Support for tims tof data

[tomthun]

Hi Michael,

is there a plan to support tims tof data (.d format) in general and ion mobility?

Best,

Tom

[lazear]

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.

[tomthun]

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. ;)

[lazear]

Thanks Tom.

Stay tuned, I hope to have a very exciting update for you soon

[jspaezp]

Hey @lazear! Along these lines ... I worked on a prototype to use IMS predictions during the prediction stage (branch diffs: https://github.com/lazear/sage/compare/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, Sebastian

[lazear]

@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

[tomthun]

Hey, sorry to bother once again. Are the changes regarding the ims_model already merged? Thanks! :)

[jspaezp]

@tomthun not quite yet!

There is a pretty good discussion here >> https://github.com/lazear/sage/pull/98 << on where to go with the feature (long story short, the utility is less than I was expecting in most datasets) On the other hand, support for searching .d files is already implemented (but LFQ is not)

[lazear]

The ims_model feature has been merged and is included in the newly released v0.14.6!

[tomthun]

So .d directories are now natively supported right: https://github.com/lazear/sage/issues/117#issuecomment-1928514516? I just ran some quick tests on some test data and got the following:

(base) PS D:\Data\tools\SAGE> sage .\current_config.json [2024-02-09T11:03:06Z INFO sage] generated 111120583 fragments, 5992882 peptides in 7285ms [2024-02-09T11:03:06Z INFO sage] processing files 0 .. 1 thread 'main' panicked at C:\Users\runneradmin.cargo\registry\src\index.crates.io-6f17d22bba15001f\timsrust-0.2.0\src\file_readers\common\sql_reader.rs:30:62: called Result::unwrap() on an Err value: SqliteFailure(Error { code: Unknown, extended_code: 1 }, Some("incomplete input")) note: run with RUST_BACKTRACE=1 environment variable to display a backtrace

I use the current_config.json

[lazear]

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?

https://github.com/MannLabs/timsrust/issues

[tomthun]

I tried another .d dataset with the same error. Hopefully someone will soon reply at #15.

[lazear]

I would strongly suggest sharing the actual file. It's going to be nigh-impossible for anyone to debug the issue otherwise.

[tomthun]

Updated with the data. Edit: Sorry, i had the wrong settings for the file, but should now work.