ratioCharge3over2: ratio of 3+ over 2+ of all MS2 known precursor charges...

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

ratio of 3+ over 2+ of all MS2 known precursor charges (MS:4000169) or ratio of 3+ over 2+ of identified MS2 known precursor charges (MS:4000170)

Description

MS:4000169
"The ratio of 3+ over 2+ MS2 precursor charge count of all spectra. Higher ratios of 3+/2+ MS2 precursor charge count may preferentially favor longer e.g. peptides." [PSI:MS]

MS:4000170
"The ratio of 3+ over 2+ MS2 precursor charge count of identified spectra. Higher ratios of 3+/2+ MS2 precursor charge count may preferentially favor longer e.g. peptides. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability." [PSI:MS]

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,
  identificationLevel = c("all", "identified", "unidentified"),
  ...
)

Arguments

spectra	Spectra object
msLevel	integer
identificationLevel	character(1), one of "all", "identified", or "unidentified"
...	not used here

Details

MS:4000169
is_a: MS:4000001 ! QC metric
is_a: MS:4000003 ! single value
is_a: MS:4000009 ! ID free metric
relationship: has_metric_category MS:4000012 ! single run based metric
relationship: has_metric_category MS:4000020 ! ion source metric
relationship: has_metric_category MS:4000022 ! MS2 metric
synonym: "IS-3B" RELATED [PMID:19837981]
synonym: "MS2 known precursor charges fractions" RELATED []
synonym: "MS2-PrecZ-2" RELATED [PMID:24494671]
synonym: "MS2-PrecZ-3" RELATED [PMID:24494671]

MS:4000170
is_a: MS:4000001 ! QC metric
is_a: MS:4000003 ! single value
is_a: MS:4000008 ! ID based
relationship: has_metric_category MS:4000012 ! single run based metric
relationship: has_metric_category MS:4000020 ! ion source metric
relationship: has_metric_category MS:4000022 ! MS2 metric
synonym: "IS-3B" RELATED [PMID:19837981]
synonym: "MS2 known precursor charges fractions" RELATED []
synonym: "MS2-PrecZ-2" RELATED [PMID:24494671]
synonym: "MS2-PrecZ-3" RELATED [PMID:24494671]

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

An attribute containing the PSI:MS term will only be returned if identificationLevel is either "all" or "identified".

Value

numeric(1)

Note

The Spectra object might contain features that were not identified. If the calculation needs to be done according to *MS:4000170*, the Spectra object should be prepared accordingly.

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

tnaake/MsQuality documentation built on Oct. 31, 2024, 2:41 a.m.