parse.seq: Parse an amino acid sequence into a set of peptides,...

In bioarch-sjh/bacollite: Analysis of MALDI and LC-MS/MS spectral data using sequence data (mainly for collagen)

Parse an amino acid sequence into a set of peptides, incorporating hydroxylation and deamidation modifications, and calculating mass

Description

Parse an amino acid sequence into a set of peptides, incorporating hydroxylation and deamidation modifications, and calculating mass

Usage

parse.seq(
  sequence,
  cuts = "K|R",
  skip = "X",
  massmin = 800,
  massmax = 3500,
  verbose = F,
  max.missed.cleaves = 0,
  cutbefore = F
)

Arguments

cuts	a regular expression listing the amino acids that the sequence should be cut at. Defaults to Trypsing cut sites K & R
skip	any codes that mean the peptide is invalid. Defaults to "X"
massmin	the minimum mass that a peptide should be. Defaults to 800
massmax	the maximum mass that a peptide should be. Defaults to 3500
verbose	whether to print messages to console during processing. Defaults to FALSE
max.missed.cleaves	the number of missed cleaves to incorporate in the set of peptides.
seqeunce	a character string holding the sequence, e.g. "GPPGAPGPPGPP"

Examples

parse.seq("GPPGQKGPPGPQGPRGPPGPPGPM")

bioarch-sjh/bacollite documentation built on Oct. 7, 2022, 3:34 p.m.