Topdown_batch: Annotate a set of top-down MS/MS spectra

In ManuelPerisDiaz/CysMpro: Mass Spectrometry-Based Structural Analysis of Metalloproteins

Description

Annotate a set of top-down MS/MS spectra

Usage

Topdown_batch(
  mzML = TRUE,
  xy = FALSE,
  mz1 = 500,
  mz2 = 3000,
  tol = 0.15,
  txt = FALSE,
  Metal = c("Zn"),
  SNR.Th = 2,
  peak = FALSE,
  plot = FALSE,
  dir = getwd(),
  sequence,
  b,
  t,
  maxMass,
  mzw,
  NbindingMetal,
  Maxcharge,
  label = "CID"
)

Arguments

mzML	if TRUE, the experimental file is in mzML file format
xy	if TRUE, the experimental file is in xy file format
mz1	left mass
mz2	right mass
tol	mass tolerance
txt	if TRUE, the experimental file is in txt file format
Metal	Metal
SNR.Th	SNR threshold
peak	if TRUE peak picking is performed
plot	if TRUE, plot is produced
dir	Where to save results
sequence	Protein sequence
b	Filter by intensity
t	Mass error window.
maxMass	maximum mass for deconvolution
mzw	mass error window to annotate the parent ion
NbindingMetal	Number of metal ions
Maxcharge	maximum charge state for deconvolution
label	Label the results

Value

Annotate a set of top-down MS/MS spectra

ManuelPerisDiaz/CysMpro documentation built on Oct. 18, 2020, 6:44 a.m.