Export other detectors data from raw file

[Adafede]

Hi, since you were so amazingly reactive with solutions last time, I'll give it a try:

Could you find a way to also export other types of data from the .raw? (UV, Light Scattering, CAD, ...)

For UV (2D data), the export in .netCDF from Waters works fine, for 1D data like Corona CAD and so on, maybe an additional CSV would be great.

Thanks and good evening

[caetera]

@nielshulstaert @ypriverol do you think this feature mounts naturally to batch XIC extraction?

[nielshulstaert]

Hi could you give some output examples for the 2D and the 1D data?

[Adafede]

@nielshulstaert

Hi,

Thank you for your answer. I have no real example since what I'm asking for currently does not exist, if I'm not mistaking.
Actually, what I'm doing is opening the .raw file, where all 3 signals (MS, UV, CAD) are encoded. I can visualize the traces in Xcalibur or other Thermo softwares and export them as .csv.
To work with other softwares, I need to convert the files in .mz(X)mL. But when doing it of course, I loose the UV and CAD signal.
I know there is an existing solution for UV with Databridge (from Waters), since it is 2D data ( intensity, wavelength), like MS( intensity, m/z). They convert it to .CDF instead and you can then load your UV signal. For CAD, I have no idea, that is why I am asking you.

[Adafede]

Is there so any answer?

In other words, for 1D Data, you simply got an intensity at a given retention time. ( X = ret tim, Y = Int). It is the case for some detectors which signal is encoded in the raw file...
For 2D data like UV or MS (that your converter mainly converts), you got 3 dimensions: intensity, retention time and m/z or the wavelength, so you get X,Y,Z points and not X,Y only. I'm interested in extracting not only the MS signal but also the other ones from the .raw file. Waters Databridge does it for UV signal in netCDF as example. Since you got the metadata option I think you could maybe write it there...

[edeutsch]

Note that mzML has a section of the schema specifically designed to hold this kind of data.

[caetera]

Hi @Adafede I will try to find time soon to implement it. Is it important to have it as netCDF?

@edeutsch am I correct that this kind of data belongs to <chromatogramList> ?

[Adafede]

Hi @caetera , thank you very much for your prompt response! It would really be an enormous plus. No, it absolutely doesn’t need to be netCDF, or even more: please don’t make it netCDF mzML is Perfect. I was just mentioning it because it is the only actual solution I know

[edeutsch]

Correct, <chromatogramList> is for any intensity vs. time series data such as UV. I think msconvert will already export UV data to <chromatogramList>, although I am not certain.

[caetera]

@Adafede ok. That will be mzML then. One more thing. I do not have any raw files with UV data, could you share some? You can use this link if necessary to upload large files: https://filesender.deic.dk/?s=upload&vid=4ffb472c-ff60-3499-58fa-0887a714f989

[Adafede]

@caetera Thank you very much!

I did send 5 files to your link. ( https://filesender.deic.dk/?s=download&token=489ce23a-d71c-319f-c438-6897b0f2f652)

1. 2 files with MS DDA (2D) and UV (2D) signals
2. 1 file with MS vDIA (2D) and UV (2D) signals
3. 2 files with MS DDA (2D), UV (2D) and CAD (1D) signals

@edeutsch Thank you also very much for your help!

Just to try clarifying once again: our UV data has same dimensionality as MS because it is PhotoDiodeArray data. So you have not intensity vs time only but also wavelength (like m/z in MS)

CAD is only time vs intensity. I don't know how it appears in the RAW...

[edeutsch]

Ah, I see, I misunderstood, I thought it was 1D data. If it's 2D, then I assume the usual part of the schema should be used? Maybe try running these files through msconvert to see what it does with the UV data if anything? or see if Matt Chambers has a comment on how msconvert handles this?

[edeutsch]

I don't know what the current status is, but this thread seems to imply that the latest msconvert code will convert UV and CAD data to mzML:

https://sourceforge.net/p/proteowizard/mailman/message/36687814/

[chambm]

MSconvert will convert PDA spectra (from PDA detector as shown by qualbrowser) as mzml spectra (wavelength is the x axis) and UV traces (from UV detector) as mzml chromatograms. Other detectors like A/d card are if ignored iirc.