From ba33812504cf0e3d65a4d40c95e5737ea99368b7 Mon Sep 17 00:00:00 2001
From: RalfG <ralfg@hotmail.be>
Date: Mon, 18 Mar 2024 18:59:32 +0100
Subject: [PATCH 1/2] docs: Add instructions for adding fixed terminal
 modifications. See #125, compomics/psm_utils#71, and hupo-psi/proforma#6

---
 docs/source/userguide/configuration.rst | 26 +++++++++++++++++++++++--
 1 file changed, 24 insertions(+), 2 deletions(-)

diff --git a/docs/source/userguide/configuration.rst b/docs/source/userguide/configuration.rst
index 52036aa7..8b68ea45 100644
--- a/docs/source/userguide/configuration.rst
+++ b/docs/source/userguide/configuration.rst
@@ -123,7 +123,7 @@ be configured separately. For instance:
   .. code-block:: json
 
     "fixed_modifications": {
-      "C": "U:Carbamidomethyl"
+      "U:Carbamidomethyl": ["C"]
     }
 
 .. tab:: TOML
@@ -131,7 +131,7 @@ be configured separately. For instance:
     .. code-block:: toml
 
       [ms2rescore.fixed_modifications]
-      "Carbamidomethyl" = ["C"]
+      "U:Carbamidomethyl" = ["C"]
 
 .. tab:: GUI
 
@@ -140,6 +140,28 @@ be configured separately. For instance:
     :alt: fixed modifications configuration in GUI
 
 
+Fixed terminal modifications can be added by using the special labels ``N-term`` and ``C-term``.
+For example, to additionally add TMT6plex to the N-terminus and lysine residues, the following
+configuration can be used:
+
+.. tab:: JSON
+
+  .. code-block:: json
+
+    "fixed_modifications": {
+      "U:Carbamidomethyl": ["C"],
+      "U:TMT6plex": ["N-term", "K"]
+    }
+
+.. tab:: TOML
+
+    .. code-block:: toml
+
+      [ms2rescore.fixed_modifications]
+      "U:Carbamidomethyl" = ["C"]
+      "U:TMT6plex" = ["N-term", "K"]
+
+
 .. caution::
   Most search engines DO return fixed modifications as part of the modified peptide sequences.
   In these cases, they must NOT be added to the ``fixed_modifications`` configuration.

From 60e69996087dc065c2e345eca7058a2a6d51eb3c Mon Sep 17 00:00:00 2001
From: RalfG <ralfg@hotmail.be>
Date: Mon, 8 Apr 2024 17:01:35 +0200
Subject: [PATCH 2/2] Version bump

---
 ms2rescore/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/ms2rescore/__init__.py b/ms2rescore/__init__.py
index 509fc99e..16f7dfd4 100644
--- a/ms2rescore/__init__.py
+++ b/ms2rescore/__init__.py
@@ -1,6 +1,6 @@
 """MS²Rescore: Sensitive PSM rescoring with predicted MS² peak intensities and RTs."""
 
-__version__ = "3.0.2"
+__version__ = "3.0.3"
 
 from warnings import filterwarnings