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(ms1Settings, ms2Settings, groupBy = c("replication",
  "ETDReactionTime"), replications = 2, mz, massLabeling = TRUE,
  nMs2perMs1 = 10, duration = 0.5, randomise = TRUE,
  pattern = "method-%s.xml", exps, verbose = interactive())

Arguments

ms1Settings

list, named list of MS1 settings, see e.g. defaultMs1Settings().

ms2Settings

list, named list of MS2 settings, see e.g. defaultMs2Settings().

groupBy

character, split files by groupBy entries.

replications

integer, number of replications of experiments.

mz

matrix, two columns (column 1: mass, column 2: z).

massLabeling

logical, should mz values used for ID labeling?

nMs2perMs1

integer, how many MS2 scans should be run after a MS1 scan?

duration

double, how long should the scan be?

randomise

logical, should the MS2 scan settings randomised?

pattern

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

exps

list, generated by e.g. createExperimentsFragmentOptimisation()

verbose

logical, verbose output?

Details

Please note: in topdownr version < 1.5 it was used to generate all possible combinations. This interface is still available but deprecated and will be removed in the next bioconductor release (topdownr version >= 1.7)

DEPRECATED 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 1.6.0 Index]