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Support for tims tof data #73
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I am interested in adding support for Bruker data/IM eventually... but I wouldn't say there is a plan yet. This represents a fairly large amount of work (writing a native .d parser, re-writing LFQ to support IM dimension, etc); and I have no personal Bruker or TIMS data in house, but more Thermo data than you can shake a stick at. As such, there is no timeline for when (or if) this feature might be added. If anyone is interested in collaborating on this, please reach out. |
The new Sage documentation site is great! Thanks for the great overview. Also i am eager to here if there are updates regarding this issue. ;) |
Thanks Tom. Stay tuned, I hope to have a very exciting update for you soon |
Hey @lazear! Along these lines ... I worked on a prototype to use IMS predictions during the prediction stage (branch diffs: master...jspaezp:sage:feature/ims_model), and even though the model gives very modest change in ID numbers (<1% most of the times, even if the model has R2 > 0.95); The branch also implements the ion mobility field in the spectra and its extraction from .mzml data. let me know if you would like a PR that adds that to sage; either only the preservation of the IMS data or that in conjunction with the ion mobility model (which I would polish a bit and do some minor feature engineering). I could also wait for the merge of the bruker branch/use that branch as a base so both .mzml and .d files provide the mobility data. Best, |
@jspaezp this looks pretty good - let's wait to merge in the bruker branch first. I'm going to try and start reviewing it this week |
Hey, sorry to bother once again. Are the changes regarding the ims_model already merged? Thanks! :) |
The ims_model feature has been merged and is included in the newly released v0.14.6! |
So .d directories are now natively supported right: #117 (comment)? (base) PS D:\Data\tools\SAGE> sage .\current_config.json I use the current_config.json |
Is this ddaPASEF? The error suggests that this is an issue in Bruker's timsrust library. Can you please open an issue there and share your data with them? |
I tried another .d dataset with the same error. Hopefully someone will soon reply at #15. |
I would strongly suggest sharing the actual file. It's going to be nigh-impossible for anyone to debug the issue otherwise. |
Updated with the data. |
Hi Michael,
is there a plan to support tims tof data (.d format) in general and ion mobility?
Best,
Tom
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