Add "best score delta mass only" score.

Nesvilab · Jan 28, 2024 · 2224d68 · 2224d68
1 parent 801a240
commit 2224d68
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Showing 3 changed files with 7 additions and 3 deletions.
diff --git a/lib/id/pep.go b/lib/id/pep.go
@@ -112,6 +112,7 @@ type MSFraggerLoc struct {
 	MSFraggerLocalizationScores                 string
 	MSFraggerScoreAll                           string
 	MSFraggerScoreOnlyShifted                   string
+	MSFraggerBestScoreOnlyShifted               string
 	MSFraggerLocalizationScoreWithPTMIons       string
 	MSFraggerLocalizationSecondScoreWithPTMIons string
 	MSFraggerLocalizationScoreWithoutPTMIons    string
@@ -505,6 +506,7 @@ func processSpectrumQuery(sq spc.SpectrumQuery, mods mod.Modifications, decoyTag
 				MSFraggerLocalizationScores:                 i.PTMResult.LocalizationScores,
 				MSFraggerScoreAll:                           i.PTMResult.ScoreAll,
 				MSFraggerScoreOnlyShifted:                   i.PTMResult.ScoreOnlyShifted,
+				MSFraggerBestScoreOnlyShifted:               i.PTMResult.BestScoreOnlyShifted,
 				MSFraggerLocalizationScoreWithPTMIons:       i.PTMResult.BestScoreWithPTMIons,
 				MSFraggerLocalizationSecondScoreWithPTMIons: i.PTMResult.SecondBestScoreWithPTMIons,
 				MSFraggerLocalizationScoreWithoutPTMIons:    i.PTMResult.ScoreWithoutPTMIons,

diff --git a/lib/rep/psm.go b/lib/rep/psm.go
@@ -236,7 +236,7 @@ func (evi PSMEvidenceList) PSMReport(workspace, brand, decoyTag string, channels
 	}
 
 	if hasLoc {
-		header += "\tMSFragger Localization\tBest Score with Delta Mass\tBest Matched Ions with Delta Mass\tSecond Best Score with Delta Mass\tSecond Best Matched Ions with Delta Mass\tBest Score without Delta Mass\tMatched Ions without Delta mass\tLocalization Scores\tScore All\tMatched Ions All\tScore Delta Mass Only\tMatched Ions Delta Mass Only"
+		header += "\tMSFragger Localization\tBest Score with Delta Mass\tBest Matched Ions with Delta Mass\tSecond Best Score with Delta Mass\tSecond Best Matched Ions with Delta Mass\tBest Score without Delta Mass\tMatched Ions without Delta mass\tLocalization Scores\tScore All\tMatched Ions All\tScore Delta Mass Only\tMatched Ions Delta Mass Only\tBest Score Delta Mass Only"
 	}
 
 	if hasIonMob {
@@ -618,7 +618,7 @@ func (evi PSMEvidenceList) PSMReport(workspace, brand, decoyTag string, channels
 			if MSFraggerLoc == nil {
 				MSFraggerLoc = &id.MSFraggerLoc{}
 			}
-			line = fmt.Sprintf("%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s",
+			line = fmt.Sprintf("%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s",
 				line,
 				MSFraggerLoc.MSFragerLocalization,
 				MSFraggerLoc.MSFraggerLocalizationScoreWithPTM,
@@ -631,7 +631,8 @@ func (evi PSMEvidenceList) PSMReport(workspace, brand, decoyTag string, channels
 				MSFraggerLoc.MSFraggerScoreAll,
 				MSFraggerLoc.MSFraggerScoreAllIons,
 				MSFraggerLoc.MSFraggerScoreOnlyShifted,
-				MSFraggerLoc.MSFraggerScoreOnlyShiftedIons)
+				MSFraggerLoc.MSFraggerScoreOnlyShiftedIons,
+				MSFraggerLoc.MSFraggerBestScoreOnlyShifted)
 		}
 
 		if hasIonMob {

diff --git a/lib/spc/pepxml.go b/lib/spc/pepxml.go
@@ -228,4 +228,5 @@ type PTMResult struct {
 	ScoreAllIons               string `xml:"score_all_matched_ions,attr"`
 	ScoreOnlyShifted           string `xml:"score_only_shifted,attr"`
 	ScoreOnlyShiftedIons       string `xml:"score_only_shifted_matched_ions,attr"`
+	BestScoreOnlyShifted       string `xml:"best_score_only_shifted,attr"`
 }