diff --git a/dquartic/cli.py b/dquartic/cli.py
index 1118b47..ea2b2c9 100644
--- a/dquartic/cli.py
+++ b/dquartic/cli.py
@@ -77,12 +77,13 @@ def train(
     parquet_directory = config['data']['parquet_directory']
     ms2_data_path = config['data']['ms2_data_path']
     ms1_data_path = config['data']['ms1_data_path']
+    feature_mask_file=config["data"]["feature_mask_path"],
     batch_size = config['model']['batch_size']
     checkpoint_path = config['model']['checkpoint_path']
     use_wandb = config['wandb']['use_wandb']
     threads = config['threads']
 
-    dataset = DIAMSDataset(parquet_directory, ms2_data_path, ms1_data_path, normalize=config['data']['normalize'])
+    dataset = DIAMSDataset(parquet_directory, ms2_data_path, ms1_data_path, feature_mask_file, normalize=config['data']['normalize'])
     data_loader = DataLoader(dataset, batch_size=batch_size, shuffle=True, num_workers=threads)
     device = torch.device("cuda" if torch.cuda.is_available() else "cpu")
 
diff --git a/dquartic/utils/config_loader.py b/dquartic/utils/config_loader.py
index d1faba5..190c70a 100644
--- a/dquartic/utils/config_loader.py
+++ b/dquartic/utils/config_loader.py
@@ -24,6 +24,9 @@ def load_train_config(config_path: str, **kwargs):
     
     if "ms1_data_path" not in config_params["data"]:
         config_params["data"]["ms1_data_path"] = None
+    
+    if "feature_mask_path" not in config_params["data"]:
+        config_params["data"]["feature_mask_path"] = None
 
     # Override the config params with the keyword arguments
     if "parquet_directory" in kwargs:
@@ -37,6 +40,10 @@ def load_train_config(config_path: str, **kwargs):
     if "ms1_data_path" in kwargs:
         if kwargs["ms1_data_path"] is not None:
             config_params["data"]["ms1_data_path"] = kwargs["ms1_data_path"]
+            
+    if "feature_mask_path" in kwargs:
+        if kwargs["feature_mask_path"] is not None:
+            config_params["data"]["feature_mask_path"] = kwargs["feature_mask_path"]
 
     if "batch_size" in kwargs:
         if kwargs["batch_size"] is not None:
@@ -69,6 +76,7 @@ def generate_train_config(config_path: str):
             "parquet_directory": "data/",
             "ms2_data_path": None,
             "ms1_data_path": None,
+            "feature_mask_path": None,  # Add feature mask path
             "normalize": "minmax",
         },
         "model": {
diff --git a/dquartic/utils/data_loader.py b/dquartic/utils/data_loader.py
index 454a987..f0a8fbf 100644
--- a/dquartic/utils/data_loader.py
+++ b/dquartic/utils/data_loader.py
@@ -30,12 +30,20 @@ class DIAMSDataset(Dataset):
         __getitem__(idx): Retrieves an item from the dataset.
     """
 
-    def __init__(self, parquet_directory=None, ms2_file=None, ms1_file=None, normalize: Literal[None, "minmax"] = None):
+    def __init__(self, parquet_directory=None, ms2_file=None, ms1_file=None, feature_mask_file=None, normalize: Literal[None, "minmax"] = None):
         if parquet_directory is None and ms1_file is not None and ms2_file is not None:
             self.ms2_data = np.load(ms2_file, mmap_mode="r")
-            self.ms1_data = np.load(ms1_file, mmap_mode="r")
-            self.data_type = "npy"
-            print(f"Info: Loaded  {len(self.ms2_data)} MS2 slice samples and {len(self.ms1_data)} MS1 slice samples from NPY files.")
+            # Use feature mask instead of MS1 if provided
+            if feature_mask_file is not None:
+                self.ms1_data = np.load(feature_mask_file, mmap_mode="r")
+                print(f"Info: Using feature masks instead of MS1 data")
+                self.data_type = "npy"
+                print(f"Info: Loaded {len(self.ms2_data)} MS2 samples and {len(self.ms1_data)} conditioning samples")
+            else:
+                self.ms1_data = np.load(ms1_file, mmap_mode="r")
+                self.data_type = "npy"
+                print(f"Info: Loaded  {len(self.ms2_data)} MS2 slice samples and {len(self.ms1_data)} MS1 slice samples from NPY files.")
+            
         elif parquet_directory is not None and ms1_file is None and ms2_file is None:
             self.meta_df = self.read_parquet_meta(parquet_directory)
             self.parquet_directory = parquet_directory