1. Supported TMT labelled peptides;

2. Fixed issues: #74 and #71.
wenbostar · Apr 28, 2024 · e1ddd03 · e1ddd03
1 parent d01fb49
commit e1ddd03
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Showing 3 changed files with 32 additions and 16 deletions.
diff --git a/pom.xml b/pom.xml
@@ -5,7 +5,7 @@
     <groupId>PDV</groupId>
     <artifactId>PDV</artifactId>
     <packaging>jar</packaging>
-    <version>2.0.0</version>
+    <version>2.0.1-beta</version>
     <name>PDV</name>
     <url>https://github.com/wenbostar/PDV</url>
     <description>An integrative proteomics viewer</description>

diff --git a/src/main/java/PDVGUI/gui/utils/GetPredictedOnline.java b/src/main/java/PDVGUI/gui/utils/GetPredictedOnline.java
@@ -1,14 +1,12 @@
 package PDVGUI.gui.utils;
 
-import com.compomics.util.experiment.identification.spectrum_assumptions.PeptideAssumption;
 import com.compomics.util.experiment.massspectrometry.Charge;
 import com.compomics.util.experiment.massspectrometry.MSnSpectrum;
 import com.compomics.util.experiment.massspectrometry.Peak;
 import com.compomics.util.experiment.massspectrometry.Precursor;
 import org.apache.commons.lang3.StringUtils;
 import org.json.JSONArray;
 import org.json.JSONObject;
-import org.kohsuke.rngom.util.Uri;
 
 import java.io.BufferedReader;
 import java.io.IOException;
@@ -17,7 +15,6 @@
 import java.math.BigDecimal;
 import java.net.HttpURLConnection;
 import java.net.MalformedURLException;
-import java.net.ProtocolException;
 import java.net.URL;
 import java.nio.charset.StandardCharsets;
 import java.util.ArrayList;
@@ -105,7 +102,7 @@ private void generateInputString(){
                 // TODO: C-term modification
                 if(index == 0){
                     // N-term modification
-                    aa_list[0] = aa_list[0]+newMods.get(index);
+                    aa_list[0] = newMods.get(index) + "-"+ aa_list[0];
                 }else{
                     aa_list[index-1] = aa_list[index-1]+newMods.get(index);
                 }
@@ -157,7 +154,8 @@ private void generateInputString(){
 //                    " ] }] }";
 //        }
         else if (model.equals("Prosit_2020_intensity_TMT")){
-            modPep = "[UNIMOD:737]-" + modPep;
+            // modPep = "[UNIMOD:737]-" + modPep;
+            // System.out.println(modPep);
             inputString = "{ \"id\": \"0\", \"inputs\": [ { \"name\": \"peptide_sequences\", \"shape\": [ 1, 1 ], " +
                     "\"datatype\": \"BYTES\", \"data\": [ \"" + modPep + "\" ] }, { \"name\": \"precursor_charges\", " +
                     "\"shape\": [ 1, 1 ], \"datatype\": \"INT32\", \"data\": [ "+ precursorCharge + " ] }, { \"name\": " +

diff --git a/src/main/java/PDVGUI/gui/utils/ImportPredictedDialog.java b/src/main/java/PDVGUI/gui/utils/ImportPredictedDialog.java
@@ -11,8 +11,6 @@
 import javax.swing.*;
 import javax.swing.table.DefaultTableModel;
 import java.awt.*;
-import java.awt.event.MouseAdapter;
-import java.awt.event.MouseEvent;
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.Objects;
@@ -256,6 +254,14 @@ private String getModificationString(String originalMod) {
                 if (Math.abs(ptmFactory.getPTM(originalMod).getMass() - 0.984016) < 0.01) {
                     modificationString = "[UNIMOD:7]";
                 }
+            } else if(originalMod.contains("of K")){
+                if (Math.abs(ptmFactory.getPTM(originalMod).getMass() - 229.162932) < 0.01) {
+                    modificationString = "[UNIMOD:737]";
+                }
+            } else if(originalMod.contains("of N-term") || originalMod.contains("of peptide N-term")){
+                if (Math.abs(ptmFactory.getPTM(originalMod).getMass() - 229.162932) < 0.01) {
+                    modificationString = "[UNIMOD:737]";
+                }
             } else{
                 System.out.println("This modification is not supported:"+originalMod);
             }
@@ -270,10 +276,18 @@ private String getModificationString(String originalMod) {
                 if (Math.abs(ptmFactory.getPTM(originalMod).getMass() -57.021464) < 0.01) {
                     modificationString = "[UNIMOD:4]";
                 }
-            } else if (originalMod.contains("of M")){
-                if (Math.abs(ptmFactory.getPTM(originalMod).getMass() -15.994915) < 0.01) {
+            } else if (originalMod.contains("of M")) {
+                if (Math.abs(ptmFactory.getPTM(originalMod).getMass() - 15.994915) < 0.01) {
                     modificationString = "[UNIMOD:35]";
                 }
+            } else if(originalMod.contains("of K") && modelListComboBox.getSelectedIndex() == 6){
+                if (Math.abs(ptmFactory.getPTM(originalMod).getMass() - 229.162932) < 0.01) {
+                    modificationString = "[UNIMOD:737]";
+                }
+            } else if((originalMod.contains("of N-term") || originalMod.contains("of peptide N-term")) && modelListComboBox.getSelectedIndex() == 6){
+                if (Math.abs(ptmFactory.getPTM(originalMod).getMass() - 229.162932) < 0.01) {
+                    modificationString = "[UNIMOD:737]";
+                }
             } else{
                 System.out.println("This modification is not supported:"+originalMod);
             }
@@ -299,11 +313,11 @@ private void submissionButtonActionPerformed(java.awt.event.ActionEvent evt) {
                 newMods.put((int) modificationJTable.getValueAt(i, 1), mod);
             }
         }
-        if (modelListComboBox.getSelectedIndex() == 6) {
-            JOptionPane.showMessageDialog(
-                    null, "This model will add a TMT tag to the N-term of the peptide.",
-                    "Warning", JOptionPane.WARNING_MESSAGE);
-        }
+        //if (modelListComboBox.getSelectedIndex() == 6) {
+        //    JOptionPane.showMessageDialog(
+        //            null, "This model will add a TMT tag to the N-term of the peptide.",
+        //            "Warning", JOptionPane.WARNING_MESSAGE);
+        //}
 
         ProgressDialogX progressDialogX = new ProgressDialogX(spectrumMainPanel.parentFrame,
                 Toolkit.getDefaultToolkit().getImage(getClass().getResource("/icons/SeaGullMass.png")),
@@ -418,7 +432,11 @@ public Object getValueAt(int row, int column) {
                 case 0:
                     return modificationMatch.getTheoreticPtm();
                 case 1:
-                    return modificationMatch.getModificationSite();
+                    if(modificationMatch.getTheoreticPtm().contains("of N-term") || modificationMatch.getTheoreticPtm().contains("of peptide N-term")){
+                        return 0;
+                    }else{
+                        return modificationMatch.getModificationSite();
+                    }
                 case 2:
                     return getModificationString(modificationMatch.getTheoreticPtm());
                 case 3: