Fixed calculating b ion mass for unlabeled peptides

Added test case for Sean MHC peptide
white-lab · Jan 28, 2019 · 9fe7941 · 9fe7941
1 parent e31c423
commit 9fe7941
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Showing 3 changed files with 45 additions and 9 deletions.
diff --git a/pycamv/fragment/fragments.py b/pycamv/fragment/fragments.py
@@ -82,7 +82,7 @@ def _internal_fragment_ions(
                 [("C=O", ())]
             )
 
-            mass = _sequence_mass(fragment)
+            mass = _sequence_mass(fragment) + masses.PROTON
             name = _sequence_name(fragment)
 
             # Also calculate any potential neutral losses from this fragment
@@ -383,8 +383,7 @@ def fragment_ions(
         parent_max_charge = charge
 
     if fragment_max_charge is None:
-        # TODO: This correct?
-        fragment_max_charge = parent_max_charge - 1
+        fragment_max_charge = parent_max_charge
 
     if any_losses is None:
         any_losses = PEPTIDE_LOSSES

diff --git a/pycamv/fragment/masses.py b/pycamv/fragment/masses.py
@@ -81,7 +81,7 @@ def exact_mass(atoms):
 PROTON = exact_mass({"H": [1]})
 
 C_TERM = exact_mass({"H": [1], "O": [1]})
-N_TERM = exact_mass({"H": [1]})
+N_TERM = 0
 
 # iTRAQ Masses not exact due to mass differences between isotopes
 ITRAQ_4_PLEX = exact_mass({"C": [4, 3], "N": [1, 1], "O": [1], "H": [12]})
@@ -194,11 +194,11 @@ def exact_mass(atoms):
     ("Y", "Phospho"): PHOSPHO_TYROSINE,
 
     # TMT / iTRAQ
-    ("N-term", "iTRAQ4plex"): ITRAQ_4_PLEX - N_TERM,
-    ("N-term", "iTRAQ8plex"): ITRAQ_8_PLEX - N_TERM,
-    ("N-term", "TMT6plex"): TMT_6_PLEX - N_TERM,
-    ("N-term", "TMT10plex"): TMT_10_PLEX - N_TERM,
-    ("N-term", "TMT11plex"): TMT_11_PLEX - N_TERM,
+    ("N-term", "iTRAQ4plex"): ITRAQ_4_PLEX,
+    ("N-term", "iTRAQ8plex"): ITRAQ_8_PLEX,
+    ("N-term", "TMT6plex"): TMT_6_PLEX,
+    ("N-term", "TMT10plex"): TMT_10_PLEX,
+    ("N-term", "TMT11plex"): TMT_11_PLEX,
     ("K", "iTRAQ4plex"): ITRAQ_4_PLEX,
     ("K", "iTRAQ8plex"): ITRAQ_8_PLEX,
     ("K", "TMT6plex"): TMT_6_PLEX,

diff --git a/tests/fragments_test.py b/tests/fragments_test.py
@@ -6,6 +6,42 @@
 class FragmentIonsTest(TestCase):
     def test_fragment_ions(self):
         test_peptides = {
+            (
+                (
+                    ("N-term", ()),
+                    ("R", ()),
+                    ("V", ()),
+                    ("D", ()),
+                    ("E", ()),
+                    ("N", ()),
+                    ("N", ()),
+                    ("P", ()),
+                    ("E", ()),
+                    ("Y", ()),
+                    ("C-term", ()),
+                ),
+                2,
+            ): {
+                "a_{1}^{+}": 129.11347,
+                "a_{2}^{+}": 228.18189,
+                "b_{1}^{+}": 157.10839,
+                "b_{2}^{+}": 256.17680,
+                "b_{3}^{+}": 371.20374,
+                "b_{4}^{+}": 500.24634,
+                "b_{5}^{+}": 614.28926,
+                "b_{6}^{+}": 728.33219,
+                "b_{6}^{+2}": 364.66973,
+                "b_{7}^{+}": 825.38496,
+                "b_{8}^{+}": 954.42755,
+                "y_{1}^{+}": 182.08117,
+                "y_{2}^{+}": 311.12376,
+                "y_{3}^{+}": 408.17653,
+                "y_{4}^{+}": 522.21945,
+                "y_{5}^{+}": 636.26238,
+                "y_{6}^{+}": 765.30497,
+                "y_{7}^{+}": 880.33192,
+                "y_{8}^{+}": 979.40033,
+            },
             (
                 (
                     ("N-term", ("TMT6plex",)),
@@ -195,6 +231,7 @@ def test_fragment_ions(self):
 
             for name, mz in hits.items():
                 self.assertIn(name, frag_ions)
+                print(name, frag_ions[name], mz)
                 self.assertLess(abs(frag_ions[name] - mz), 0.01)
 
     def test_no_by_losses(self):