MetaDBparse (version 2.0.0)

searchCMMR: Search CMMR

Description

Queries Ceu Mass Mediator through their API

Usage

searchCMMR(
  cmm_url = "http://ceumass.eps.uspceu.es/mediator/api/v3/batch",
  metabolites_type = "all-except-peptides",
  databases = "[\"all-except-mine\"]",
  masses_mode = "mz",
  ion_mode = "positive",
  adducts = switch(ion_mode, positive =
    "[\"M+H\", \"M+2H\", \"M+Na\", \"M+K\", \"M+NH4\", \"M+H-H2O\"]",
    negative = "[\"M-H\", \"M+Cl\", \"M+FA-H\", \"M-H-H2O\"]"),
  tolerance = 10,
  tolerance_mode = "ppm",
  unique_mz
)

Arguments

cmm_url

API base url, Default: 'http://ceumass.eps.uspceu.es/mediator/api/v3/batch'

metabolites_type

Which type of metabolites to consider?, Default: 'all-except-peptides'

databases

Which databases to consider?, Default: '["all-except-mine"]'

masses_mode

Format of input compound, Default: 'mz'

ion_mode

Which ion mode was the compound found in?, Default: 'positive'

adducts

Adducts to be considered, Default: switch(ion_mode, positive = "[\"M+H\", \"M+2H\", \"M+Na\", \"M+K\", \"M+NH4\", \"M+H-H2O\"]", negative = "[\"M-H\", \"M+Cl\", \"M+FA-H\", \"M-H-H2O\"]")

tolerance

Error margin, units of 'tolerance_mode', Default: 10

tolerance_mode

Mode of error margin, Default: 'ppm'

unique_mz

M/z(s) to use in query

Value

Data table with match results

See Also

create_batch_body POST,content_type,content fromJSON progress_bar rbindlist

Examples

# NOT RUN {
searchCMMR(unique_mz = "170.09240307", ion_mode = "positive")
# }