advanced_batch_search {cmmr}

Encapsulation of CEU Mass Mediator advanced batch search API.

Description

advanced_batch_search returns the body string of a POST request. using the following code to install the dependencies: install.packages(c("httr", "progress", "RJSONIO"))

Usage

  advanced_batch_search(cmm_url = paste0("http://ceumass.eps.uspceu.es/mediator/api/v3/",
  "advancedbatch"), chemical_alphabet = "all", modifiers_type = "none",
  metabolites_type = "all-except-peptides", databases = "[\"hmdb\"]",
  masses_mode = "mz", ion_mode = "positive", adducts = "[\"all\"]",
  deuterium = "false", tolerance = "7.5", tolerance_mode = "ppm",
  masses = "[400.3432, 288.2174]", all_masses = "[]",
  retention_times = "[18.842525, 4.021555]",
  all_retention_times = "[]",
  composite_spectra = paste0("[[{ \"mz\": 400.3432, \"intensity\": 307034.88 }, ",
  "{ \"mz\": 311.20145, \"intensity\": 400.03336 }]]"))

Arguments

cmm_url

'http://ceumass.eps.uspceu.es/mediator/api/v3/advancedbatch' or your local one

chemical_alphabet

"CHNOPS", "CHNOPSCL", "ALL"

modifiers_type

"none", "NH3", "HCOO", "CH3COO", "HCOONH3", "CH3COONH3"

metabolites_type

"all-except-peptides", "only-lipids", "all-including-peptides"

databases

"all", "all-except-mine", "HMDB", "LipidMaps", "Metlin", "Kegg", "in-house", "mine"

masses_mode

"neutral", "mz"

ion_mode

"positive", "negative"

adducts

for positive mode ["M+H", "M+2H", "M+Na", "M+K", "M+NH4", "M+H-H2O"] for negative mode ["M-H", "M+Cl", "M+FA-H", "M-H-H2O"], for neutral ["M"]

deuterium

boolean 'true' 'false'

tolerance

double (Range: [0..100])

tolerance_mode

"ppm", "mDa"

masses

double

all_masses

array of doubles

retention_times

double

all_retention_times

array of doubles

composite_spectra

array of arrays of spectra_object

Value

If all inputs are all correctly formatted, a dataframe will be returned for the result.

Author(s)

Yaoxiang Li [e-mail]

Georgetown University, USA

License: GPL (>= 3)

Examples

df <- advanced_batch_search(
cmm_url             = paste0(
  'http://ceumass.eps.uspceu.es/mediator/api/v3/',
  'advancedbatch'),
chemical_alphabet   = 'all',
modifiers_type      = 'none',
metabolites_type    = 'all-except-peptides',
databases           = '["hmdb"]',
masses_mode         = 'mz',
ion_mode            = 'positive',
adducts             = '["all"]',
deuterium           = 'false',
tolerance           = '7.5',
tolerance_mode      = 'ppm',
masses              = '[400.3432, 288.2174]',
all_masses          = '[]',
retention_times     = '[18.842525, 4.021555]',
all_retention_times = '[]',
composite_spectra   = paste0(
  '[[{ "mz": 400.3432, "intensity": 307034.88 }, ',
  '{ "mz": 311.20145, "intensity": 400.03336 }]]'
))