Merge pull request #476 from OpenMS/cbielow-patch-1

fix PSM_to_features tutorial

Author: cbielow

docs/source/user_guide/PSM_to_features.rst

@@ -69,7 +69,10 @@ Use the configured `IDMapper` to link peptide IDs to the FeatureMap:
 
 .. code-block:: python
 
-   id_mapper.annotate(feature_map, peptide_ids, protein_ids, use_centroid_rt=True, use_centroid_mz=True, spectra=None)
+   # annotate() can optionally use the underlying raw MS data (spectra) to annotate unidentified MS/MS scans to features in the FeatureMap
+   # We don't need this here, so we provide an empty default.
+   spectra = oms.MSExperiment()
+   id_mapper.annotate(feature_map, peptide_ids, protein_ids, True, True, spectra)
 
 Step 5: Save the Annotated FeatureMap
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