expandMsConditions: Expand MS Conditions

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

Expand MS Conditions

Description

Create a data.frame of all possible combinations of the given arguments. It ensures that just arguments are applied that yield a valid MethodModification.xml file.

Usage

expandMs1Conditions(..., family = "Calcium", version = "3.2")

expandTms2Conditions(
  ActivationType = c("CID", "HCD", "ETD", "UVPD"),
  ...,
  MassList = NULL,
  family = "Calcium",
  version = "3.2"
)

Arguments

...	further named arguments, used to create the combination of conditions.
family	character, currently just Calcium is supported
version	character, currently 3.1, 3.2 (default), 3.3 are supported
ActivationType	character, ActivationType for TMS2, either CID, HCD, ETD, or UVPD.
MassList	matrix, 2 columns (mass, z) for targeted mass list, or NULL (default) to not overwrite targeted mass.

Value

data.frame with all possible combinations of conditions/settings.

See Also

validMs1Settings()

validTms2Settings(), expand.grid()

Examples

expandMs1Conditions(FirstMass=100, LastMass=400)
expandTms2Conditions(
     ActivationType="CID",
     OrbitrapResolution="R120K",
     IsolationWindow=1,
     MaxITTimeInMS=200,
     Microscans=as.integer(40),
     AgcTarget=c(1e5, 5e5, 1e6),
     CIDCollisionEnergy=c(NA, seq(7, 35, 7)),
     MassList=cbind(mz=c(560.6, 700.5, 933.7), z=rep(1, 3))
)

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