create_advanced_batch_body {cmmr}

Create POST request Body for batch search

Description

create_advanced_batch_body returns a string of advanced search POST request body.

Usage

create_advanced_batch_body(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

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)