prepare_peaks: Prepare list of peaks data into a data.frame

In ismaRP/MALDIpqi: Estimate Parchment Glutamine Index from MALDI-TOF datasets

Prepare list of peaks data into a data.frame

Description

Prepare list of peaks data into a data.frame

Usage

prepare_peaks(
  peaks,
  peptides_user,
  n_isopeaks,
  int_column = "intensity",
  q2e = NULL
)

Arguments

peaks	List of peaks matrix. Names are used as spectra name
peptides_user	A dataframe with peptide information. It must contain at least 3 columns, pep_number or ID, mass, sequence and h_hyp (# of hydroxyprolines). IF NULL, default are used, see details.
n_isopeaks	Number of isotopic peaks
q2e	Optional q2e value to calculate the theoretical distribution of a peptide with this extent of deamidation

Details

The default peptides are the ones from Nair et al. (2022). The paper contains the details on the preprocessing procedure.

Value

A data.frame with isotopic peaks detected from data, theoretical isotopic envelopes for 1 and 2 deamidations and other associated data.

ismaRP/MALDIpqi documentation built on Dec. 28, 2024, 1:08 p.m.