These functions list settings for MS1 or TMS2 that are supported by Thermo's XmlMethodChanger.
validMs1Settings(family = "Calcium", version = "3.2")
validTms2Settings(
type = c("All", "TMS2", "ETD", "CID", "HCD", "UVPD"),
family = "Calcium",
version = "3.2"
)| family |
|
|---|---|
| version |
|
| type |
|
matrix with three columns:
name: element name
class: expected R class of the value
type: MS/ActivationType, e.g. MS1/TMS2/ETD/...
validMs1Settings()
#> name class type
#> [1,] "FirstMass" "double" "MS1"
#> [2,] "LastMass" "double" "MS1"
#> [3,] "Microscans" "integer" "MS1"
#> [4,] "MaxITTimeInMS" "double" "MS1"
#> [5,] "AgcTarget" "double" "MS1"
#> [6,] "ScanDescription" "character" "MS1"
validTms2Settings()
#> name class
#> [1,] "EnableMultiplexIons" "logical"
#> [2,] "EnableMSXIds" "logical"
#> [3,] "MaxNoOfMultiplexIons" "integer"
#> [4,] "OrbitrapResolution" "R15K:R30K:R50K:R60K:R120K:R240K:R500K"
#> [5,] "AgcTarget" "double"
#> [6,] "MinAgcTarget" "logical"
#> [7,] "MaxITTimeInMS" "double"
#> [8,] "Microscans" "integer"
#> [9,] "ActivationType" "CID:HCD:ETD:UVPD"
#> [10,] "IsolationWindow" "double"
#> [11,] "ETDReactionTime" "double"
#> [12,] "ETDReagentTarget" "double"
#> [13,] "MaximumETDReagentInjectionTime" "double"
#> [14,] "UseInternalCalibratedETD" "logical"
#> [15,] "ETDSupplementalActivationEnergy" "double"
#> [16,] "ETDSupplementalActivation" "None:ETciD:EThcD"
#> [17,] "CIDCollisionEnergy" "double"
#> [18,] "CIDActivationTime" "double"
#> [19,] "CIDActivationQ" "double"
#> [20,] "HCDCollisionEnergy" "double"
#> [21,] "UVPDUseCalibratedActivationTime" "logical"
#> [22,] "UVPDActivationTime " "double"
#> [23,] "MassList" "MassListRecord"
#> [24,] "ScanDescription" "character"
#> type
#> [1,] "TMS2"
#> [2,] "TMS2"
#> [3,] "TMS2"
#> [4,] "TMS2"
#> [5,] "TMS2"
#> [6,] "TMS2"
#> [7,] "TMS2"
#> [8,] "TMS2"
#> [9,] "TMS2"
#> [10,] "TMS2"
#> [11,] "ETD"
#> [12,] "ETD"
#> [13,] "ETD"
#> [14,] "ETD"
#> [15,] "ETD"
#> [16,] "ETD"
#> [17,] "CID"
#> [18,] "CID"
#> [19,] "CID"
#> [20,] "HCD"
#> [21,] "UVPD"
#> [22,] "UVPD"
#> [23,] "TMS2"
#> [24,] "TMS2"
validTms2Settings("TMS2")
#> name class type
#> [1,] "EnableMultiplexIons" "logical" "TMS2"
#> [2,] "EnableMSXIds" "logical" "TMS2"
#> [3,] "MaxNoOfMultiplexIons" "integer" "TMS2"
#> [4,] "OrbitrapResolution" "R15K:R30K:R50K:R60K:R120K:R240K:R500K" "TMS2"
#> [5,] "AgcTarget" "double" "TMS2"
#> [6,] "MinAgcTarget" "logical" "TMS2"
#> [7,] "MaxITTimeInMS" "double" "TMS2"
#> [8,] "Microscans" "integer" "TMS2"
#> [9,] "ActivationType" "CID:HCD:ETD:UVPD" "TMS2"
#> [10,] "IsolationWindow" "double" "TMS2"
#> [11,] "MassList" "MassListRecord" "TMS2"
#> [12,] "ScanDescription" "character" "TMS2"
validTms2Settings("ETD")
#> name class type
#> [1,] "ETDReactionTime" "double" "ETD"
#> [2,] "ETDReagentTarget" "double" "ETD"
#> [3,] "MaximumETDReagentInjectionTime" "double" "ETD"
#> [4,] "UseInternalCalibratedETD" "logical" "ETD"
#> [5,] "ETDSupplementalActivationEnergy" "double" "ETD"
#> [6,] "ETDSupplementalActivation" "None:ETciD:EThcD" "ETD"
validTms2Settings(c("TMS2", "ETD"))
#> name class
#> [1,] "EnableMultiplexIons" "logical"
#> [2,] "EnableMSXIds" "logical"
#> [3,] "MaxNoOfMultiplexIons" "integer"
#> [4,] "OrbitrapResolution" "R15K:R30K:R50K:R60K:R120K:R240K:R500K"
#> [5,] "AgcTarget" "double"
#> [6,] "MinAgcTarget" "logical"
#> [7,] "MaxITTimeInMS" "double"
#> [8,] "Microscans" "integer"
#> [9,] "ActivationType" "CID:HCD:ETD:UVPD"
#> [10,] "IsolationWindow" "double"
#> [11,] "ETDReactionTime" "double"
#> [12,] "ETDReagentTarget" "double"
#> [13,] "MaximumETDReagentInjectionTime" "double"
#> [14,] "UseInternalCalibratedETD" "logical"
#> [15,] "ETDSupplementalActivationEnergy" "double"
#> [16,] "ETDSupplementalActivation" "None:ETciD:EThcD"
#> [17,] "MassList" "MassListRecord"
#> [18,] "ScanDescription" "character"
#> type
#> [1,] "TMS2"
#> [2,] "TMS2"
#> [3,] "TMS2"
#> [4,] "TMS2"
#> [5,] "TMS2"
#> [6,] "TMS2"
#> [7,] "TMS2"
#> [8,] "TMS2"
#> [9,] "TMS2"
#> [10,] "TMS2"
#> [11,] "ETD"
#> [12,] "ETD"
#> [13,] "ETD"
#> [14,] "ETD"
#> [15,] "ETD"
#> [16,] "ETD"
#> [17,] "TMS2"
#> [18,] "TMS2"