numberSpectra: number of MS1 spectra (MS:4000059) or number of MS2 spectra...

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

number of MS1 spectra (MS:4000059) or number of MS2 spectra (MS:4000060)

Description

MS:4000059
"The number of MS1 events in the run." [PSI:MS]

MS:4000060
"The number of MS2 events in the run." [PSI:MS]

For *MS:4000059*, msLevel is set to 1. For *MS:4000060*, msLevel is set to 2.

The metric is calculated as follows:
(1) the Spectra object is filtered according to the MS level,
(2) the number of the spectra are obtained (length of Spectra) and returned.

Usage

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

Arguments

spectra	Spectra object
msLevel	integer
...	not used here

Details

MS:4000059
synonym: "MS1-Count" EXACT [PMID:24494671]
is_a: MS:4000003 ! single value
relationship: has_metric_category MS:4000009 ! ID free metric
relationship: has_metric_category MS:4000012 ! single run based metric
relationship: has_metric_category MS:4000021 ! MS1 metric
relationship: has_value_type xsd:int ! The allowed value-type for this CV term
relationship: has_units UO:0000189 ! count unit

MS:4000060
synonym: "MS2-Count" EXACT [PMID:24494671]
is_a: MS:4000003 ! single value
relationship: has_metric_category MS:4000009 ! ID free metric
relationship: has_metric_category MS:4000012 ! single run based metric
relationship: has_metric_category MS:4000022 ! MS2 metric
relationship: has_value_type xsd:int ! The allowed value-type for this CV term
relationship: has_units UO:0000189 ! count unit

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

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))
sps <- Spectra(spd)
numberSpectra(spectra = sps, msLevel = 1L)
numberSpectra(spectra = sps, msLevel = 2L)

tnaake/msQC documentation built on Jan. 30, 2025, 5:25 a.m.