peptideMBR: MBR of peptides

In qzhang503/proteoQ: Processing and Informatic Analysis of Mass Spectrometrirc Data

MBR of peptides

Description

MBR of peptides

Usage

peptideMBR(
  ms1files,
  base_name,
  xvs,
  yvs,
  tvs,
  svs,
  mbr_mzs,
  mbr_ys,
  mbr_rets,
  mbr_peps,
  dat_dir,
  mbr_ret_tol = 25,
  min_y = 2e+06,
  max_mbr_fold = 20,
  step = 1e-05,
  gap = mbr_ret_tol + 45
)

Arguments

ms1files	The names of MS1 data files corresponding to a peptide table, e.g., TMTset1_LCMSinj1_Peptide_N.txt.
base_name	The basename of a peptide table.
xvs	A vector of m-over-z's.
yvs	A vector of apex intensities.
tvs	A vector of apex retention times.
svs	A vector of apex scan numbers.
mbr_mzs	Values of m-over-zs for MBR.
mbr_ys	Intensity values for MBR.
mbr_rets	Values of retention times for MBR.
mbr_peps	Sequences of peptides for MBR.
dat_dir	The working data directory.
mbr_ret_tol	The tolerance in MBR retention time in seconds.
min_y	The cut-off of intensity values in MBR. Change to a smaller value with PASEF.
max_mbr_fold	The maximum absolute fold change in MBR.
step	The mass error in ppm / 1e6.
gap	A gap in retention-time window in seconds for finding gates in the Y values of LC. The gap value need to be broad enough.

qzhang503/proteoQ documentation built on Dec. 14, 2024, 12:27 p.m.