getPredicted: Get predicted formulas and adducts from m/z value

In MetaDBparse: Annotate Mass over Charge Values with Databases and Formula Prediction

Description

Wrapper function to predict formulas and then consider adducts as well.

Usage

getPredicted(
  mz,
  ppm = 2,
  mode = "positive",
  rules = c("senior", "lewis", "hc", "chnops", "nops"),
  elements = c("C", "H", "N", "O", "P", "S"),
  search = c("PubChem", "ChemSpider"),
  detailed = TRUE,
  calc_adducts = adducts[Ion_mode == mode, ]$Name,
  adduct_table = adducts
)

Arguments

mz	M/z of interest
ppm	Error margin in parts per million, Default: 2
mode	M/z found in positive or negative mode?, Default: 'positive'
rules	Which golden rules to apply?, Default: c("senior", "lewis", "hc", "chnops", "nops")
elements	Which elements to consider?, Default: c("C", "H", "N", "O", "P", "S")
search	Check the found formulas on PubChem or ChemSpider?, Default: c("PubChem", "ChemSpider")
detailed	Look up details like description etc. if hit found? Makes things slower!, Default: TRUE
calc_adducts	Which adducts to consider?, Default: adducts[Ion_mode == mode, ]$Name
adduct_table	Adduct table to use, referred to by 'calc_adducts'. Allows use for custom 'adducts' such as in-source fragments etc.

Value

Table of found matches and associated info

See Also

rbindlist check_chemform

Examples

## Not run: getPredicted(mz = 170, ppm = 2, mode = "positive",
rules = c("hc", "chnops", "nops"),
elements = c("C","H","O"))
## End(Not run)

MetaDBparse documentation built on May 3, 2021, 5:09 p.m.