Package 'cmmr'

Advanced Batch Search using CEU Mass Mediator API

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/mediator/api/v3/advancedbatch",
  chemical_alphabet = "all",
  modifiers_type = "none",
  metabolites_type = "all-except-peptides",
  databases = list("hmdb"),
  masses_mode = "mz",
  ion_mode = "positive",
  adducts = list("all"),
  deuterium = FALSE,
  tolerance = 10,
  tolerance_mode = "ppm",
  masses = c(399.3367, 421.3169, 315.2424, 337.2234, 280.2402),
  all_masses = list(),
  retention_times = c(18.8425, 18.8425, 8.1449, 8.1449, 28.2695, 4.0216),
  all_retention_times = list(),
  composite_spectra = list(),
  all_composite_spectra = list()
)

Arguments

cmm_url	A character string specifying the CEU Mass Mediator API endpoint.
chemical_alphabet	A character string specifying the chemical alphabet to use.
modifiers_type	A character string specifying the modifier type.
metabolites_type	A character string specifying the metabolites type.
databases	A list specifying the databases to search.
masses_mode	A character string specifying the masses mode.
ion_mode	A character string specifying the ionization mode.
adducts	A list specifying the adducts to include in the search.
deuterium	Logical value indicating whether to consider deuterium substitutions.
tolerance	A numeric value specifying the mass tolerance.
tolerance_mode	A character string specifying the tolerance mode.
masses	A numeric vector of masses to search.
all_masses	A list for arrays of masses (optional).
retention_times	A numeric vector of retention times corresponding to the masses.
all_retention_times	A list for retention times arrays (optional).
composite_spectra	A list for composite spectra (optional).
all_composite_spectra	A list for all composite spectra (optional)

Value

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

Examples

df <- advanced_batch_search(
cmm_url = "https://ceumass.eps.uspceu.es/mediator/api/v3/advancedbatch",
chemical_alphabet = "all",
modifiers_type = "none",
metabolites_type = "all-except-peptides",
databases = list("hmdb"),
masses_mode = "mz",
ion_mode = "positive",
adducts = list("all"),
deuterium = FALSE,
tolerance = 10.0,
tolerance_mode = "ppm",
masses = c(399.3367, 421.31686, 315.2424, 337.2234, 280.2402),
all_masses = list(),
retention_times = c(18.842525, 18.842525, 8.144917, 8.144917, 28.269503, 4.021555),
all_retention_times = list(),
composite_spectra = list(),
all_composite_spectra = list()
)

head(df)

---

Encapsulation of CEU Mass Mediator batch search API

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

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)
)

---

Create POST request Body for advanced batch search

Description

create_advanced_batch_body creates a list for the advanced batch search POST request.

Usage

create_advanced_batch_body(
  chemical_alphabet = "all",
  modifiers_type = "none",
  metabolites_type = "all-except-peptides",
  databases = list("hmdb"),
  masses_mode = "mz",
  ion_mode = "positive",
  adducts = list("all"),
  deuterium = FALSE,
  tolerance = 10,
  tolerance_mode = "ppm",
  masses = c(399.3367, 421.3169, 315.2424, 337.2234, 280.2402),
  all_masses = list(),
  retention_times = c(18.8425, 18.8425, 8.1449, 8.1449, 28.2695, 4.0216),
  all_retention_times = list(),
  composite_spectra = list(),
  all_composite_spectra = list()
)

Arguments

chemical_alphabet	A string for the chemical alphabet: "CHNOPS", "CHNOPSCL", "ALL".
modifiers_type	A string for the modifier type: "none", "NH3", "HCOO", etc.
metabolites_type	A string for metabolites type: "all-except-peptides", "only-lipids", etc.
databases	A vector of databases to search: e.g., list("HMDB").
masses_mode	A string specifying masses mode: "neutral" or "mz".
ion_mode	A string for the ionization mode: "positive", "negative", etc.
adducts	A vector of adducts to include in the search, e.g., list("M+H", "M+Na").
deuterium	Logical value: whether to consider deuterium substitutions (TRUE or FALSE).
tolerance	Numeric value specifying the tolerance.
tolerance_mode	A string for the tolerance mode: "ppm" or "mDa".
masses	Numeric vector of masses to search.
all_masses	Empty array for all masses (optional).
retention_times	Numeric vector of retention times.
all_retention_times	Empty array for retention times (optional).
composite_spectra	Empty array for composite spectra.
all_composite_spectra	A list for all composite spectra (optional)

Value

A properly formatted JSON body for the POST request.

---

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.

---

MS/MS Search using CEU Mass Mediator API

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

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"
)

---