findmass: findmass

In RAMClustR: Mass Spectrometry Metabolomics Feature Clustering and Interpretation

findmass

Description

see if any features match a given mass, and whether they are plausibly M0

Usage

findmass(
  ramclustObj = NULL,
  mz = NULL,
  mztol = 0.02,
  rttol = 2,
  zmax = 6,
  m.check = TRUE
)

Arguments

ramclustObj	R object: the ramclustR object to explore
mz	numeric: mz value to search for
mztol	numeric: absolute mass tolerance around mz
rttol	numeric: when examining isotope patterns, feature retention time tolerance around features matching mz +- mztol
zmax	integer: maximum charge state to consider. default is 6.
m.check	logical: check whether the matching masses are plausibly M0. That is, we look for ions 1 proton mass (from charge state 1:zmax) below the target m/z at the same time that have intensities consistent with target ion being a non-M0 isotope.

Details

a convenience function to perform a targeted search of all feaures for a mass of interest. Also performs a crude plausibility check as to whether the matched feature could be M0, based on the assumption of approximately 1 carbon per 17 m/z units and natural isotopic abundance of 1.1

Value

returns a table to the console listing masses which match, their retention time and intensity, and whether it appears to be plausible as M0

Author(s)

Corey Broeckling

RAMClustR documentation built on Oct. 20, 2023, 5:08 p.m.