fix var mods for maxquant to work with the ptm model

wilhelm-lab · Nov 7, 2024 · a58f06b · a58f06b
1 parent 03b0249
commit a58f06b
Showing 1 changed file with 22 additions and 21 deletions.
diff --git a/spectrum_fundamentals/constants.py b/spectrum_fundamentals/constants.py
@@ -80,27 +80,28 @@
 ######################
 
 MAXQUANT_VAR_MODS = {
-    "(ox)": "[UNIMOD:35]",
-    "(Oxidation (M))": "[UNIMOD:35]",
-    "(tm)": "[UNIMOD:737]",
-    "_(tm)": "_[UNIMOD:737]-",
-    "K(tm)": "K[UNIMOD:737]",
-    "(i4)": "[UNIMOD:214]",
-    "_(i4)": "_[UNIMOD:214]-",
-    "K(i4)": "K[UNIMOD:214]",
-    "(i8)": "[UNIMOD:730]",
-    "_(i8)": "_[UNIMOD:730]-",
-    "K(i8)": "K[UNIMOD:730]",
-    "(tmp)": "[UNIMOD:2016]",
-    "_(tmp)": "_[UNIMOD:2016]-",
-    "K(tmp)": "K[UNIMOD:2016]",
-    "(ph)": "[UNIMOD:21]",
-    "(Phospho (STY))": "[UNIMOD:21]",
-    "(de)": "[UNIMOD:23]",
-    "(Dehydrated (ST))": "[UNIMOD:23]",
-    "K(Lys8)": "K[UNIMOD:259]",
-    "R(Arg10)": "R[UNIMOD:267]",
-    "C(Carbamidomethyl (C))": "C[UNIMOD:4]",
+    "\\(ox\\)": "[UNIMOD:35]",
+    "\\(Oxidation\\ \\(M\\)\\)": "[UNIMOD:35]",
+    "\\(tm\\)": "[UNIMOD:737]",
+    "_\\(tm\\)": "_[UNIMOD:737]-",
+    "K\\(tm\\)": "K[UNIMOD:737]",
+    "\\(i4\\)": "[UNIMOD:214]",
+    "_\\(i4\\)": "_[UNIMOD:214]-",
+    "K\\(i4\\)": "K[UNIMOD:214]",
+    "\\(i8\\)": "[UNIMOD:730]",
+    "_\\(i8\\)": "_[UNIMOD:730]-",
+    "K\\(i8\\)": "K[UNIMOD:730]",
+    "\\(tmp\\)": "[UNIMOD:2016]",
+    "_\\(tmp\\)": "_[UNIMOD:2016]-",
+    "K\\(tmp\\)": "K[UNIMOD:2016]",
+    "\\(ph\\)": "[UNIMOD:21]",
+    "\\(Phospho\\ \\(STY\\)\\)": "[UNIMOD:21]",
+    "\\(de\\)": "[UNIMOD:23]",
+    "\\(Dehydrated \\(ST\\)\\)": "[UNIMOD:23]",
+    "K\\(Lys8\\)": "K[UNIMOD:259]",
+    "R\\(Arg10\\)": "R[UNIMOD:267]",
+    "C\\(Carbamidomethyl\\ \\(C\\)\\)": "C[UNIMOD:4]",
+    "C": "C[UNIMOD:4]",
 }
 
 MAXQUANT_NC_TERM = {"^_": "", "_$": ""}