Add option MatchesPerSpectrumToKeepInMemory to parameter files

PNNL-Comp-Mass-Spec · May 21, 2021 · f45c61f · f45c61f
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diff --git a/Example_Files/MSPF_CysDehydro_LysMethDiMethTriMeth_NTermAcet_SingleInternalCleavage.txt b/Example_Files/MSPF_CysDehydro_LysMethDiMethTriMeth_NTermAcet_SingleInternalCleavage.txt
@@ -53,6 +53,10 @@ minMass=3000
 # Maximum sequence mass, in Da
 maxMass=50000
 
+# Number of matches per spectrum to keep in memory
+# These matches are used when computing spectral E-values
+MatchesPerSpectrumToKeepInMemory=3
+
 # Number of matches per spectrum to be reported
 NumMatchesPerSpec=1
 

diff --git a/...s/MSPF_MetOx_CysDehydro_LysMethDiMethTriMeth_NTermAcet_NoInternalCleavage_NoTagSearch.txt b/...s/MSPF_MetOx_CysDehydro_LysMethDiMethTriMeth_NTermAcet_NoInternalCleavage_NoTagSearch.txt
@@ -55,6 +55,10 @@ minMass=3000
 # Maximum sequence mass, in Da
 maxMass=50000
 
+# Number of matches per spectrum to keep in memory
+# These matches are used when computing spectral E-values
+MatchesPerSpectrumToKeepInMemory=3
+
 # Number of matches per spectrum to be reported
 NumMatchesPerSpec=1
 

diff --git a/Example_Files/MSPF_MetOx_CysDehydro_NTermAcet_SingleInternalCleavage.txt b/Example_Files/MSPF_MetOx_CysDehydro_NTermAcet_SingleInternalCleavage.txt
@@ -49,6 +49,10 @@ minMass=3000
 # Maximum sequence mass, in Da
 maxMass=50000
 
+# Number of matches per spectrum to keep in memory
+# These matches are used when computing spectral E-values
+MatchesPerSpectrumToKeepInMemory=3
+
 # Number of matches per spectrum to be reported
 NumMatchesPerSpec=1
 

diff --git a/...PF_MetOx_STYPhos_LysMethDiMethTriMeth_NTermAcet_CysTriOx_SingleInternalCleavage_10ppm.txt b/...PF_MetOx_STYPhos_LysMethDiMethTriMeth_NTermAcet_CysTriOx_SingleInternalCleavage_10ppm.txt
@@ -54,6 +54,10 @@ minMass=3000
 # Maximum sequence mass, in Da
 maxMass=50000
 
+# Number of matches per spectrum to keep in memory
+# These matches are used when computing spectral E-values
+MatchesPerSpectrumToKeepInMemory=3
+
 # Number of matches per spectrum to be reported
 NumMatchesPerSpec=1
 

diff --git a/Example_Files/MSPF_STYPhos_CysDehydro_NTermAcet_SingleInternalCleavage_ReportTop2.txt b/Example_Files/MSPF_STYPhos_CysDehydro_NTermAcet_SingleInternalCleavage_ReportTop2.txt
@@ -50,6 +50,10 @@ minMass=3000
 # Maximum sequence mass, in Da
 maxMass=50000
 
+# Number of matches per spectrum to keep in memory
+# These matches are used when computing spectral E-values
+MatchesPerSpectrumToKeepInMemory=3
+
 # Number of matches per spectrum to be reported
 NumMatchesPerSpec=2
 

diff --git a/Example_Files/MSPF_STYPhos_CysDehydro_NTermAcet_SingleInternalCleavage_ReportTop3.txt b/Example_Files/MSPF_STYPhos_CysDehydro_NTermAcet_SingleInternalCleavage_ReportTop3.txt
@@ -50,6 +50,10 @@ minMass=3000
 # Maximum sequence mass, in Da
 maxMass=50000
 
+# Number of matches per spectrum to keep in memory
+# These matches are used when computing spectral E-values
+MatchesPerSpectrumToKeepInMemory=4
+
 # Number of matches per spectrum to be reported
 NumMatchesPerSpec=3