Re: [proteowizard-support] No chromatograms from other detectors, Thermo RAW data

[Chambers, M. <mat...@gm...>]

Huh, that's strange. If you're seeing PDA spectra, there should definitely be a PDA (absorption) chromatogram. Are you sure the mzML was 
getting converted by the 19156 version? Maybe some other version was in your path? I'll need to see the RAW file to understand how to 
convert the CAD data. I added checks for the UV channel to only conditionally produce those chromatograms because I noticed a lot of RAW 
files have LC traces in that controller (e.g. pump pressure). But the PDA channel has no such checks.

On 6/6/2019 8:35 AM, Winget, Jason wrote:
>
> Hi Matt, Wow that was a quick response!
>
> I’ve tried the newest build (ProteoWizard 3.0.19156.f8f43942e 64-bit) and still only see 1 chromatogram as far as I can tell.
>
> The mzML shows:
>
> <chromatogramList count="1" defaultDataProcessingRef="pwiz_Reader_Thermo_conversion">
>
> and there appears to only be a TIC chromatogram in that block.
>
> I can plot that chromatogram using mzR and I see what appears to be two lines, but I haven’t been able to separate them from one another. 
> I /think/ this might just be showing MS1 and MS2 TIC, not the other detectors.
>
> I tried building pwiz directly from the GitHub repo in case the windows installer was lagging behind but the build was failing and I 
> haven’t been able to get it to succeed on my machine yet.
>
> I believe that the individual UV scans are actually included in the mzML, because I see some <spectrum> blocks about half way through the 
> file that have wavelength arrays in the binaryDataArray.
>
> CAD stands for “Charged Aerosol Detector”. When viewing my data in Qual Browser, the CAD shows up under the “UV” detector and the UV data 
> shows up under “PDA”. Clear as mud 😉
>
> Thanks again for your help.
>
> Jason
>
> *From:*Chambers, Matthew <mat...@gm...>
> *Sent:* Wednesday, June 5, 2019 10:02 AM
> *To:* Winget, Jason <win...@pg...>; pro...@li...
> *Subject:* Re: [proteowizard-support] No chromatograms from other detectors, Thermo RAW data
>
> Hi Jason,
>
> I committed a fix for this yesterday. Download the latest version and try again. It should work for UV and PDA. What is CAD?
>
> Thanks for the report,
> -Matt
>
> On 6/3/2019 11:03 AM, Winget, Jason wrote:
>
>     I’m trying to get mzML files with chromatograms from other detectors (UV, CAD) from Thermo RAW data.
>
>     There have been a few posts on this mailing list that indicate this should be possible, however I am unable to get this to work.
>
>     https://sourceforge.net/p/proteowizard/mailman/message/30695902/
>
>     https://sourceforge.net/p/proteowizard/mailman/message/36435876/
>
>     I’ve tried 34-bit and 64-bit versions of msconvert, using a variety of filters (or none at all). I’ve inspected the resulting mzML
>     files and can only find the MS chromatograms.
>
>     Does anyone have a functioning command that generates mzMLs with chromatograms from non-MS detectors?
>
>     Thanks,
>     Jason
>
>
>
>
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