findMAIN {InterpretMSSpectrum}

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
)

## S3 method for class 'findMAIN'
plot(x, rank = 1, correct_mass = NULL, ...)

## S3 method for class 'findMAIN'
print(x, ...)

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.

x

Object of class findMAIN.

rank

Rank of the suggestion to plot (can be a numeric vector).

correct_mass

If provided will indicate correct suggestion by green color.

...

Further parameters.

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. Each list element represents a potential spectra annotation, ranked according to a combined score. The spectrum is annotated with columns indicating the determined isotopic groups (isogr) and their likely charge. Further, information on the potential set of adducts and their ppm error is attached. The score aims to integrate all this information using formula S=sum(w_i x s_i). In short, we sum up i weighted score components (currently i=4). Currently these components are calculated based on the explained intensity (adduct sets which annotate a higher amount of the total spectrum intensity are better), the mass error (adduct sets with lower mass error are better), the support by isotopic peaks (adduct sets with fitting isotopes are better) and the number of adducts (adduct sets with a larger number of adducts are better). The individual scores for each adduct set are attached as an attribute to the respective list element and can be easily observed by applying the 'summary' or the 'plot' function on the 'findMAIN' object.

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::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)
attr(fmr[[1]],"scores")
plot(fmr, rank = 1:4)
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+")