msms_search {cmmr}

Encapsulation of CEU Mass Mediator batch search API.

Description

batch_search returns the dataframe of all the database search results. using the following code to install the dependencies: install.packages(c("httr", "progress", "RJSONIO"))

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,
  ionizationVoltage = "all", spectra_types = "experimental",
  cmm_url = "http://ceumass.eps.uspceu.es/mediator/api/msmssearch")

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

ionizationVoltage

ionizationVoltage

spectra_types

spectra_types

cmm_url

"http://ceumass.eps.uspceu.es/mediator/api/msmssearch" or your local one

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

ms_ms_peaks = matrix(
c(40.948, 0.174,
  56.022, 0.424,
  84.37, 53.488,
  101.50, 8.285,
  102.401, 0.775,
  129.670, 100.000,
  146.966, 20.070),
ncol = 2,
byrow = TRUE)

msms_search(ion_mass = 147, ms_ms_peaks = ms_ms_peaks, ion_mode = 'positive')