diff --git a/quantmsutils/mzml/ms1_feature_finder.py b/quantmsutils/mzml/ms1_feature_finder.py
index 0381328..4d84a0d 100644
--- a/quantmsutils/mzml/ms1_feature_finder.py
+++ b/quantmsutils/mzml/ms1_feature_finder.py
@@ -25,6 +25,8 @@
 logging.basicConfig(format="%(asctime)s [%(funcName)s] - %(message)s", level=logging.INFO)
 logger = logging.getLogger(__name__)
 
+_PYOPENMS_VERSION = tuple(int(p) for p in oms.__version__.split(".")[:2])
+
 
 class MS1FeatureDetector:
     """
@@ -51,6 +53,21 @@ def __init__(self, ms_level: int = 1):
         self.options = oms.PeakFileOptions()
         self.options.setMSLevels([self.ms_level])
 
+    @staticmethod
+    def _pick_experiment(
+        picker: oms.PeakPickerHiRes, experiment: oms.MSExperiment
+    ) -> oms.MSExperiment:
+        """Centroid an experiment, supporting both pyopenms peak-picker APIs.
+
+        pyopenms >= 3.6 returns the picked experiment; older versions fill an
+        output experiment passed by reference.
+        """
+        if _PYOPENMS_VERSION >= (3, 6):
+            return picker.pickExperiment(experiment, False)
+        picked = oms.MSExperiment()
+        picker.pickExperiment(experiment, picked, False)
+        return picked
+
     def _calc_tic(self, experiment: oms.MSExperiment) -> float:
         """
         Calculate all the TIC in the MS experiment, summing all intensities from all scans.
@@ -249,12 +266,9 @@ def process_file(
             experiment = oms.MSExperiment()
             picker = oms.PeakPickerHiRes()
 
-            filtered_experiment = oms.MSExperiment()
-
             file_handler.setOptions(self.options)
             file_handler.load(str(input_path), experiment)
-            picker.pickExperiment(experiment, filtered_experiment, False)
-            experiment = filtered_experiment
+            experiment = self._pick_experiment(picker, experiment)
 
             filtered_experiment = oms.MSExperiment()
             for spec in experiment:
diff --git a/quantmsutils/psm/psm_conversion.py b/quantmsutils/psm/psm_conversion.py
index f113197..c365b57 100644
--- a/quantmsutils/psm/psm_conversion.py
+++ b/quantmsutils/psm/psm_conversion.py
@@ -103,9 +103,11 @@ def convert_psm(
     else:
         search_engines = [prot_ids[0].getSearchEngine()]
 
-    reference_file_name = os.path.splitext(
-        prot_ids[0].getMetaValue("spectra_data")[0].decode("UTF-8")
-    )[0]
+    spectra_data = prot_ids[0].getMetaValue("spectra_data")[0]
+    # pyopenms < 3.6 returns bytes here, >= 3.6 returns str
+    if isinstance(spectra_data, bytes):
+        spectra_data = spectra_data.decode("UTF-8")
+    reference_file_name = os.path.splitext(spectra_data)[0]
     spectra_df = pd.read_parquet(ms2_file) if ms2_file else None
 
     if spectra_df is not None: