Title: CEU Mass Mediator RESTful API
Version: 1.0.3
Depends: R (≥ 4.4.0)
Imports: httr, progress, RJSONIO, cli
Description: CEU (CEU San Pablo University) Mass Mediator is an on-line tool for aiding researchers in performing metabolite annotation. 'cmmr' (CEU Mass Mediator RESTful API) allows for programmatic access in R: batch search, batch advanced search, MS/MS (tandem mass spectrometry) search, etc. For more information about the API Endpoint please go to https://github.com/YaoxiangLi/cmmr.
License: GPL-3
Encoding: UTF-8
URL: https://github.com/YaoxiangLi/cmmr
RoxygenNote: 7.3.2
Suggests: testthat
NeedsCompilation: no
Packaged: 2024-10-04 17:47:54 UTC; bach
Author: Yaoxiang Li ORCID iD [aut, cre], Alberto Gil de la Fuente [aut], Charles Hinzman [aut], Amrita Cheema [aut]
Maintainer: Yaoxiang Li <liyaoxiang@outlook.com>
Repository: CRAN
Date/Publication: 2024-10-04 20:10:34 UTC

Description

advanced_batch_search performs an advanced batch search on the CEU Mass Mediator API and returns a dataframe of search results.

Usage

advanced_batch_search(
  cmm_url = "https://ceumass.eps.uspceu.es/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 = NULL,
  all_masses = "[]",
  retention_times = NULL,
  all_retention_times = "[]",
  composite_spectra = NULL
)

Arguments

cmm_url

A character string specifying the CEU Mass Mediator API endpoint. Default is "https://ceumass.eps.uspceu.es/api/v3/advancedbatch".

chemical_alphabet

A character string specifying the chemical alphabet to use. Options are "CHNOPS", "CHNOPSCL", or "ALL".

modifiers_type

A character string specifying the modifier type. Options are "none", "NH3", "HCOO", "CH3COO", "HCOONH3", or "CH3COONH3".

metabolites_type

A character string specifying the metabolites type. Options are "all-except-peptides", "only-lipids", or "all-including-peptides".

databases

A JSON-formatted character string specifying the databases to search. Examples include '["all"]', '["HMDB"]', '["LipidMaps"]'.

masses_mode

A character string specifying the masses mode. Options are "neutral" or "mz".

ion_mode

A character string specifying the ionization mode. Options are "positive", "negative", or "neutral".

adducts

A JSON-formatted character string specifying the adducts to include in the search. Examples include '["M+H","M+Na"]' for positive mode.

deuterium

A logical value indicating whether to consider deuterium substitutions. TRUE or FALSE.

tolerance

A numeric value specifying the mass tolerance (Range: 0 to 100).

tolerance_mode

A character string specifying the tolerance mode. Options are "ppm" or "mDa".

masses

A numeric vector of masses to search.

all_masses

A JSON-formatted character string representing an array of mass arrays.

retention_times

A numeric vector of retention times corresponding to the masses.

all_retention_times

A JSON-formatted character string representing an array of retention time arrays.

composite_spectra

A JSON-formatted character string representing composite spectra.

Value

A dataframe containing the search results from the CEU Mass Mediator API.

Examples

## Not run: 
df <- advanced_batch_search(
  cmm_url = "https://ceumass.eps.uspceu.es/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 = c(400.3432, 288.2174),
  all_masses = "[]",
  retention_times = c(18.842525, 4.021555),
  all_retention_times = "[]",
  composite_spectra = paste0(
    '[ [ { "mz": 400.3, "intensity": 307034.9 },',
    '   { "mz": 311.2, "intensity": 400.1 } ] ]'
  )
)

## End(Not run)

Description

batch_search returns a dataframe with the results from the database search.

Usage

batch_search(
  cmm_url = "https://ceumass.eps.uspceu.es/api/v3/batch",
  metabolites_type = "all-except-peptides",
  databases = "[\"all-except-mine\"]",
  masses_mode = "mz",
  ion_mode = "positive",
  adducts = "[\"M+H\",\"M+Na\"]",
  tolerance = 10,
  tolerance_mode = "ppm",
  unique_mz
)

Arguments

cmm_url

A URL string for the CEU Mass Mediator or a local API endpoint.

metabolites_type

Search metabolites type: "all-except-peptides", "only-lipids", or "all-including-peptides".

databases

A JSON array of databases to search: e.g., "all", "HMDB", "LipidMaps", etc.

masses_mode

Masses mode: "neutral" or "mz".

ion_mode

Ionization mode: "positive" or "negative".

adducts

A JSON array of adducts to include in the search, e.g., '["M+H", "M+Na"]'.

tolerance

A numeric tolerance value (range: 0-100).

tolerance_mode

Tolerance mode: "ppm" or "mDa".

unique_mz

A numeric vector of unique m/z values for the search.

Value

A dataframe containing search results.

Examples

## Not run: 
df_pos <- batch_search(
  "https://ceumass.eps.uspceu.es/api/v3/batch",
  "all-except-peptides",
  '["all-except-mine"]',
  "mz",
  "positive",
  '["M+H","M+Na"]',
  10,
  "ppm",
  c(670.4623, 1125.2555, 602.6180)
)

## End(Not run)

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.

Create POST request Body for batch search

Description

create_batch_body returns a string of a POST request body.

Usage

create_batch_body(
  metabolites_type = "all-except-peptides",
  databases = "[\"all-except-mine\"]",
  masses_mode = "mz",
  ion_mode = "positive",
  adducts = "[\"M+H\",\"M+Na\"]",
  tolerance = 10,
  tolerance_mode = "ppm",
  unique_mz
)

Arguments

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]

tolerance

double (Range: [0..100])

tolerance_mode

"ppm", "mDa"

unique_mz

An array of unique m/zs

Value

If all inputs are all correctly formatted, a string of a POST request will be returned for the result.

Examples


batch_body <- create_batch_body(
  "all-except-peptides",
  '["all-except-mine"]',
  "mz",
  "positive",
  '["M+H","M+Na"]',
  10,
  "ppm",
  c(670.4623, 1125.2555, 602.6180)
)

batch_body <- create_batch_body(
  "all-except-peptides",
  '["all-except-mine"]',
  "mz",
  "negative",
  '["M-H","M+Cl"]',
  10,
  "ppm",
  c(670.4623, 1125.2555, 602.6180)
)

## Not run: 
create_batch_body(c(670.4623, 1125.2555, 602.6180))

## End(Not run)

Create MS/MS search POST request body

Description

create_msms_body returns a string of a POST request body.

Usage

create_msms_body(
  ion_mass,
  ms_ms_peaks,
  precursor_ion_tolerance = 500,
  precursor_ion_tolerance_mode = "mDa",
  precursor_mz_tolerance = 1000,
  precursor_mz_tolerance_mode = "mDa",
  ion_mode = "positive",
  ionization_voltage = "all",
  spectra_types = "experimental"
)

Arguments

ion_mass

ion_mass

ms_ms_peaks

ms_ms_peaks

precursor_ion_tolerance

precursor_ion_tolerance

precursor_ion_tolerance_mode

precursor_ion_tolerance_mode

precursor_mz_tolerance

precursor_mz_tolerance

precursor_mz_tolerance_mode

precursor_mz_tolerance_mode

ion_mode

ion_mode

ionization_voltage

ionization_voltage

spectra_types

spectra_types

Value

If all inputs are all correctly formatted, a string of a POST request will be returned for the result.

Description

msms_search performs an MS/MS search on the CEU Mass Mediator API and returns a dataframe with the search results.

Usage

msms_search(
  ion_mass,
  ms_ms_peaks,
  precursor_ion_tolerance = 100,
  precursor_ion_tolerance_mode = "mDa",
  precursor_mz_tolerance = 500,
  precursor_mz_tolerance_mode = "mDa",
  ion_mode,
  ionization_voltage = "all",
  spectra_types = "experimental",
  cmm_url = "https://ceumass.eps.uspceu.es/api/msmssearch"
)

Arguments

ion_mass

Numeric. Mass of the ion to search for.

ms_ms_peaks

Matrix. The MS/MS peaks, with two columns representing mass and intensity.

precursor_ion_tolerance

Numeric. Tolerance for the precursor ion (default: 100.0).

precursor_ion_tolerance_mode

Character. Tolerance mode for precursor ion: "ppm" or "mDa" (default: "mDa").

precursor_mz_tolerance

Numeric. Tolerance for the m/z (default: 500.0).

precursor_mz_tolerance_mode

Character. Tolerance mode for precursor m/z: "ppm" or "mDa" (default: "mDa").

ion_mode

Character. Ionization mode: "positive" or "negative".

ionization_voltage

Character. Ionization voltage to use (default: "all").

spectra_types

Character. Spectra types: "experimental" or other supported types.

cmm_url

Character. URL for the CEU Mass Mediator API (default: "https://ceumass.eps.uspceu.es/api/msmssearch").

Value

A dataframe containing the search results from the CEU Mass Mediator API.

Examples

## Not run: 
ms_ms_peaks <- matrix(
  c(
    40.948, 0.174,
    56.022, 0.424,
    84.370, 53.488,
    101.500, 8.285,
    102.401, 0.775,
    129.670, 100.000,
    146.966, 20.070
  ),
  ncol = 2,
  byrow = TRUE
)

df <- msms_search(
  ion_mass = 147,
  ms_ms_peaks = ms_ms_peaks,
  ion_mode = "positive"
)

## End(Not run)