InterpretMSSpectrum

Interpreting High Resolution Mass Spectra


License
GPL-3.0

Documentation

InterpretMSSpectrum

CRAN status R-CMD-check codecov

The goal of InterpretMSSpectrum is to provides a set of R functions to annotate mass spectra from Electrospray-Ionization and Atmospheric-Pressure-Chemical-Ionization derived data in positive and negative ionization mode.

Installation

You can install the CRAN or the development version of InterpretMSSpectrum from GitHub with:

# install the CRAN version als usual
install.packages("InterpretMSSpectrum")

# devtools is required to install from GitHub
# install.packages("devtools")
devtools::install_github("janlisec/InterpretMSSpectrum")

Example

In the simplest case InterpretMSSpectrum will provide an informed guess for the potential sum formula of an arbitrary mass spectrum.

library(InterpretMSSpectrum)

# load APCI test data
apci_spectrum <- InterpretMSSpectrum::apci_spectrum

# find the most probable sum formula for the spectrum
# (will print to the console and open a new plot)
InterpretMSSpectrum(spec=apci_spectrum)

The function can be tweaked with numerous parameters to limit the results, speed up calculations and more.

The other high level function of the package allows to predict the precursor of ESI spectra.

# load ESI test data
esi_spectrum <- InterpretMSSpectrum::esi_spectrum

# find the most likely precursor for the spectrum
(fmr <- findMAIN(spec=esi_spectrum))
plot(fmr)

Also in findMAIN multiple user options exist to provide individual adduct lists, thresholds and rule sets.

Finally, InterpretMSSpectrum provides a number of helper functions.

# CountChemicalElements
CountChemicalElements(x = "C6H12O6")
sapply(c("C6H12O6", "CH3"), CountChemicalElements, ele=c("C","H","O"))

# get_exactmass
get_exactmass(c("C6H12O6", "Na", "H1"))

# is.subformula
# findiso
# GetIsotopeDistribution
# GetGroupFactor
# PlausibleFormula

Detailed documentation

You might read the publications on either APCI spectra processing which explains the idea of using the in source fragments for prediction of potential sum formulas or on ESI spectra processing which explains the strategy to infer the correct precursor of ESI mass spectra.