Add Signal to Noise data to ReadScan about rawdiag HOT 6 CLOSED

Hi David,

to my knowledge S/N is not something that gets written into the raw file, but is rather estimated for each peak by an offline algorithm that examines the local surrounding. Where does your info come from that it is written into the file?

Best,
Tobi

from rawdiag.

Thanks for the reply, Tobi!

You are correct. We need the noise or background information stored for each peak.

from rawdiag.

Hello Tobi,

It seems I may have been unclear. We would still like to add signal/background information to the object returned by ReadScans. We believe this value is stored in one of the ThermoFisher DLLs, likely ThermoFisher.CommonCore.RawFileReader.dll. Here's a reference: https://github.com/PNNL-Comp-Mass-Spec/Thermo-Raw-File-Reader/blob/master/XRawFileIO.cs#L2508

Thank you!

from rawdiag.

Hi David,

in general DLLs do not store any values:

https://support.microsoft.com/en-us/help/815065/what-is-a-dll

In short, DLLs are code modules. The code line you linked above:

var data = mXRawFile.GetCentroidStream(scan, false);

references the method GetCentroidStream and to my knowledge it returns a set of position and intensity values in array format. Position is equivalent to m/z and intensity is the abs. abundance aka the signal. Noise is not stored in a raw file can can be estimated by analysing the local/global environment of any signal.

@cpanse Is this correct?

Best,
Tobi

from rawdiag.

btw: I guess the only person that really KNOWs what is inside raw files is [email protected]
I could also be that the .NET assemblies do not make it accessible. :-(

from rawdiag.

Hello Tobi,

The GetCentroidStream returns an array of position, intensity, resolutions, baselines, noises, and charges. We would like the noises added to ReadScans. https://github.com/PNNL-Comp-Mass-Spec/Thermo-Raw-File-Reader/blob/master/XRawFileIO.cs#L2520

Thank you!

-David

from rawdiag.