PerformSearch: Search MS/MS spectra with MSeQUiP

In chrismckennan/MSeQUiP: Quantifying uncertainty in peptide-spectrum matches

Description

Computes MSeQUiP Bayes factors for each candidate peptide

Usage

PerformSearch(
  Spectra,
  Headers = NULL,
  data.F,
  clean.database = F,
  match.charge = T,
  append.file = "_Train.Q9.lowpH",
  scale = c("Quant90", "base-peak", "none"),
  path.spline = "<path to>/NoiseObserved",
  rt.path = "<path to>/RetentionTime",
  byInt.path = "<path to>/BYInt",
  byMA.path = "<path to>/BYMassAccuracy",
  byObs.path = "<path to>/BYObserved",
  NoiseInt.path = "<path to>/NoiseInt",
  Noise.MA.path = "<path to>/NoiseMassAccuracy",
  Int0.path = NULL,
  ppm.precursor = 10,
  min.peaks = 20,
  delta.ppm = 20,
  delta.ppm.prec = 20,
  scale.obs = NA,
  include.scale = T,
  append.noise = NULL,
  include.pep.IDs = T
)

Arguments

Spectra	A list of MS and MS/MS spectra. Can be obtained using mzR, or Deisotope.
Headers	A data frame of headers. Can be obtained using mzR, or Deisotope.
data.F	Spectral library. This can be obtained from Prosit.
clean.database	Should the spectral library be cleaned. Defaults to F.
match.charge	Should inferred fragment charges obtained from Deisotope be used. Defaults to T.
append.file	Name of training parameters to use. Detaults to "_Train.Q9.lowpH".
scale	Type of intensity normalization to use. Can be one of "Quant90" (normalize by the 0.9 quantile), "base-peak" (normalize by the base peak), or "none" (no normalization). Defaults to "Quant90".
path.spline	Path to parameters to define lambda(m), the probability a noise peak was generated around a predicted m/z m
rt.path	Path to retention time parameters.
byInt.path	Path to signal b/y intensity parameters.
byMA.path	Path to signal mass accuracy parameters.
byObs.path	Path to parameters determine the probability a b/y ion is observed.
NoiseInt.path	Path to parameters describing the noise intensity.
Noise.MA.path	Path to parameters describing the noise mass accuracy.
ppm.precursor	Precursor mass accuracy, on the ppm scale. Defaults to 10.
min.peaks	Minimum number of peaks in the MS/MS spectrum. Defaults to 20.
delta.ppm	MS/MS fragment mass accuracy, on the ppm scale. Defaults to 20.
delta.ppm.prec	Maximum difference between the precursors observed in MS and MS/MS spectra.
scale.obs	The intensity scale, if available. The default of NA will almost always be appropriate.
include.scale	If scale.obs is available, should it be used. Defaults to T.
append.noise	Name of training parameters to use. Detaults to append.file.
include.pep.IDs	Should peptide IDs be included in the results. Defaults to T.

Value

A list.

MS2.indices	The indices of Spectra that are MS/MS spectra.
Results	A list. List element FM contains the results, and is a list of matrices giving the MSeQUiP scores and other statistics for each scored peptide. The sum of the first 4 columns gives the log Bayes factor for the peptide. The element RM is NA.

chrismckennan/MSeQUiP documentation built on Dec. 19, 2021, 4:01 p.m.