CorMID {CorMID}

CorMID.

Description

CorMID will compute a MID (Mass Isotopomer Distribution) based on measured ion intensities in GC-APCI-MS.

Usage

CorMID(
  int = NULL,
  fml = "",
  r = NULL,
  penalize = 7,
  mid_fix = NULL,
  trace_steps = FALSE,
  prec = 0.01
)

## S3 method for class 'CorMID'
plot(x, ...)

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

Arguments

int

Named numeric vector of measured ion intensities of a fragment. Names will give position of values relative to M+H (see details).

fml

Chemical formula of the fragment as string.

r

Either a character vector giving fragments to be considered OR a named numeric giving relative amounts of fragments OR NULL (all known fragments will be estimated) OR a 2-row matrix giving the lower and upper allowed ratio (see examples).

penalize

Numeric exponent penalizing solutions with low M+H occurrence. Formula is 1+3*(1-x)^penalty. NA to omit penalizing.

mid_fix

May provide a numeric vector used as a given MID. Allows to estimate r individually.

trace_steps

For testing purposes. Print the results of intermediate steps to console.

prec

Precision of the estimation of MID, set to 1% as default.

x

Object of class CorMID.

...

Further plotting parameters.

Details

Let's assume we measured the ion intensities of all 3 isotopes of an individual compound containing 2 carbons and observe a vector of 978,22,0. We may calculate the enrichment E out of this data, i.e. the relative proportion of 13C vs total carbon which will amount to about 1.1% (the natural 13C abundance) under standard conditions. The equivalent corMID vector would be 1,0,0, indicating that the non-labeled isotopologue (where non-labeled means non-labeled above the natural 1.1%) is the only component observed. During a labeling experiment we may change the measurement values in different ways (either labeling only one carbon or both), which potentially can translate into similar values for E being larger 1.1%. The MIDs will provide additional information about the isotopologue fraction which gave rise to the observed E's (cf. examples). The r parameter indicates an overlay of chemical rearrangements which may occur.

Value

Estimated percent representation of each isotopologue measured (corMID).

References

<doi:10.3390/metabo12050408>

Examples

# make up some fake measurement data for Pyruvic acid 2TMS with 3 biological carbon
# assuming 10% labeling at M3 and 2 fragments
fml <- "C9H20O3Si2"
mid <- c(0.9,0,0,0.1)
r <- unlist(list("M+H"=0.8, "M+H2O-CH4"=0.2))
int <- CorMID::recMID(mid=mid, r=r, fml=fml)
plot(int)

# full estimation of M and r
out <- CorMID::CorMID(int=int, fml=fml)
plot(out)

# get an improved result setting r to the correct values
CorMID::CorMID(int=int, fml=fml, r=r, prec=0.0001)

# provoke a wrong estimation using a fixed r
CorMID::CorMID(int=int, fml=fml, r=unlist(list("M+H"=1)))

# calculate r if you know the true corMID for a compound
r <- attr(CorMID::CorMID(int=int, fml=fml, mid_fix=c(0.9,0,0,0.1)), "ratio")
round(CorMID::CorMID(int=int, fml=fml, r=r, prec=0.0001),3)

# deal with missing intensity values
CorMID::CorMID(int=int[-3], fml=fml)


# perform estimation with banded r and observation of optimization steps
r <- matrix(c(0.5,1,0,0.5,0,0.5), nrow=2, dimnames=list(NULL,c("M+H","M+","M+H2O-CH4")))
CorMID::CorMID(int=int, fml=fml, r=r, trace=TRUE)

#process Gln data from publication
utils::data("prep", package = "CorMID")
int <- prep[[24]][["int"]][,6]
fml <- prep[[24]]$fml
CorMID::CorMID(int=int, fml=fml, trace=TRUE)

# check the effect of the penalize parameter on selection of adducts
int <- c(1560, 119203, 41927, 16932, 4438)
names(int) <- c(-2, 0, 1, 2, 3)
fml <- "C19H37NO4Si3"
CorMID::CorMID(int=int, fml=fml, r=NULL, trace=TRUE)
CorMID::CorMID(int=int, fml=fml, r=NULL, trace=TRUE, penalize=7)