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

- `exps`: a named tree-like `list` object generated by e.g. `createExperimentsFragmentOptimisation()`. Its names are used as filename.

- `pattern`: The file name pattern used to name different method files. It must contain a `"%s"` that is replaced by the conditions defined in `groupBy`.

DEFUNCT options:

- `ms1Settings`: A `list` of MS1 settings. This has to be a named `list`. Valid MS1 settings are: `c("FirstMass", "LastMass", "Microscans", "MaxITTimeInMS", "AgcTarget")`

- `ms2Settings`: A `list` of MS2 settings. This has to be a named `list`. Valid MS2 settings are: `c("ActivationType", "IsolationWindow", "EnableMultiplexIons", "EnableMSXIds", "MaxNoOfMultiplexIons", "OrbitrapResolution", "AgcTarget", "MinAgcTarget", "MaxITTimeInMS", "Microscans", "ETDReactionTime", "ETDReagentTarget", "MaximumETDReagentInjectionTime", "UseInternalCalibratedETD", "ETDSupplementalActivationEnergy", "ETDSupplementalActivation")`

- `groupBy`: The `groupBy` parameter is used to split methods into different files. Valid entries are all settings that could be used in `ms2Settings` and `"replication"`.

- `massLabeling`: The Orbitrap Fusion devices seems not to respect the start and end times of the runs given in the method.xml files. That's why it is nearly impossible to identify the run with its conditions based on the timings. If `massLabeling` is `TRUE` (default) the mass values given in `mz` are rounded to the first decimal place and the second to fourth decimal place is used as numeric identifier.

### 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 1.12.0 Index]