ticQuantileRtFraction: TIC quantile RT fraction (MS:4000183)

In tnaake/msQC: MsQuality - Quality metric calculation from Spectra and MsExperiment objects

TIC quantile RT fraction (MS:4000183)

Description

MS:4000183 "The interval when the respective quantile of the TIC accumulates divided by retention time duration. The number of values in the tuple implies the quantile mode." [PSI:MS]

The metric informs about the dynamic range of the acquisition along the chromatographic separation. The metric provides information on the sample (compound) flow along the chromatographic run, potentially revealing poor chromatographic performance, such as the absence of a signal for a significant portion of the run.

The metric is calculated as follows:
(1) the Spectra object is ordered according to the retention time,
(2) the cumulative sum of the ion count is calculated (TIC),
(3) the quantiles are calculated according to the probs argument, e.g. when probs is set to c(0, 0.25, 0.5, 0.75, 1) the 0%, 25%, 50%, 75%, and 100% quantile is calculated,
(4) the retention time/relative retention time (retention time divided by the total run time taking into account the minimum retention time) is calculated,
(5) the (relative) duration of the LC run after which the cumulative TIC exceeds (for the first time) the respective quantile of the cumulative TIC is calculated and returned.

Usage

ticQuantileRtFraction(
  spectra,
  probs = seq(0, 1, 0.25),
  msLevel = 1L,
  relative = TRUE,
  ...
)

Arguments

spectra	Spectra object
probs	numeric defining the quantiles. See probs = seq(0, 1, 0.25).
msLevel	integer
relative	logical, if set to TRUE the relative retention time will be returned instead of the abolute retention time
...	not used here

Details

MS:4000183 synonym: "RT-TIC-Q1" RELATED [PMID:24494671]
synonym: "RT-TIC-Q2" RELATED [PMID:24494671]
synonym: "RT-TIC-Q3" RELATED [PMID:24494671]
synonym: "RT-TIC-Q4" RELATED [PMID:24494671]
is_a: MS:4000004 ! n-tuple
relationship: has_metric_category MS:4000009 ! ID free metric
relationship: has_metric_category MS:4000012 ! single run based metric
relationship: has_metric_category MS:4000016 ! retention time metric
relationship: has_metric_category MS:4000017 ! chromatogram metric
relationship: has_units UO:0000191 ! fraction
relationship: has_value_concept STATO:0000291
relationship: has_value_type xsd:float
#'

Value

numeric of length equal to length probs with the relative duration (duration divided by the total run time) after which the TIC exceeds the respective quantile of the TIC.

Author(s)

Thomas Naake, Johannes Rainer

Examples

library(S4Vectors)
library(Spectra)

spd <- DataFrame(
    msLevel = c(2L, 2L, 2L),
    polarity = c(1L, 1L, 1L),
    id = c("HMDB0000001", "HMDB0000001", "HMDB0001847"),
    name = c("1-Methylhistidine", "1-Methylhistidine", "Caffeine"))
## Assign m/z and intensity values
spd$mz <- list(
    c(109.2, 124.2, 124.5, 170.16, 170.52),
    c(83.1, 96.12, 97.14, 109.14, 124.08, 125.1, 170.16),
    c(56.0494, 69.0447, 83.0603, 109.0395, 110.0712,
        111.0551, 123.0429, 138.0662, 195.0876))
spd$intensity <- list(
    c(3.407, 47.494, 3.094, 100.0, 13.240),
    c(6.685, 4.381, 3.022, 16.708, 100.0, 4.565, 40.643),
    c(0.459, 2.585, 2.446, 0.508, 8.968, 0.524, 0.974, 100.0, 40.994))
spd$rtime <- c(9.44, 9.44, 15.84)
sps <- Spectra(spd)
ticQuantileRtFraction(spectra = sps, msLevel = 2L)

tnaake/msQC documentation built on Jan. 30, 2025, 5:25 a.m.