Comments (5)
Dear @papanlipotype,
the S/N values are never stored in the raw file. They need to be calculated. This is for instance done by the plot
method for rawrrSpectrum
objects in case SN = TRUE
:
plot.rawrrSpectrum <- function(x, relative = TRUE, centroid = FALSE, SN = FALSE,
legend = TRUE, diagnostic = FALSE, ...){
stopifnot(is.rawrrSpectrum(x))
if (centroid) {
stopifnot(x$centroidStream)
if (SN) {
plot(x = x$centroid.mZ, y = x$centroid.intensity/x$noise,
type = "h",
xlim = x$massRange,
xlab = "Centroid m/z",
ylab = "Centroid Signal/Noise",
frame.plot = FALSE, ...
)
Currently the plot function only supports this for centroided data, although it has meanwhile become clear that the noise attribute is also available for (reduced) profile mode data.
But you could easily write a function that combines data retrieval and S/N calculation.
Hope this helps,
Tobi
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Apparently reduced profile mode is what the Q Exactive series uses when you select profile mode in the instrument method. see #37. I also thought that full profile mode would be triggered by selecting profile mode acquisition, but that doesn't seem to be the case.
I had a look at recent data from our Q Exactive for a "FTMS + p NSI Full ms [350.0000-1500.0000]" scan. rawrr
just gives access to the intensity and m/z values (no noise attributes). But I guess the noise was written to the raw file. Most likely to a different data stream that our managed code currently ignores (again, have a look at issue #37).
@cpanse We should really push the code changes to make this stream available!
btw: I already filed a GitHub project for this: Support for reduced profile mode spectra
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ok. We will try to do our best to make this happen in the near future, since quite some people requested this already!
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Related Issues (20)
- Get information on gradient HOT 1
- Enhancement - Complete readIndex() function HOT 9
- Peak charges for MS1 spectras HOT 4
- Spectrum scan centroid mZ, intensity and noises values do not match HOT 2
- Error in Example: Length of "x" and "y" are not matching HOT 3
- Read noise value for profile mode mass spectra HOT 4
- Read_Spectrum - Sum Spectra
- unit should be minute / auc computation in seconds HOT 24
- validate_rawrrSpectrum 'StartTime' HOT 4
- "Error: line 1 did not have 9 elements" for readIndex() and readChromatogram() + "Error : No scan vector is provided"for readSpectrum HOT 9
- Problem executing readChromatogram inside Singularity container HOT 5
- Add a check if `input` file exists and is not empty
- Error in if (rvs != "No RAW file specified!") { : the condition has length > 1 HOT 16
- Switch to RawFileReader 5.0.93 HOT 2
- different total number of Spectra in msconvert, compomics/ThermoRawFileParser and thermofisherlsms/RawFileReader HOT 2
- Request for auc.rawrrChromatogram HOT 3
- profile mode in readSpectrum HOT 11
- speed up readIndex/readSpectrum by base::textConnection HOT 14
- rawrr::buildRawrrExe() fails HOT 6
- auc.rawrrChromatogram question
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