extentIdentifiedPrecursorIntensity: Extent of identified precursor intensity (QC:4000125)

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

Extent of identified precursor intensity (QC:4000125)

Description

"Ratio of 95th over 5th percentile of precursor intensity for identified peptides" [PSI:QC] id: QC:4000125

The metric is calculated as follows: (1) the 'Spectra' object is filtered according to the MS level,

(2) the intensities of the precursor ions are obtained,

(3) the 5% and 95% quantile of these intensities are obtained ('NA' values are removed),

(4) the ratio between the 95% and the 5% intensity quantile is calculated and returned.

Usage

extentIdentifiedPrecursorIntensity(spectra, msLevel = 1L, ...)

Arguments

spectra	'Spectra' object
msLevel	'integer'
...	not used here

Details

Can be used to approximate the dynamic range of signal is_a: QC:4000003 ! single value is_a: QC:4000009 ! ID based is_a: QC:4000001 ! QC metric

Precursor intensity values that are 'NA' are removed.

Value

'numeric(1)'

Note

The 'Spectra' object might contain features that were not identified. If the calculation needs to be done according to *QC:4000125*, the 'Spectra' object should be prepared accordingly, i.e. being subsetted to spectra with identification data.

Author(s)

Thomas Naake, [e-mail]

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, 100, 100)
sps <- Spectra(spd)
extentIdentifiedPrecursorIntensity(spectra = sps, msLevel = 2L)

tnaake/msQC documentation built on March 1, 2023, 8:11 p.m.