msSignal10xChange: MS1 signal jump (10x) count (MS:4000097) or MS1 signal fall...

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

MS1 signal jump (10x) count (MS:4000097) or MS1 signal fall (10x) count (MS:4000098)

Description

MS:4000097
"The number of times where MS1 TIC increased more than 10-fold between adjacent MS1 scans. An unusual high count of signal jumps or falls can indicate ESI stability issues." [PSI:MS]

MS:4000098
"The number of times where MS1 TIC decreased more than 10-fold between adjacent MS1 scans. An unusual high count of signal jumps or falls can indicate ESI stability issues." [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 intensity values of the features are obtained via the ion count,
(4) the signal jumps/declines of the intensity values with the two subsequent intensity values is calculated,
(5) in the case of *MS:4000097*, the signal jumps by a factor of ten or more are counted and returned;
in the case of *MS:4000098*, the signal declines by a factor of ten or more are counted and returned.

Usage

msSignal10xChange(spectra, change = "jump", msLevel = 1L, ...)

Arguments

spectra	Spectra object
change	character(1), one of "jump" or "fall"
msLevel	integer
...	not used here

Details

MS:4000097
is_a: MS:4000003 ! single value
relationship: has_metric_category MS:4000009 ! ID free metric
relationship: has_metric_category MS:4000021 ! MS1 metric
relationship: has_units UO:0000189 ! count unit
relationship: has_value_type xsd:integer ! The allowed value-type for this CV term
synonym: "IS-1A" RELATED []

MS:4000098
is_a: MS:4000003 ! single value
relationship: has_metric_category MS:4000009 ! ID free metric
relationship: has_metric_category MS:4000021 ! MS1 metric
relationship: has_units UO:0000189 ! count unit
relationship: has_value_type xsd:integer ! The allowed value-type for this CV term
synonym: "IS-1B" RELATED []

The function msSignal10xChange uses the function ionCount as an equivalent to the TIC.

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

Value

numeric(1)

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$rtime <- c(9.44, 9.44, 15.84)
sps <- Spectra(spd)
msSignal10xChange(spectra = sps, change = "jump", msLevel = 2L)
msSignal10xChange(spectra = sps, change = "fall", msLevel = 2L)

tnaake/msQC documentation built on Feb. 25, 2024, 7:33 p.m.