diff --git a/pyproteininference/datastore.py b/pyproteininference/datastore.py
index 207fe80..eebc8f7 100644
--- a/pyproteininference/datastore.py
+++ b/pyproteininference/datastore.py
@@ -62,6 +62,8 @@ class DataStore(object):
         "q-value": "qvalue",
         "posterior_error_prob": "pepvalue",
         "posterior_error_probability": "pepvalue",
+        "MS:1001493": "pepvalue",  # Added to make sure custom input for pep/qval accession gets mapped to pep/qval
+        "MS:1001491": "qvalue",
     }
 
     CUSTOM_SCORE_KEY = "custom_score"
@@ -1179,6 +1181,12 @@ def _check_target_decoy_split(self):
         decoys = [
             x for x in self.digest.protein_to_peptide_dictionary.keys() if self.parameter_file_object.decoy_symbol in x
         ]
+        if len(decoys) == 0:
+            raise ValueError(
+                "No decoy proteins found in digest file with decoy symbol: {}. Please double check your decoy symbol and make sure decoy proteins are present in your input file(s).".format(
+                    self.parameter_file_object.decoy_symbol
+                )
+            )
         ratio = float(len(targets)) / float(len(decoys))
         logger.info("Number of Target Proteins in Digest: {}".format(len(targets)))
         logger.info("Number of Decoy Proteins in Digest: {}".format(len(decoys)))
diff --git a/pyproteininference/physical.py b/pyproteininference/physical.py
index eefa87e..90453e3 100644
--- a/pyproteininference/physical.py
+++ b/pyproteininference/physical.py
@@ -330,6 +330,7 @@ def assign_main_score(self, score):
         if score not in self.SCORE_ATTRIBUTE_NAMES:
             raise ValueError("Scores must either be one of: '{}'".format(", ".join(self.SCORE_ATTRIBUTE_NAMES)))
         else:
+            score_attribute = getattr(self, score)
             self.main_score = getattr(self, score)
 
 
diff --git a/pyproteininference/pipeline.py b/pyproteininference/pipeline.py
index 2cad67f..a397457 100644
--- a/pyproteininference/pipeline.py
+++ b/pyproteininference/pipeline.py
@@ -210,9 +210,7 @@ def _as_list(x: Union[str, List[str]]) -> List[str]:
             else (
                 _as_list(self.decoy_files)
                 if self.decoy_files
-                else _as_list(self.combined_files)
-                if self.combined_files
-                else list()
+                else _as_list(self.combined_files) if self.combined_files else list()
             )
         )
         extensions = set([os.path.splitext(x)[1].lower() for x in input_files])
diff --git a/pyproteininference/reader.py b/pyproteininference/reader.py
index 327a5c8..d4cffc6 100644
--- a/pyproteininference/reader.py
+++ b/pyproteininference/reader.py
@@ -1111,13 +1111,13 @@ def __init__(
         if self.scoring_variable != self.Q_VALUE and self.scoring_variable != self.POSTERIOR_ERROR_PROB:
             self.load_custom_score = True
             logger.info(
-                "Pulling custom column based on parameter file input for score, Column: {}".format(
+                "Pulling custom column based on parameter file input for score, Attribute: {}".format(
                     self.scoring_variable
                 )
             )
         else:
             logger.info(
-                "Pulling no custom columns based on parameter file input for score, using standard Column: {}".format(
+                "Pulling no custom columns based on parameter file input for score, using standard Attribute: {}".format(
                     self.scoring_variable
                 )
             )
diff --git a/pyproteininference/scoring.py b/pyproteininference/scoring.py
index e5e8176..e61af6d 100644
--- a/pyproteininference/scoring.py
+++ b/pyproteininference/scoring.py
@@ -120,6 +120,8 @@ def score_psms(self, score_method="multiplicative_log"):
             >>> score.score_psms(score_method="best_peptide_per_protein")
         """
 
+        self._validate_scoring_input()
+
         if score_method not in self.SCORE_METHODS:
             raise ValueError(
                 "score method '{}' is not a proper method. Score method must be one of the following: '{}'".format(
@@ -472,3 +474,18 @@ def additive(self):
         self.data.protein_score = self.ADDITIVE
         self.data.short_protein_score = self.SHORT_ADDITIVE
         self.data.scored_proteins = all_scores
+
+    def _validate_scoring_input(self):
+        validated_psm_scores = all(x.main_score is not None for x in self.data.get_psm_data())
+        if validated_psm_scores:
+            logger.info(
+                "PSM scores validated. Score: {} read from file correctly for all PSMs".format(
+                    self.data.parameter_file_object.psm_score
+                )
+            )
+        else:
+            raise ValueError(
+                "PSM scores not validated. Score: {} not read from file correctly for all PSMs".format(
+                    self.data.parameter_file_object.psm_score
+                )
+            )