permutatePeptideMass: permutatePeptideMass
In mjhelf/MassTools: R package for mass and molecular formula calculations

Description Usage Arguments Details See Also Examples

Apply a set of mass modifications to a peptide with a known mass

1 2	permutatePeptideMass(df, modifications, sequenceCol = "seq", massCol = "mz", chargeCol = NULL)

`df`	data.frame with at least two columns, one with a non-empty sequence string and one with a mass for that sequence
`modifications`	a data.frame with colums `AAs`
`sequenceCol`	name of the sequence column in df
`massCol`	name of the mass column in df
`chargeCol`	name of column that specifies charge state (used to adjust modification masses)

modifications

Columns that need to be in the modifications data.frame:

AAs: containing letters for the amino acids (e.g. "TS") affected by this modification
min: minimum number of times this modification can be applied
max: maximum number of times this modification can be applied
mass: mass of this modification
tag: label for this modification (will automatically be preceded by number of these modifications applied)

min and max can be positive, negative or 0. The larger *absolute* value has to be in the max column

permutateMass

peptides = data.frame(seq = "ASDFGHKLIPYTREWQCNM",mz = 2295.056)
mods = data.frame(AAs = c("TS", ""),
 min = c(0,1), max = c(-10,2),
  mass = c(18.01,12.0), tag = c("DH","C") )

permutatePeptideMass(peptides, mods)