IDBacApp
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chasemc
Will not process data
When using mzML, the box in the bottom right corner will show up and then disappear and the screen greys out and stays there.
I am using 1.1.10. I sound if I convert my .d file to mzML then convert to mzXML then it will work. Is there a way to tell idbac to cluster multiple runs as it does when uploading bruker files?
On Fri, Sep 2, 2022 at 11:05 AM Chase Clark @.***> wrote:
What version are you using?
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I'm not sure what format .d is from, so probably not.
If you can share how your files are organized I may be able to help with an msconvert command that could group them
The .d file format is off of a Bruker TimsTOF.
Each file is a folder and each folder is labeled with the well it came from, with one run per well and 4 wells are one bacteria.
On Fri, Sep 2, 2022 at 12:09 PM Chase Clark @.***> wrote:
I'm not sure what format .d is from, so probably not.
If you can share how your files are organized I may be able to help with an msconvert command that could group them
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TimsTOF wasn't really around when IDBac was first written and I couldn't get hold of any TimsTOF data when I was actively working on IDBac so there's currently limited support (there's ongoing active work on putting all the analyses online instead).
If could you share a few of the TimsTOF data files, I can try and work on it, though it may take some time.
@gtluu has also tried but I'm not sure if he ever got it to work or not.
Sure! In this GoogleDrive, there are 8 files from two different bacteria, one bacteria in column 6 one in column 7.
https://drive.google.com/drive/folders/1i4vMJ0IxfQl4_-aKw-RImX7tcfeIyiHK?usp=sharing
On Fri, Sep 2, 2022 at 2:30 PM Chase Clark @.***> wrote:
TimsTOF wasn't really around when IDBac was first written and I couldn't get hold of any TimsTOF data when I was actively working on IDBac so there's currently limited support (there's ongoing active work on putting all the analyses online instead).
If could you share a few of the TimsTOF data files, I can try and work on it, though it may take some time.
@gtluu https://github.com/gtluu has also tried but I'm not sure if he ever got it to work or not.
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Sorry for the delay. We are working on making this part of the process easier for the new web app, which might make it easier for this version of IDBac as well. If you'd like help in the meantime we could set up a Zoom call and work through getting the files converted/grouped, just let me know
Hi Chase,
That would be great! I have figured out a system that works, but I am curious if you have a more streamlined method. Let me know when is best for you.
Thank you,
Paige Banks (she/her)
Ph.D. Candidate
Mevers Lab | Department of Chemistry
@.***
On Thu, Oct 20, 2022 at 5:41 PM Chase Clark @.***> wrote:
Sorry for the delay. We are working on making this part of the process easier for the new web app, which might make it easier for this version of IDBac as well. If you'd like help in the meantime we could set up a Zoom call and work through getting the files converted/grouped, just let me know
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Hi Paige and Chase,
I work with .d files from a Bruker timsTOF and I have a similar issue uploading/ processing data to IDBac. Did you come up with a solution? Paige, would you let me know your workaround? Thank you both!
Casey Heaney Sanchez Lab UCSC
Was able to figure out a work around. The data conversion tool I was using was not readily compatible with IDBac.
Hi @chasemc @PaigeBanks . I'm late to the party here but for future reference for anyone using small molecule data from the timsTOF fleX, I was able to get IDBac 1.1.0 working by having replicate spectra grouped by sample/strain. So in timsControl's AutoXecute Run Editor menu, replicate samples should be grouped into the same Spectra Folder, meaning those multiple spectra will be output to a single .d file (example screenshot attached). This can be converted using TIMSCONVERT or MSConvert and loaded into IDBac to run the small molecule workflow. If you are using TIMSCONVERT you will need to use the --barebones_metadata flag as I had some errors in IDBac when incompatible CV params were introduced into the converted mzML files I was working with.
