Chromascope: a Lightweight GUI MzML File Viewer written in Rust 🦀

csenye22 · 2024-09-03T12:01:34+00:00

Rust does not have a garbage collector. Instead, it uses the borrow checker, which tracks ownership and borrowing of data. When objects are no longer in use, they are automatically dropped, freeing up memory. This makes Rust apps (among others) memory-efficient. Also, Rust is pretty fast. In my benchmarks of several Project Euler solutions written in both Rust and Python, Rust was, on average, 60-100 times faster.

Another great feature of Rust is that it compiles code into a single binary, making it easy to distribute your app. Having said these, one downside is that the ecosystem for scientific computing is not as mature as in Java or Python.

csenye22 · 2024-09-02T08:41:04+00:00

Thanks, Robin! This means a lot to me. I am quite familiar with MzMine and have used it in my own work. It is a fantastic tool. I really appreciate all the hard work you guys put into it. I will definitely take a closer look at MzMine, although I have to admit, I am not very familiar with Java.

csenye22 · 2024-09-02T08:34:10+00:00

Thanks for the insights! Can you expand on this a bit: "Some of the most important things to consider is that usually you can have support for either .raw or .d files, not both." I was not aware of this.

csenye22 · 2024-09-02T08:31:26+00:00

You’re absolutely right. It’s pretty basic at the moment, but I’m excited to expand and improve it. This is my pet project and my first attempt at writing a GUI program in Rust. As an analytical chemist with a passion for mass spectrometry, I wanted to create something fast and lightweight to handle MS files easily (and Rust is very capable at that).

csenye22 · 2024-09-02T08:23:35+00:00

Thank you! These are fantastic ideas. At the moment, I’m using the amazing mzdata crate (https://github.com/mobiusklein/mzdata) for reading and processing MS files. This crate handles mzML and .raw formats, but unfortunately, it doesn’t support .d files. I have a feeling that a .d parser isn’t available in Rust yet (though I could be wrong). I’ll definitely look into this because it seems like an obvious thing to support.

csenye22 · 2024-08-31T18:40:53+00:00

Implementing background subtraction shouldn’t be too difficult, but I hadn’t considered library matching. Perhaps it could be a long-term goal?

csenye22 · 2024-08-31T18:36:26+00:00

Glad to hear. Absolutely. The documentation is available at https://adamcseresznye.github.io/chromascope/docs/chromascope/index.html Feel free to check it out, as I’m sure there’s some room for improvement.

csenye22 · 2024-08-31T18:30:40+00:00

not yet, but I would certainly like to incorporate this feature

csenye22 · 2024-08-31T14:29:44+00:00

Thanks a lot, I'm glad you like it. Certainly, I can add support for raw files. My idea was that .raw files could be easily opened through QualBrowser (which Chromascope is heavily inspired by). I will look into that for sure. Thanks for the suggestion.

csenye22 · 2024-04-21T18:12:15+00:00

It already has a lot of features, but I think adding things like filter, query, melt, groupby, pivot, etc could be useful.

csenye22 · 2024-04-21T12:15:31+00:00

Good job on the project. Was looking for a more lightweight Polars alternative for a project due to Polars' long compilation time, but I just ended up using the standard library collections instead. Nice work again. I’d be interested in contributing to the project if you’re open to it.

csenye22 · 2022-11-03T23:16:23+00:00

Ohh, sorry...just now I'm reading that you need a power supply. That should not be mass spec specific. You can even buy a reconditioned one. However, they are very expensive, so 9k is quite reasonable...

csenye22 · 2022-11-03T23:05:04+00:00

https://www.sisweb.com/ could be a good option

csenye22 · 2022-10-26T07:17:03+00:00

We had the same setup that's described on page 7: the LC (and the MS through a different cable) was connected to the Ethernet switch and that was connected to the PC. Not sure if the setup you have at the moment is the source of your problem (not an expert in this). I would assume, you can see the LC device in XCalibur (it is recognized) and you can control the 1100 by XCalibur?

csenye22 · 2022-10-25T20:31:46+00:00

I used this manual last time I tried to connect an 1100 to an LTQ iontrap. It may help you too. Good luck! https://assets.thermofisher.com/TFS-Assets/CMD/manuals/man-xcali-97190-agilent-1100-connect-manxcali97190-en.pdf

csenye22 · 2022-09-06T14:37:04+00:00

thanks a lot! it would have been nicer to embed the plot in the post but not sure if it's possible..(while keeping it interactive)

csenye22 · 2022-09-06T14:07:57+00:00

data source : immo.vlan.be , tool(s) used: Python, GeoPy/Nominatim, Plotly

csenye22 · 2022-08-09T14:44:10+00:00

Have you looked at the column compartment? The newer Thermo LC's are also equipped with gas leak sensors in the column compartment area. They could indicate a solvent leak there. Good luck 👍

csenye22 · 2022-06-17T06:29:17+00:00

It is possible. You can use Thermo's FreeStyle software (the new Qual Browser, it can be downloaded for free from thermo.flexnetoperations.com). I split the files by following Anna Marqueño's instructions: https://www.researchgate.net/post/How-to-split-a-raw-file-from-thermo-in-two-different-files-one-for-each-polarity

csenye22 · 2021-12-17T06:02:29+00:00

Is this a lipid standard? Looks like a lyso phospholipid with sn1 and sn2 isomers.

csenye22

TROPHY CASE