✨ Add parsing of attributes for MaxQuant 1.5

- from 1.6 onwords, information is given explicitly
Proteobench · Nov 19, 2023 · 5a95fa0 · 5a95fa0
1 parent df208d2
commit 5a95fa0
Show file tree

Hide file tree

Showing 3 changed files with 123 additions and 1 deletion.
diff --git a/proteobench/io/params/maxquant.py b/proteobench/io/params/maxquant.py
@@ -54,6 +54,8 @@ def add_record(data: dict, tag: str, record) -> dict:
 def read_xml_record(element: ET.Element) -> dict:
     """Read entire record in a nested dict structure."""
     data = dict()
+    if element.attrib:
+        data.update(element.attrib)
     for child in element:
         if len(child) > 1 and child.tag:
             # if there is a list, process each element one by one
@@ -125,7 +127,7 @@ def flatten_dict_of_dicts(d: dict, parent_key: str = "") -> dict:
 def build_Series_from_records(records, index_length=4):
     records = flatten_dict_of_dicts(records)
     idx = pd.MultiIndex.from_tuples(
-        (extend_tuple(k, index_length) for (k, v) in records)
+        (extend_tuple(k, index_length) for (k, _) in records)
     )
     return pd.Series((v for (k, v) in records), index=idx)
 

diff --git a/test/params/mqpar1.5.3.30_MBR.csv b/test/params/mqpar1.5.3.30_MBR.csv
@@ -1,4 +1,20 @@
 ,,,,run_identifier
+aifSilWeight,,,,0
+aifIsoWeight,,,,0
+aifTopx,,,,0
+aifCorrelation,,,,0
+aifCorrelationFirstPass,,,,0
+aifMinMass,,,,0
+aifMsmsTol,,,,0
+aifSecondPass,,,,false
+aifIterative,,,,false
+aifThresholdFdr,,,,0
+writeMsScansTable,,,,true
+writeMsmsScansTable,,,,true
+writeMs3ScansTable,,,,true
+writeAllPeptidesTable,,,,true
+writeMzRangeTable,,,,true
+disableMd5,,,,false
 name,,,,Session1
 maxQuantVersion,,,,1.5.3.30
 tempFolder,,,,
@@ -187,15 +203,59 @@ numberOfCandidatesMultiplexedMsms,,,,25
 numberOfCandidatesMsms,,,,15
 massDifferenceMods,,,,
 mainSearchMaxCombinations,,,,200
+msmsParamsArray,msmsParams,Name,,FTMS
+msmsParamsArray,msmsParams,MatchToleranceInPpm,,true
+msmsParamsArray,msmsParams,DeisotopeToleranceInPpm,,true
+msmsParamsArray,msmsParams,DeNovoToleranceInPpm,,true
+msmsParamsArray,msmsParams,Deisotope,,true
+msmsParamsArray,msmsParams,Topx,,12
+msmsParamsArray,msmsParams,HigherCharges,,true
+msmsParamsArray,msmsParams,IncludeWater,,true
+msmsParamsArray,msmsParams,IncludeAmmonia,,true
+msmsParamsArray,msmsParams,DependentLosses,,true
+msmsParamsArray,msmsParams,Recalibration,,false
 msmsParamsArray,msmsParams,MatchTolerance,,20
 msmsParamsArray,msmsParams,DeisotopeTolerance,,7
 msmsParamsArray,msmsParams,DeNovoTolerance,,10
+msmsParamsArray,msmsParams,Name,,ITMS
+msmsParamsArray,msmsParams,MatchToleranceInPpm,,false
+msmsParamsArray,msmsParams,DeisotopeToleranceInPpm,,false
+msmsParamsArray,msmsParams,DeNovoToleranceInPpm,,false
+msmsParamsArray,msmsParams,Deisotope,,false
+msmsParamsArray,msmsParams,Topx,,8
+msmsParamsArray,msmsParams,HigherCharges,,true
+msmsParamsArray,msmsParams,IncludeWater,,true
+msmsParamsArray,msmsParams,IncludeAmmonia,,true
+msmsParamsArray,msmsParams,DependentLosses,,true
+msmsParamsArray,msmsParams,Recalibration,,false
 msmsParamsArray,msmsParams,MatchTolerance,,0.5
 msmsParamsArray,msmsParams,DeisotopeTolerance,,0.15
 msmsParamsArray,msmsParams,DeNovoTolerance,,0.25
+msmsParamsArray,msmsParams,Name,,TOF
+msmsParamsArray,msmsParams,MatchToleranceInPpm,,true
+msmsParamsArray,msmsParams,DeisotopeToleranceInPpm,,false
+msmsParamsArray,msmsParams,DeNovoToleranceInPpm,,false
+msmsParamsArray,msmsParams,Deisotope,,true
+msmsParamsArray,msmsParams,Topx,,10
+msmsParamsArray,msmsParams,HigherCharges,,true
+msmsParamsArray,msmsParams,IncludeWater,,true
+msmsParamsArray,msmsParams,IncludeAmmonia,,true
+msmsParamsArray,msmsParams,DependentLosses,,true
+msmsParamsArray,msmsParams,Recalibration,,false
 msmsParamsArray,msmsParams,MatchTolerance,,40
 msmsParamsArray,msmsParams,DeisotopeTolerance,,0.01
 msmsParamsArray,msmsParams,DeNovoTolerance,,0.02
+msmsParamsArray,msmsParams,Name,,Unknown
+msmsParamsArray,msmsParams,MatchToleranceInPpm,,false
+msmsParamsArray,msmsParams,DeisotopeToleranceInPpm,,false
+msmsParamsArray,msmsParams,DeNovoToleranceInPpm,,false
+msmsParamsArray,msmsParams,Deisotope,,false
+msmsParamsArray,msmsParams,Topx,,8
+msmsParamsArray,msmsParams,HigherCharges,,true
+msmsParamsArray,msmsParams,IncludeWater,,true
+msmsParamsArray,msmsParams,IncludeAmmonia,,true
+msmsParamsArray,msmsParams,DependentLosses,,true
+msmsParamsArray,msmsParams,Recalibration,,false
 msmsParamsArray,msmsParams,MatchTolerance,,0.5
 msmsParamsArray,msmsParams,DeisotopeTolerance,,0.15
 msmsParamsArray,msmsParams,DeNovoTolerance,,0.25

diff --git a/test/params/mqpar1.5.3.30_MBR.json b/test/params/mqpar1.5.3.30_MBR.json
@@ -1,4 +1,20 @@
 {
+    "aifSilWeight": "0",
+    "aifIsoWeight": "0",
+    "aifTopx": "0",
+    "aifCorrelation": "0",
+    "aifCorrelationFirstPass": "0",
+    "aifMinMass": "0",
+    "aifMsmsTol": "0",
+    "aifSecondPass": "false",
+    "aifIterative": "false",
+    "aifThresholdFdr": "0",
+    "writeMsScansTable": "true",
+    "writeMsmsScansTable": "true",
+    "writeMs3ScansTable": "true",
+    "writeAllPeptidesTable": "true",
+    "writeMzRangeTable": "true",
+    "disableMd5": "false",
     "name": "Session1",
     "maxQuantVersion": "1.5.3.30",
     "tempFolder": null,
@@ -425,27 +441,71 @@
     "msmsParamsArray": [
         {
             "msmsParams": {
+                "Name": "FTMS",
+                "MatchToleranceInPpm": "true",
+                "DeisotopeToleranceInPpm": "true",
+                "DeNovoToleranceInPpm": "true",
+                "Deisotope": "true",
+                "Topx": "12",
+                "HigherCharges": "true",
+                "IncludeWater": "true",
+                "IncludeAmmonia": "true",
+                "DependentLosses": "true",
+                "Recalibration": "false",
                 "MatchTolerance": "20",
                 "DeisotopeTolerance": "7",
                 "DeNovoTolerance": "10"
             }
         },
         {
             "msmsParams": {
+                "Name": "ITMS",
+                "MatchToleranceInPpm": "false",
+                "DeisotopeToleranceInPpm": "false",
+                "DeNovoToleranceInPpm": "false",
+                "Deisotope": "false",
+                "Topx": "8",
+                "HigherCharges": "true",
+                "IncludeWater": "true",
+                "IncludeAmmonia": "true",
+                "DependentLosses": "true",
+                "Recalibration": "false",
                 "MatchTolerance": "0.5",
                 "DeisotopeTolerance": "0.15",
                 "DeNovoTolerance": "0.25"
             }
         },
         {
             "msmsParams": {
+                "Name": "TOF",
+                "MatchToleranceInPpm": "true",
+                "DeisotopeToleranceInPpm": "false",
+                "DeNovoToleranceInPpm": "false",
+                "Deisotope": "true",
+                "Topx": "10",
+                "HigherCharges": "true",
+                "IncludeWater": "true",
+                "IncludeAmmonia": "true",
+                "DependentLosses": "true",
+                "Recalibration": "false",
                 "MatchTolerance": "40",
                 "DeisotopeTolerance": "0.01",
                 "DeNovoTolerance": "0.02"
             }
         },
         {
             "msmsParams": {
+                "Name": "Unknown",
+                "MatchToleranceInPpm": "false",
+                "DeisotopeToleranceInPpm": "false",
+                "DeNovoToleranceInPpm": "false",
+                "Deisotope": "false",
+                "Topx": "8",
+                "HigherCharges": "true",
+                "IncludeWater": "true",
+                "IncludeAmmonia": "true",
+                "DependentLosses": "true",
+                "Recalibration": "false",
                 "MatchTolerance": "0.5",
                 "DeisotopeTolerance": "0.15",
                 "DeNovoTolerance": "0.25"