digestMod {adductomicsR}R Documentation

modified Digest function (from OrgMassSpecR package)

Description

allows maxCharge to be set to calculate precursor m/z

Usage

digestMod(sequence, enzyme = "trypsin", missed = 0, 
maxCharge = 8,IAA = TRUE, N15 = FALSE, custom = list())

Arguments

sequence

a character string representing the amino acid sequence.

enzyme

is the enzyme to perform in silico digestion with

missed

the maximum number of missed cleavages. Must be an integer of 0 (default) or greater. An error will result if the specified number of missed cleavages is greater than the maximum possible number of missed cleavages.

maxCharge

numeric max charge charge for predicted precursor m/z

IAA

logical. TRUE specifies iodoacetylated cysteine and FALSE specifies unmodified cysteine. Used only in determining the elemental formula, not the three letter codes.

N15

logical indicating if the nitrogen-15 isotope should be used in place of the default nitrogen-14 isotope. calculation

custom

list of custom masses

Details

see Digest for details of further function arguments.

Value

dataframe

Examples

digestMod('MKWVTFISLLFLFSSAYSRGVFRRDAHKSEVAHRFKDLGEENFKALVLIA',
enzyme = "trypsin", missed = 0, maxCharge = 8,IAA = TRUE, N15 = FALSE, 
custom = list()) 

[Package adductomicsR version 1.8.0 Index]