
+                            try (BufferedWriter writer = new BufferedWriter(
+                                    new FileWriter(calibrationPeptideFilePath + ".txt"))) {
+                                for (String peptide : entry.getValue()) {
+                                    writer.write(peptide);
+                                    writer.newLine();
+                                }
+                            } catch (IOException e) {
+                                e.printStackTrace();
+                            }
+                        }
                     }
                 }
                 if (featuresList.contains("deltaRTlinear")) {
@@ -564,6 +604,8 @@ public static void editPin(PinMzmlMatcher pmMatcher, String[] features, String o
                     mzml.setLOESS(Constants.imLoessRegressionSize, Constants.loessBandwidth, Constants.robustIters, "IM");
                     mzml.predictIMLOESS(executorService);
 
+                    CalibrationFigure cf = null;
+                    boolean writePeptides = false;
                     for (int charge : mzml.expAndPredIMsHashMap.keySet()) {
                         boolean plot = false;
                         for (Map.Entry<String, double[][]> entry : mzml.expAndPredIMsHashMap.get(charge).entrySet()) {
@@ -573,8 +615,47 @@ public static void editPin(PinMzmlMatcher pmMatcher, String[] features, String o
                             }
                         }
                         if (plot) {
-                            new IMCalibrationFigure(mzml, pinFiles[i].getCanonicalPath(), 0.2f,
+                            cf = new IMCalibrationFigure(mzml, pinFiles[i].getCanonicalPath(), 0.2f,
                                     mzml.expAndPredIMsHashMap.get(charge), mzml.IMLOESS.get(charge - 1), charge);
+                            writePeptides = true;
+
+                            //individual figures by mass
+                            //separate figures
+                            for (String mass : mzml.expAndPredIMsHashMap.get(charge).keySet()) {
+                                if (!mass.isEmpty()) {
+                                    HashMap<String, double[][]> miniMassToData = new HashMap<>();
+                                    miniMassToData.put(mass, mzml.expAndPredIMsHashMap.get(charge).get(mass));
+                                    HashMap<String, Function1<Double, Double>> miniLoessFunctions = new HashMap<>();
+                                    miniLoessFunctions.put(mass, mzml.IMLOESS.get(charge - 1).get(mass));
+                                    new IMCalibrationFigure(mzml,
+                                            pinFiles[i].getCanonicalPath().substring(0,
+                                                    pinFiles[i].getCanonicalPath().length() - 4) + "_" + mass + ".pin",
+                                            0.2f, miniMassToData, miniLoessFunctions, charge);
+                                }
+                            }
+                        }
+                    }
+                    if (writePeptides) {
+                        //write peptides used
+                        File f = new File(pinFiles[i].getCanonicalPath());
+                        String calibrationPeptideFilePathBase =
+                                f.getParent() + File.separator + "MSBooster_plots" + File.separator + cf.folderString +
+                                        File.separator + f.getName().substring(0, f.getName().length() - 4) +
+                                        "_IMcalibrationPeptides";
+                        for (Map.Entry<String, ArrayList<String>> entry : mzml.IMpeptides.entrySet()) {
+                            String calibrationPeptideFilePath = calibrationPeptideFilePathBase;
+                            if (!entry.getKey().isEmpty()) {
+                                calibrationPeptideFilePath += "_" + entry.getKey();
+                            }
+                            try (BufferedWriter writer = new BufferedWriter(
+                                    new FileWriter(calibrationPeptideFilePath + ".txt"))) {
+                                for (String peptide : entry.getValue()) {
+                                    writer.write(peptide);
+                                    writer.newLine();
+                                }
+                            } catch (IOException e) {
+                                e.printStackTrace();
+                            }
                         }
                     }
                 }
diff --git a/src/main/java/Features/RTFunctions.java b/src/main/java/Features/RTFunctions.java
index 2130ecc..86c6e0b 100644
--- a/src/main/java/Features/RTFunctions.java
+++ b/src/main/java/Features/RTFunctions.java
@@ -55,7 +55,9 @@ public static float normalizeRT(float[] betas, float expRT) {
     //assumes peptide objects already set
     //TODO: only supporting getting PSMs for supported PTMs
     public static float[] getBetas(MzmlReader mzml, int RTregressionSize) throws FileParsingException {
-        double[][] RTs = LoessUtilities.getArrays(mzml, RTregressionSize, "RT", 0).get("");
+        HashMap<String, double[][]> arrays = (HashMap<String, double[][]>)
+                LoessUtilities.getArrays(mzml, RTregressionSize, "RT", 0)[0];
+        double[][] RTs = arrays.get("");
         return StatMethods.linearRegression(RTs[0], RTs[1]);
     }