create.spectral.lib: Creates a spectral library with intensities and retention...
In MarcIsak/MSLibrarian: What the Package Does (One Line, Title Case)

create.spectral.lib

R Documentation

Creates a spectral library with intensities and retention times from Prosit

Description

Creates a spectral library with intensities and retention times from Prosit

Usage

create.spectral.lib(
  calibrationLib = NULL,
  projectFolder = NULL,
  msFile = NULL,
  fasta,
  outputLib = NULL,
  format = "spectronaut",
  ceMode = "length_charge",
  threads = detectCores(),
  saveObj = F
)

Arguments

`calibrationLib`	path to processed calibration library (RData format)
`projectFolder`	path to project folder containing a processed calibration library.
`msFile`	path to representative pseudo ms/ms file used to create the calibration library (could be extracted from the calibration library file later...)
`fasta`	path to protein sequence FASTA file from Uniprot
`outputLib`	path to desired output library
`format`	output library format c("spectronaut", "openswath")
`ceMode`	Collision energy optimization setting. Possible values are c("length_only", "length_charge", "charge", scalar(fixed collision energy))
`saveObj`	Determines whether a MSLibrarian object will be saved. Possible values are "TRUE" or "FALSE" (default)