rtOverMSQuarters: MS1/MS2 quantiles RT fraction (QC:4000055/QC:4000056)

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

Description

"The interval used for acquisition of the first, second, third, and fourth quarter of all MS1 events divided by RT-Duration." [PSI:QC] id: QC:4000055

"The interval used for acquisition of the first, second, third, and fourth quarter of all MS2 events divided by RT-Duration." [PSI:QC] id: QC:4000056

The metric is calculated as follows: (1) the retention time duration of the whole 'Spectra' object is determined (taking into account all the MS levels),

(2) the 'Spectra' object is filtered according to the MS level and subsequently ordered according to the retention time

(3) the MS events are split into four (approximately) equal parts,

(4) the relative retention time is calculated (using the retention time duration from (1) and taking into account the minimum retention time),

(5) the relative retention time values associated to the MS event parts are returned.

Usage

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

Arguments

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

Details

is_a: QC:4000004 ! n-tuple is_a: QC:4000010 ! ID free is_a: QC:4000021 ! retention time metric is_a: QC:4000023 ! MS1 metric

Value

'numeric(4)'

Note

'rtDuration' considers the total runtime (including MS1 and MS2 scans).

Author(s)

Thomas Naake, [e-mail], Johannes Rainer

Examples

library(S4Vectors)
library(Spectra)

spd <- DataFrame(
    msLevel = c(2L, 2L, 2L, 2L),
    polarity = c(1L, 1L, 1L, 1L),
    id = c("HMDB0000001", "HMDB0000001", "HMDB0001847", "unknown"),
    name = c("1-Methylhistidine", "1-Methylhistidine", "Caffeine", "unknown"))
## Assign m/z and intensity values
spd$mz <- list(
    c(109.2, 124.2, 124.5, 170.16, 170.52),
    c(83.1, 96.12, 97.14, 109.14, 124.08, 125.1, 170.16),
    c(56.0494, 69.0447, 83.0603, 109.0395, 110.0712,
        111.0551, 123.0429, 138.0662, 195.0876),
    c(83.0603, 195.0876))
spd$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),
    c(3.146, 61.611))
spd$rtime <- c(9.44, 9.44, 15.84, 15.81)
sps <- Spectra(spd)
rtOverMsQuarters(spectra = sps, msLevel = 2L)

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