R/queryPubchem.R

In jasenfinch/pubchemPIP: Putative Ionisation Product querying of the pubchem database

queryPubchem <- function(mz,ppm,mode,db_path){
  if(mode=="p"){
    adducts <- c("[M+2Na]2+","[M+H+K]2+","[M+H+Na]2+","[M+H+NH4]2+","[M+2H]2+","[M+2H-H2O-NH3]2+","[2M+K]1+","[2M+Na]1+","[2M+NH4]1+","[2M+H]1+","[M+2K-H]1+","[M+2Na-H]1+","[M+K]1+","[M+Na]1+","[M+Na]1+","[M+H]1+","[M1+.]1+","[M+H-NH3]1+","[M+H-H2O]1+","[M+H-FA]1+")
  }
  if(mode=="n"){
    adducts <- c("[2M+Na-2H]1-","[2M-H]1-","[M+K-2H]1-","[M+Cl]1-","[M+Na-2H]1-","[M1-.]1-","[M-H]1-","[M-2H]2-")
  }
  if(mode=="ne"){
    adducts <- c("M")
  }
  res <- lapply(adducts,getAdduct,mz=mz,ppm=ppm,db_path=db_path)
  res <- ldply(res)
  return(res)
}