writeMethodXmls {topdownr}R Documentation

Create Orbitrap Fusion Lumos method.xml files.

Description

This function is used to create Orbitrap Fusion Lumos method files from a tree-like list experiment generated by e.g. createExperimentsFragmentOptimisation().

Usage

writeMethodXmls(exps, pattern = "method-%s.xml", verbose = interactive())

Arguments

exps

list, generated by e.g. createExperimentsFragmentOptimisation()

pattern

character, file name pattern for the method.xml files.

verbose

logical, verbose output?

Details

DEFUNCT options:

Author(s)

Sebastian Gibb mail@sebastiangibb.de, Pavel V. Shliaha pavels@bmb.sdu.dk

See Also

createExperimentsFragmentOptimisation()

Examples

ms1 <- expandMs1Conditions(FirstMass=400, LastMass=1200, Microscans=as.integer(10))

targetMz <- cbind(mz=c(560.6, 700.5, 933.7), z=rep(1, 3))
common <- list(
    OrbitrapResolution="R120K",
    IsolationWindow=1,
    MaxITTimeInMS=200,
    Microscans=as.integer(40),
    AgcTarget=c(1e5, 5e5, 1e6)
)
cid <- expandTms2Conditions(
    MassList=targetMz,
    common,
    ActivationType="CID",
    CIDCollisionEnergy=seq(7, 35, 7)
)
hcd <- expandTms2Conditions(
    MassList=targetMz,
    common,
    ActivationType="HCD",
    HCDCollisionEnergy=seq(7, 35, 7)
)
etd <- expandTms2Conditions(
    MassList=targetMz,
    common,
    ActivationType="ETD",
    ETDReagentTarget=c(1e6, 5e6, 1e7),
    ETDReactionTime=c(2.5, 5, 10, 15, 30, 50),
    ETDSupplementalActivation=c("None", "ETciD", "EThcD"),
    ETDSupplementalActivationEnergy=seq(7, 35, 7)
)
exps <- createExperimentsFragmentOptimisation(ms1=ms1, cid, hcd, etd,
    groupBy=c("AgcTarget", "replication"), nMs2perMs1=10, scanDuration=0.5,
    replications=2, randomise=TRUE
)
writeMethodXmls(exps=exps)

[Package topdownr version 1.15.1 Index]