diff --git a/tests/test_preprocessing.py b/tests/test_preprocessing.py
new file mode 100644
index 0000000..3436530
--- /dev/null
+++ b/tests/test_preprocessing.py
@@ -0,0 +1,137 @@
+#!python -m unittest tests.test_utils
+"""This module provides unit tests for alphamap.cli."""
+
+# builtin
+import unittest
+
+import os
+import pandas as pd
+import numpy as np
+from pyteomics import fasta
+import warnings
+
+# local
+from alphamap.preprocessing import extract_uniprot_id, \
+    expand_protein_ids, \
+    pep_position_helper, \
+    get_peptide_position, \
+    get_ptm_sites, \
+    get_modifications, \
+    format_input_data
+
+THIS_FOLDER = os.path.dirname(__file__)
+TEST_FOLDER = os.path.join(
+    f"{os.path.dirname(THIS_FOLDER)}",
+    "nbs",
+    "testdata",
+)
+
+test_df = pd.DataFrame(data={'all_protein_ids': ["A0A024R161;A0A087WT10;A0A087WTH1", 
+                                                 "A0A024R161;A0A087WT10", 
+                                                 "A0A087WTH5","A0A087WTH5",
+                                                 "Nonsense"], 
+                            'modified_sequence': ["PEPT[Phospho (STY)]IDER", 
+                                                  "SEQ[GlyGly (K)]UENCE[GlyGly (K)]R", 
+                                                  "VIEWER","NONSEQ",
+                                                  "NONSENSE"],
+                            'naked_sequence': ["PEPTIDER", 
+                                               "SEQUENCER", 
+                                               "VIEWER","NONSEQ",
+                                               "NONSENSE"]})
+
+test_df_expanded = pd.DataFrame(data={'unique_protein_id': ["A0A024R161", "A0A087WT10", "A0A087WTH1", 
+                                                            "A0A024R161", "A0A087WT10", 
+                                                            "A0A087WTH5","A0A087WTH5",
+                                                            "Nonsense"], 
+                                      'modified_sequence': ["PEPT[Phospho (STY)]IDER", "PEPT[Phospho (STY)]IDER", "PEPT[Phospho (STY)]IDER",
+                                                            "SEQ[GlyGly (K)]UENCE[GlyGly (K)]R", "SEQ[GlyGly (K)]UENCE[GlyGly (K)]R", 
+                                                            "VIEWER","NONSEQ",
+                                                            "NONSENSE"],
+                                      'naked_sequence': ["PEPTIDER", "PEPTIDER", "PEPTIDER", 
+                                                         "SEQUENCER", "SEQUENCER", 
+                                                         "VIEWER","NONSEQ",
+                                                         "NONSENSE"],
+                                      'all_protein_ids': ["A0A024R161;A0A087WT10;A0A087WTH1", "A0A024R161;A0A087WT10;A0A087WTH1", "A0A024R161;A0A087WT10;A0A087WTH1", 
+                                                 "A0A024R161;A0A087WT10", "A0A024R161;A0A087WT10", 
+                                                 "A0A087WTH5","A0A087WTH5",
+                                                 "Nonsense"]})
+     
+test_df_expanded_peptide_position = pd.DataFrame(data={'unique_protein_id': ["A0A024R161", "A0A087WT10", "A0A087WTH1", 
+                                                                             "A0A024R161", "A0A087WT10", 
+                                                                             "A0A087WTH5"], 
+                                                       'modified_sequence': ["PEPT[Phospho (STY)]IDER", "PEPT[Phospho (STY)]IDER", "PEPT[Phospho (STY)]IDER",
+                                                                             "SEQ[GlyGly (K)]UENCE[GlyGly (K)]R", "SEQ[GlyGly (K)]UENCE[GlyGly (K)]R", 
+                                                                             "VIEWER"],
+                                                       'naked_sequence': ["PEPTIDER", "PEPTIDER", "PEPTIDER", 
+                                                                          "SEQUENCER", "SEQUENCER", 
+                                                                          "VIEWER"],
+                                                       'all_protein_ids': ["A0A024R161;A0A087WT10;A0A087WTH1", "A0A024R161;A0A087WT10;A0A087WTH1", "A0A024R161;A0A087WT10;A0A087WTH1", 
+                                                                             "A0A024R161;A0A087WT10", "A0A024R161;A0A087WT10", 
+                                                                             "A0A087WTH5"],
+                                                       'start':[3,28,107,95,150,1],
+                                                       'end':[10,35,114,103,158,6]})
+
+test_df_modifications = pd.DataFrame(data={'unique_protein_id': ["A0A024R161", "A0A087WT10", "A0A087WTH1", 
+                                                                             "A0A024R161", "A0A087WT10", 
+                                                                             "A0A087WTH5"], 
+                                            'modified_sequence': ["PEPT[Phospho (STY)]IDER", "PEPT[Phospho (STY)]IDER", "PEPT[Phospho (STY)]IDER",
+                                                                             "SEQ[GlyGly (K)]UENCE[GlyGly (K)]R", "SEQ[GlyGly (K)]UENCE[GlyGly (K)]R", 
+                                                                             "VIEWER"],
+                                            'naked_sequence': ["PEPTIDER", "PEPTIDER", "PEPTIDER", 
+                                                                          "SEQUENCER", "SEQUENCER", 
+                                                                          "VIEWER"],
+                                           'all_protein_ids': ["A0A024R161;A0A087WT10;A0A087WTH1", "A0A024R161;A0A087WT10;A0A087WTH1", "A0A024R161;A0A087WT10;A0A087WTH1", 
+                                                                             "A0A024R161;A0A087WT10", "A0A024R161;A0A087WT10", 
+                                                                             "A0A087WTH5"],
+                                                       'start':[3,28,107,95,150,1],
+                                                       'end':[10,35,114,103,158,6], 
+                                           'PTMsites':[[3],[3],[3],[2,7],[2,7],[]],
+                                           'PTMtypes':[["[Phospho (STY)]"],["[Phospho (STY)]"],["[Phospho (STY)]"],["[GlyGly (K)]","[GlyGly (K)]"],["[GlyGly (K)]","[GlyGly (K)]"],[]]})
+
+test_fasta = fasta.IndexedUniProt(os.path.join(TEST_FOLDER,'test.fasta'))
+
+class TestPreprocessing(unittest.TestCase):
+    def test_extract_uniprot_id(self, ):
+        prot_id_1 = 'sp|P02769|ALBU_BOVIN'
+        assert 'P02769' == extract_uniprot_id(prot_id_1)
+        prot_id_2 = 'CON__P02769'
+        assert 'P02769' == extract_uniprot_id(prot_id_2)
+
+    def test_expand_protein_ids(self, ):
+        res = expand_protein_ids(test_df)
+        pd.testing.assert_frame_equal(res,test_df_expanded)
+
+    def test_pep_position_helper(self, ):
+        start, end = pep_position_helper("PEPTIDER","A0A024R161",test_fasta)
+        np.testing.assert_equal([start, end], [3,10])
+
+    def test_get_peptide_position(self, ):
+        with warnings.catch_warnings(record=True) as w:
+            res = get_peptide_position(test_df_expanded, test_fasta)
+            assert len(w) == 2
+            assert "Peptide sequence NONSEQ could not be mached" in str(w[0].message)
+            assert "No matching entry for Nonsense" in str(w[1].message)
+        pd.testing.assert_frame_equal(res,test_df_expanded_peptide_position)
+
+    def test_get_ptm_sites(self, ):
+        myPep = "PEPT[Phospho]IDE[GlyGly (K)]R"
+        res = get_ptm_sites(myPep, modification_reg=r'\[.*?\]')
+        np.testing.assert_equal(res, [3,6])
+        myPep = "[Ac]PEPTIDE[GlyGly (K)]R"
+        res = get_ptm_sites(myPep, modification_reg=r'\[.*?\]')
+        np.testing.assert_equal(res, [0,6])
+
+    def test_get_modifications(self, ):
+        res = get_modifications(test_df_expanded_peptide_position, mod_reg = r'\[.*?\]')
+        pd.testing.assert_frame_equal(res, test_df_modifications)
+
+    def test_format_input_data(self, ):
+        with warnings.catch_warnings(record=True) as w:
+            res = format_input_data(df=test_df, fasta = test_fasta, modification_exp = r'\[.*?\]')
+            assert len(w) == 2
+            assert "Peptide sequence NONSEQ could not be mached" in str(w[0].message)
+            assert "No matching entry for Nonsense" in str(w[1].message)   
+        pd.testing.assert_frame_equal(res, test_df_modifications)
+
+if __name__ == "__main__":
+    unittest.main()