From e5c848e715c4b26320f8ccab166b206cc1053d47 Mon Sep 17 00:00:00 2001
From: ArthurDeclercq <Arthur.Declercq@UGent.be>
Date: Fri, 8 Sep 2023 13:29:06 +0200
Subject: [PATCH 1/4] timstof_models

---
 ms2pip/constants.py | 15 +++++++++++++++
 1 file changed, 15 insertions(+)

diff --git a/ms2pip/constants.py b/ms2pip/constants.py
index 12e222f3..13440c96 100644
--- a/ms2pip/constants.py
+++ b/ms2pip/constants.py
@@ -143,5 +143,20 @@
             "model_20220104_CID_TMT_Y.xgboost": "299539179ca55d4ac82e9aed6a4e0bd134a9a41e",
         },
     },
+    "timsTOF": {
+        "id": 12,
+        "ion_types": ["B", "Y"],
+        "peaks_version": "general",
+        "features_version": "normal",
+        "xgboost_model_files": {
+            "b": "phospho_timsTOF_b_maxdepth.xgboost",
+            "y": "phospho_timsTOF_y_maxdepth.xgboost",
+        },
+        "model_hash": {
+            "phospho_timsTOF_b_maxdepth.xgboost": "87ee90fbdb2033380fc6f2b543173016404b782b",
+            "phospho_timsTOF_y_maxdepth.xgboost": "8c1d062ba86415e5cf5bf16a0cc161f11da2d87e",
+        },
+    },
 }
+
 MODELS["HCD"] = MODELS["HCD2021"]

From 70a3f6d245f954f8eb4d5636b28b0c2567f8fe70 Mon Sep 17 00:00:00 2001
From: ArthurDeclercq <Arthur.Declercq@UGent.be>
Date: Tue, 12 Sep 2023 13:48:39 +0200
Subject: [PATCH 2/4] add ms2pip timsTOF models

---
 ms2pip/constants.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/ms2pip/constants.py b/ms2pip/constants.py
index 13440c96..d895f107 100644
--- a/ms2pip/constants.py
+++ b/ms2pip/constants.py
@@ -149,12 +149,12 @@
         "peaks_version": "general",
         "features_version": "normal",
         "xgboost_model_files": {
-            "b": "phospho_timsTOF_b_maxdepth.xgboost",
-            "y": "phospho_timsTOF_y_maxdepth.xgboost",
+            "b": "11092023_172748_training_datafeature_vector_b.xgboost",
+            "y": "12092023_103353_training_datafeature_vector_inverse_y.xgboost",
         },
         "model_hash": {
-            "phospho_timsTOF_b_maxdepth.xgboost": "87ee90fbdb2033380fc6f2b543173016404b782b",
-            "phospho_timsTOF_y_maxdepth.xgboost": "8c1d062ba86415e5cf5bf16a0cc161f11da2d87e",
+            "11092023_172748_training_datafeature_vector_b.xgboost": "6beb557052455310d8c66311c86866dda8291f4b",
+            "12092023_103353_training_datafeature_vector_inverse_y.xgboost": "8edd87e0fba5f338d0a0881b5afbcf2f48ec5268",
         },
     },
 }

From 2b4d66a673c3c83a75bf68d4114463afb27763ac Mon Sep 17 00:00:00 2001
From: ArthurDeclercq <Arthur.Declercq@UGent.be>
Date: Tue, 12 Sep 2023 13:48:51 +0200
Subject: [PATCH 3/4] fix training data function

---
 ms2pip/core.py | 15 ++++++++++++---
 1 file changed, 12 insertions(+), 3 deletions(-)

diff --git a/ms2pip/core.py b/ms2pip/core.py
index e40448fd..32ccab5d 100644
--- a/ms2pip/core.py
+++ b/ms2pip/core.py
@@ -769,9 +769,18 @@ def _assemble_training_data(results: List[ProcessingResult], model: str) -> pd.D
         ]
     )
     for ion_type in ion_types:
-        training_data[f"target_{ion_type}"] = np.concatenate(
-            [r.observed_intensity[ion_type] for r in results if r.feature_vectors is not None]
-        )
+        if ion_type in ["a", "b", "b2", "c"]:
+            training_data[f"target_{ion_type}"] = np.concatenate(
+                [r.observed_intensity[ion_type] for r in results if r.feature_vectors is not None]
+            )
+        elif ion_type in ["x", "y", "y2", "z"]:
+            training_data[f"target_{ion_type}"] = np.concatenate(
+                [
+                    r.observed_intensity[ion_type][::-1]
+                    for r in results
+                    if r.feature_vectors is not None
+                ]
+            )
 
     # Reorder columns
     training_data = training_data[

From 4d48c1c3ec13ec8fe1fd90217a2ead07e3937199 Mon Sep 17 00:00:00 2001
From: ArthurDeclercq <Arthur.Declercq@UGent.be>
Date: Tue, 12 Sep 2023 15:54:07 +0200
Subject: [PATCH 4/4] changed model filenames

---
 ms2pip/constants.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/ms2pip/constants.py b/ms2pip/constants.py
index d895f107..2838bc79 100644
--- a/ms2pip/constants.py
+++ b/ms2pip/constants.py
@@ -149,12 +149,12 @@
         "peaks_version": "general",
         "features_version": "normal",
         "xgboost_model_files": {
-            "b": "11092023_172748_training_datafeature_vector_b.xgboost",
-            "y": "12092023_103353_training_datafeature_vector_inverse_y.xgboost",
+            "b": "model_20230912_timsTOF_B.xgboost",
+            "y": "model_20230912_timsTOF_Y.xgboost",
         },
         "model_hash": {
-            "11092023_172748_training_datafeature_vector_b.xgboost": "6beb557052455310d8c66311c86866dda8291f4b",
-            "12092023_103353_training_datafeature_vector_inverse_y.xgboost": "8edd87e0fba5f338d0a0881b5afbcf2f48ec5268",
+            "model_20230912_timsTOF_B.xgboost": "6beb557052455310d8c66311c86866dda8291f4b",
+            "model_20230912_timsTOF_Y.xgboost": "8edd87e0fba5f338d0a0881b5afbcf2f48ec5268",
         },
     },
 }