findMAIN: findMAIN.

In InterpretMSSpectrum: Interpreting High Resolution Mass Spectra

findMAIN.

Description

findMAIN will evaluate an ESI spectrum for the potential main adducts, rank obtained suggestions and allow the deduction of the neutral mass of the measured molecule.

Usage

findMAIN(
  spec,
  adductmz = NULL,
  ionmode = c("positive", "negative")[1],
  adducthyp = NULL,
  ms2spec = NULL,
  rules = NULL,
  mzabs = 0.01,
  ppm = 5,
  mainpkthr = 0.005,
  collapseResults = TRUE
)

Arguments

spec	A mass spectrum. Either a matrix or data frame, the first two columns of which are assumed to contain the 'mz' and 'intensity' values, respectively.
adductmz	Manually specified peak for which adducthyp should be tested, or 'NULL' (default), to test all main peaks. What is a main peak, is governed by mainpkthr.
ionmode	Ionization mode, either "positive" or "negative". Can be abbreviated.
adducthyp	Adduct hypotheses to test for each main peak. Defaults to c("[M+H]+","[M+Na]+","[M+K]+") for positive mode and c("[M-H]-","[M+Cl]-","[M+HCOOH-H]-") for negative mode.
ms2spec	Second spectrum limiting main peak selection. If available, MS^E or bbCID spectra may allow further exclusion of false positive adduct ions, as ions of the intact molecule (protonated molecule, adduct ions) should have lower intensity in the high-energy trace than in low-energy trace.
rules	Adduct/fragment relationships to test, e.g. c("[M+Na]+", "[M+H-H2O]+"), or 'NULL' for default set (see Adducts)
mzabs	Allowed mass error, absolute (Da).
ppm	Allowed mass error, relative (ppm), which is _added_ to 'mzabs'.
mainpkthr	Intensity threshold for main peak selection, relative to base peak.
collapseResults	If a neutral mass hypothesis was found more than once (due to multiple adducts suggesting the same neutral mass), return only the one with the highest adduct peak. Should normally kept at TRUE, the default.

Details

Electrospray ionization (ESI) mass spectra frequently contain a number of different adduct ions, multimers and in-source fragments [M+H]+, [M+Na]+, [2M+H]+, [M+H-H2O]+, making it difficult to decide on the compound's neutral mass. This functions aims at determining the main adduct ion and its type (protonated, sodiated etc.) of a spectrum, allowing subsequent database searches e.g. using MS-FINDER, SIRIUS or similar.

Value

A list-like 'findMAIN' object for which 'print', 'summary' and 'plot' methods are available.

References

Jaeger C, Meret M, Schmitt CA, Lisec J (2017), <doi:10.1002/rcm.7905>.

Examples

utils::data(esi_spectrum, package = "InterpretMSSpectrum")
fmr <- InterpretMSSpectrum::findMAIN(esi_spectrum)
plot(fmr)
head(summary(fmr))
InterpretMSSpectrum(fmr[[1]], precursor=263, param="ESIpos")
fmr <- InterpretMSSpectrum::findMAIN(esi_spectrum[6:9,], adducthyp = "[M+H]+")
plot(fmr)

# set up a spectrum containing a double charged peak
spec <- data.frame(mz = c(372.1894, 372.6907, 373.1931, 380), int = c(100, 40, 8, 2))
InterpretMSSpectrum:::findiso(spec)
# allow a double charged adduct hypothesis (not standard)
fmr <- InterpretMSSpectrum::findMAIN(spec, adducthyp = c("[M+H]+", "[M+2H]2+"))
summary(fmr)
plot(fmr, rank = 1)
plot(fmr, rank = 2)

# add the correct M+H to this spectrum as a minor peak
spec <- rbind(spec, c(742.3648+1.007, 10))
(fmr <- InterpretMSSpectrum::findMAIN(spec, adducthyp = c("[M+H]+", "[M+2H]2+")))
summary(fmr)
plot(fmr, rank = 1)
plot(fmr, rank = 2)

# compare specific hypotheses manually
# get correct result
InterpretMSSpectrum::findMAIN(spec, adductmz = 743.3718, adducthyp = "[M+H]+")
# enforce wrong result
InterpretMSSpectrum::findMAIN(spec, adductmz = 743.3718, adducthyp = "[M+2H]2+")

InterpretMSSpectrum documentation built on July 9, 2023, 5:58 p.m.