View source: R/function_Spectra_metrics.R
ratioCharge3over2 | R Documentation |
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.
ratioCharge3over2(
spectra,
msLevel = 1L,
identificationLevel = c("all", "identified", "unidentified"),
...
)
spectra |
|
msLevel |
|
identificationLevel |
|
... |
not used here |
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"
.
numeric(1)
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.
Thomas Naake
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)
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