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How to access S/N values #46

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papanlipotype opened this issue Jan 17, 2022 · 5 comments
Open

How to access S/N values #46

papanlipotype opened this issue Jan 17, 2022 · 5 comments
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@cpanse
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enhancement New feature or request

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@papanlipotype
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Dear all,
is there a way of accessing the S/N values from a readSpectrum-Object? I cant seem to find the info in the list.
Thanks
@tobiasko
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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

@papanlipotype
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papanlipotype commented Feb 14, 2022 via email

@tobiasko
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tobiasko commented Feb 14, 2022 •
edited

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

@papanlipotype
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papanlipotype commented Feb 14, 2022 via email

@tobiasko tobiasko added the enhancement New feature or request label Feb 17, 2022
@tobiasko
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tobiasko commented Feb 17, 2022 •
edited

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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@cpanse @tobiasko @papanlipotype