cmmr (version 1.0.3)

msms_search: 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"
)

Value

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

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").

Examples

if (FALSE) {
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"
)
}