msSignal10XChange: MS1 signal jump/fall (10x) count (QC:4000172/QC:4000173)

Description Usage Arguments Details Value Author(s) Examples

Description

"The count of MS1 signal jump (spectra sum) by a factor of ten or more (10x) between two subsequent scans" [PSI:QC] id: QC:4000172

"The count of MS1 signal decline (spectra sum) by a factor of ten or more (10x) between two subsequent scans" [PSI:QC] id: QC:4000173

#' 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 'spectra' 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 *QC:4000172*, the signal jumps by a factor of ten or more are counted and returned; in the case of *QC:4000173*, the signal declines by a factor of ten or more are counted and returned.

Usage

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

Arguments

spectra

'Spectra' object

change

'character(1)', one of '"jump"' or '"fall"'

msLevel

'integer'

...

not used here

Details

is_a: QC:4000003 ! single value is_a: QC:4000010 ! ID free is_a: QC:4000001 ! QC metric

An unusual high count of signal jumps or falls can indicate ESI stability issues.

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

Value

'numeric(1)'

Author(s)

Thomas Naake, thomasnaake@googlemail.com

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
21
22
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/MsQuality documentation built on Jan. 14, 2022, 7:34 p.m.