ratioCharge3over2: Charged peptides ratio 3+ over 2+ (QC:4000175) or charged...

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

Charged peptides ratio 3+ over 2+ (QC:4000175) or charged spectra ratio 3+ over 2+ (QC:4000180)

Description

"Ratio of 3+ peptide count over 2+ peptide count in identified spectra" [PSI:QC] id: QC:4000175

"Ratio of 3+ peptide count over 2+ peptide count in all MS2" [PSI:QC] id: QC:4000180

The metric is calculated as follows: (1) the 'Spectra' object is filtered according to the MS level,

(2) the precursor charge is obtained,

(3) the number of precursors with charge 3+ is divided by the number of precursors with charge 2+ and the ratio is returned.

Usage

ratioCharge3over2(spectra, msLevel = 1L, ...)

Arguments

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

Details

is_a: QC:4000003 ! single value is_a: QC:4000009 ! ID based is_a: QC:4000001 ! QC metric

'NA' is returned if there are no features with precursor charge of 2+ or 3+.

Value

'numeric(1)'

Note

The 'Spectra' object might contain features that were not identified. If the calculation needs to be done according to *QC:4000175*, the 'Spectra' object should be prepared accordingly.

Author(s)

Thomas Naake, [e-mail]

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$precursorCharge <- c(1L, 1L, 1L)
sps <- Spectra(spd)
ratioCharge3over2(spectra = sps, msLevel = 2L)

tnaake/msQC documentation built on March 1, 2023, 8:11 p.m.