Read CID/EAD mode from wiff2 files

[david-cox-sciex]

Use DataAPI for wiff2 to get detailed experiment information which includes fragmentation mode for spectra.

[chambm]

Looks good except tabs need to be converted to spaces. Can this wait for the EAD energy term to be approved and the CV updated in pwiz? I will do the latter although it may be more involved than usual because it looks like they've been messing around with embedding other ontologies inside the OBO.

[david-cox-sciex]

I'll take care of the tabs to spaces now. I think the EAD term is now in psi-ms.

[david-cox-sciex]

@chambm
I converted tabs to spaces.

Should I run the update_cv.bat, and then include the file changes it generates? I see it bringing in the electron beam energy term, it also makes some other changes to obo file that I think are okay but I'm not certain.

[chambm]

I will handle that part. I'm waiting for the temperature term to go in so I can do that later without having another CV update. Since you ran the update already, does it actually compile?

[david-cox-sciex]

Yes. I run this and get a functioning MSConvertGUI.exe
quickbuild.bat --i-agree-to-the-vendor-licenses address-model=64 debug

[chambm]

One thing that's missing here is a new test data set. Do you think you can get a tiny WIFF/WIFF2 set with a few EAD spectra? One neat feature of Thermo QualBrowser I discovered is it can export a single spectrum as a RAW file. The spectrum metadata is preserved although file-level metadata is lost. But that's still useful for testing that different spectrum types are converted properly! I'm not sure if Sciex software has any analogous capability.

[david-cox-sciex]

I have a ~15 MB file I've been using as a manual test.
Can you point me at where the tests are defined?

[chambm]

Reader_ABI_Test.cpp . All WIFF and WIFF2 files in the .data directory are tested. 15MB is rather big though. Any way to get it down to just a few spectra?

[david-cox-sciex]

that is the smallest one I can find.

Should I put these files in
\pwiz\data\vendor_readers\ABI\Reader_ABI_Test.data

7600ZenoTOFMSMS_EAD_TestData.zip

[chambm]

OK, if you've reviewed the mzML and it's converting ok, go ahead and add it. Thanks!

[david-cox-sciex]

OK. the example files are added. If everything is okay, will you (@chambm) be doing the merge. For me it is blocked.

[david-cox-sciex]

Did the Skyline PR Perf check fail because of this one extra file?
https://teamcity.labkey.org/buildConfiguration/ProteoWizard_SkylinePrPerfAndTutorialTestsWindowsX8664/3127062?buildTab=log&linesState=82&logView=flowAware

[chambm]

Sorry I was out sick yesterday. Is this a DIA file? I'm wondering why it's not getting isolation width.

[david-cox-sciex]

Not DIA, just a looped MSMS. It's possible we only show isolation width on DIA experiments.

[chambm]

It turns out that only all WIFF files in that directory are tested; WIFF2 files have to be added by name. I also added some index subsetting to keep the size of the reference mzML down.

[chambm]

Thanks for adding this @david-cox-sciex !