medianPrecursorMZ: Precursor median m/z for IDs (QC:4000065)

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

Description

"Median m/z value for all identified peptides (unique ions) after FDR." [PSI:QC] id: QC:4000065

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

(2) the precursor m/z values are obtained,

(3) the median value is returned ('NAs' are removed).

Usage

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

Arguments

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

Details

is_a: QC:4000003 ! single value is_a: QC:4000009 ! ID based is_a: QC:4000023 ! MS1 metric is_a: QC:4000025 ! ion source metric

Value

'numeric(1)'

Note

'medianPrecursorMz' will calculate the *precursor* median m/z of all Spectra within 'spectra'. If the calculation needs be done according to *QC:4000065*, the 'Spectra' object should be prepared accordingly, i.e. filtered with e.g. [filterPrecursorMz()] or 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$precursorMz <- c(170.16, 170.16, 195.0876)
sps <- Spectra(spd)
medianPrecursorMz(spectra = sps, msLevel = 2L)

tnaake/MsQuality documentation built on Jan. 14, 2022, 7:34 p.m.