From 3185c2ba02267ce1f5e3f0d6af5e01c581194e46 Mon Sep 17 00:00:00 2001
From: jalew188 <jalew188@gmail.com>
Date: Mon, 4 Sep 2023 14:44:06 +0200
Subject: [PATCH 1/2] FIX do nothing in _add_missing_columns_to_psm_df for DIA

---
 alpharaw/match/psm_match.py | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/alpharaw/match/psm_match.py b/alpharaw/match/psm_match.py
index 7ab815a..201fc2b 100644
--- a/alpharaw/match/psm_match.py
+++ b/alpharaw/match/psm_match.py
@@ -566,6 +566,12 @@ class PepSpecMatch_DIA(PepSpecMatch):
     min_frag_mz: float = 200.0
     rt_query_window: float = 20.0/60.0 # 20 seconds
 
+    def _add_missing_columns_to_psm_df(self,
+        psm_df:pd.DataFrame, raw_data=None
+    ):
+        # DIA results do not have spec_idx in psm_df, nothing to merge
+        return psm_df
+    
     def _prepare_matching_dfs(self):
 
         fragment_mz_df = self.get_fragment_mz_df()

From fc7cfb1fe83e63cf5c182631948ecbfab6fe33ef Mon Sep 17 00:00:00 2001
From: jalew188 <jalew188@gmail.com>
Date: Thu, 7 Sep 2023 13:45:46 +0200
Subject: [PATCH 2/2] REQ: alphabase>=1.1.0

---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index bfa3c4e..da82bba 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -7,4 +7,4 @@ pandas
 numpy
 sqlalchemy
 
-alphabase
\ No newline at end of file
+alphabase>=1.1.0
\ No newline at end of file