precursorIntensityRange: MS2 precursor intensity range (MS:4000160)

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

MS2 precursor intensity range (MS:4000160)

Description

MS:4000160
"Minimum and maximum MS2 precursor intensity recorded. The intensity range of the precursors informs about the dynamic range of the acquisition." [PSI:MS]

The metric is calculated as follows:
(1) the Spectra object is filtered according to the MS level,
(2) the intensity of the precursor ions within the Spectra object are obtained,
(3) the minimum and maximum precursor intensity values are obtained and returned.

Usage

precursorIntensityRange(spectra, msLevel = 1, ...)

Arguments

spectra	Spectra object
msLevel	integer
...	not used here

Details

MS:4000160
is_a: MS:4000001 ! QC metric
is_a: MS:4000004 ! n-tuple
is_a: MS:4000009 ! ID free
relationship: has_metric_category MS:4000022 ! MS2 metric

Value

numeric(2)

Author(s)

Thomas Naake

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$precursorIntensity <- c(100.0, 100.0, 100.0)
sps <- Spectra(spd)
precursorIntensityRange(spectra = sps, msLevel = 2L)

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