rtOverMsQuarters: MS1 quarter RT fraction (MS:4000055) or MS2 quarter RT...

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

MS1 quarter RT fraction (MS:4000055) or MS2 quarter RT fraction (MS:4000056)

Description

MS:4000055
"The interval used for acquisition of the first, second, third, and fourth quarter of all MS1 events divided by retention time duration." [PSI:MS]

MS:4000056
"The interval used for acquisition of the first, second, third, and fourth quarter of all MS2 events divided by retention time duration." [PSI:MS]

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

MS:4000055
synonym: "RT-MS-Q1" RELATED [PMID:24494671]
synonym: "RT-MS-Q2" RELATED [PMID:24494671]
synonym: "RT-MS-Q3" RELATED [PMID:24494671]
synonym: "RT-MS-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:4000021 ! MS1 metric
relationship: has_value_type xsd:float ! The allowed value-type for this CV term
relationship: has_units UO:0000191 ! fraction

MS:4000056
synonym: "RT-MSMS-Q1" RELATED [PMID:24494671]
synonym: "RT-MSMS-Q2" RELATED [PMID:24494671]
synonym: "RT-MSMS-Q3" RELATED [PMID:24494671]
synonym: "RT-MSMS-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:4000022 ! MS2 metric
relationship: has_value_type xsd:float ! The allowed value-type for this CV term
relationship: has_units UO:0000191 ! fraction

The function returns c(NaN, NaN, NaN, NaN) if the filtered spectra object has less than 4 scan events.

An attribute containing the PSI:MS term will only be returned if msLevel is 1 or 2.

Value

numeric(4)

Note

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

Author(s)

Thomas Naake, 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 Oct. 31, 2024, 2:41 a.m.