Merge pull request #340 from Proteobench/fix_338_mq_2_6

🐛 Close 338 parsing MQ 2.6 (minPepLen)
Proteobench · Aug 9, 2024 · c804897 · c804897
2 parents cd7ed36 + b0239c7
commit c804897
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Showing 7 changed files with 2,315 additions and 2 deletions.
diff --git a/proteobench/io/params/maxquant.py b/proteobench/io/params/maxquant.py
@@ -154,7 +154,12 @@ def extract_params(fname, ms2frac="FTMS") -> ProteoBenchParameters:
     params.allowed_miscleavages = record.loc[
         pd.IndexSlice["parameterGroups", "parameterGroup", "maxMissedCleavages", :]
     ].squeeze()
-    params.min_peptide_length = record.loc["minPepLen"].squeeze()
+    try:
+        params.min_peptide_length = record.loc["minPepLen"].squeeze()
+    except KeyError:
+        # Version 2.6 and above
+        params.minPeptideLength = record.loc["minPeptideLength"].squeeze()
+    # minPeptideLengthForUnspecificSearch (what is it?)
     params.max_peptide_length = None
     # fixed mods
     if params.software_version > "1.6.0.0":
@@ -192,6 +197,7 @@ def extract_params(fname, ms2frac="FTMS") -> ProteoBenchParameters:
         "../../../test/params/mqpar_MQ1.6.3.3_MBR.xml",
         "../../../test/params/mqpar_MQ2.1.3.0_noMBR.xml",
         "../../../test/params/mqpar1.5.3.30_MBR.xml",
+        "../../../test/params/mqpar_mq2.6.2.0_1mc_MBR.xml",
     ]:
         print(f"{test_file = }")
         record = read_file(test_file)

diff --git a/test/params/mqpar1.5.3.30_MBR_sel.json b/test/params/mqpar1.5.3.30_MBR_sel.json
@@ -18,4 +18,4 @@
     "max_mods": "5",
     "min_precursor_charge": null,
     "max_precursor_charge": "7"
-}
+}