writeMethodXmls: Create Orbitrap Fusion Lumos method.xml files.

In sgibb/topdownr: Investigation of Fragmentation Conditions in Top-Down Proteomics

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 [e-mail], Pavel V. Shliaha [e-mail]

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)

sgibb/topdownr documentation built on Jan. 16, 2024, 12:14 a.m.