CorMID: CorMID.

In CorMID: Correct Mass Isotopologue Distribution Vectors

CorMID.

Description

CorMID will compute a MID (Mass Isotopologues 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,
  algo = c("CorMID", "Rdisop")
)

## 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. Set to 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.
algo	The algorithm used to estimate the isotopic distribution of a chemical formula.
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)
out
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)

CorMID documentation built on Oct. 2, 2024, 5:06 p.m.