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fgcz / rawrr

Access Orbitrap data in R lang using C# mono assembly - bioconductor package
https://bioconductor.org/packages/rawrr/
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Read noise value for profile mode mass spectra #56

Closed Taoq888 closed 1 year ago

Taoq888 commented 2 years ago

First the rawrr package is so amazing, which will greatly facilitate my data analysis. I have now realized that I cannot extract the Resolution R, noise, and charge z values from my own data. At the begining, I thought it could be that our instrument is LTQ Orbitrap Velos, which is slightly different with the one QE in the paper. While, I found the noise can be read when a centroid mass spectrum as an input. So seems it can't access to the noise values in the profile mode mass data. I am wondering if it is possible to obtain these values, as this information is present in the raw data.

image for the centriod mass spectrum

image for the profile mass spectrum

same mass spectrometer is used to obtain these data. (LTQ Orbitrap velos)

Thank you very much!

tobiasko commented 2 years ago

Hi @Taoq888,

that is true. For reduced profile mode (FTMS + p) the noise values are written to a different slot (stream). But @cpanse recently made some changes to our code so these can also be accessed. But these changes haven't made it to a stable package release yet.

tobiasko commented 2 years ago

Please try this one here: https://github.com/fgcz/rawrr/issues/37#issuecomment-1241155140

cpanse commented 2 years ago

or install via install.packages("https://fgcz-ms.uzh.ch/~cpanse/rawrr/rawrr_1.5.3.tar.gz", repo = NULL)

Taoq888 commented 2 years ago

or install via `install.packages("https://fgcz-ms.uzh.ch/~cpanse/rawrr/rawrr_1.5.3.tar.gz", repo = NULL)

Thank you for your reply. Yes, I have tried this verison, and I still can not get the noise information. It is still cool to direct read intensity data using this amazing package. Thank you very much!!