Protein_feature_list_fun: Protein_feature_list_fun

In MASHUOA/HiTMaP: A collection of tools for imaging MS data processing

Protein_feature_list_fun

Description

This is a function that prepare the candiate list for maldi imaging data qualitative or quantitative analysis. this function will read the fasta file and generate mz for the adducts list defined in "adducts".

Usage

Protein_feature_list_fun(
  workdir = getwd(),
  database,
  Digestion_site = "[G]",
  missedCleavages = 0:1,
  Multiple_mode = c("sequential", "parallel"),
  adducts = c("M+H", "M+NH4", "M+Na"),
  BPPARAM = bpparam(),
  Decoy_search = T,
  Decoy_mode = c("adducts", "elements", "isotope", "sequence"),
  Decoy_adducts = c("M+He", "M+Ne", "M+Ar", "M+Kr", "M+Xe", "M+Rn"),
  Substitute_AA = list(AA = c(NULL), AA_new_formula = c(NULL), Formula_with_water =
    c(NULL)),
  mzrange = c(500, 4000),
  output_candidatelist = T,
  Modifications = list(fixed = NULL, fixmod_position = NULL, variable = NULL,
    varmod_position = NULL),
  use_previous_candidates = F,
  Protein_desc_of_exclusion = NULL,
  Database_stats = F
)

Arguments

workdir	the folder that contains fasta file
database	the file name of fasta file
Digestion_site	Digestion pattern, this is the
missedCleavages	Define a number range for misscleaved peptides to be considered
adducts	the adducts list to be used for generating the PMF search candidates
BPPARAM	parallel processing parameter for BiocParallel

Value

a table of peptide candiate list

Examples

Protein_feature_list_fun(database="lipid candidates.csv",adducts=c("M+H","M+NH4","M+Na"))

MASHUOA/HiTMaP documentation built on April 5, 2024, 5:48 p.m.