Tobias Kroniger

GitHub - kronigert/timsCompare: A desktop application for mass spectrometry users to load, view, compare timsTOF methods and export isolation schemes and method reports from Bruker's .d method directo... A desktop application for mass spectrometry users to load, view, compare timsTOF methods and export isolation schemes and method reports from Bruker's .d method directories. - kronigert/timsCom...

timsCompare v1.3 has a few new functionalities:
- a new report wizard that allows batch exports and comparison reports
- segment comparison mode
- session management to revisit a comparison later without the raw data
- "remove all" button
- better AIP support
- better UI scaling for smaller displays

Release timsCompare v1.1 · kronigert/timsCompare Some people reported false-positive flagging of the tool by some AV softwares. This was due using pyinstaller in the previous build. This version has been compiled with Nuitka and should not be fla...

I just pushed an update to the timsCompare GitHub.
- compiled with Nuitka preventing false-flagging by AV software
- startup parameters can now be customized
- plots can now be resized to the measured mass range
- extraction of used instrument and used timsControl version

github.com/kronigert/ti...

Very happy to hear that! It should be quite stable for "standard" proteomics methods. Can be a bit trickier for stepping or multi-segment methods, but even these should work as far as I have tested

I sure hope that there wont be too many, haha. But I you encounter some, please report them! Happy testing :)

Yes, that should be unnecessary now!

What things did you adapt via notepad++? The polygon for dda measurements?

Thank you! Yes, also TME only works for same instrument type. timsCompare works instrument independent! Can also be a great tool to recover a dia-PASEF scheme from a PRIDE repository for example.

GitHub - kronigert/timsCompare: A desktop application for mass spectrometry users to load, view, compare timsTOF methods and export isolation schemes and method reports from Bruker's .d method directo... A desktop application for mass spectrometry users to load, view, compare timsTOF methods and export isolation schemes and method reports from Bruker's .d method directories. - kronigert/timsCom...

timsCompare is free, open-source, and available now on GitHub! All feedback, bug reports, and feature ideas are welcome.

github.com/kronigert/ti...

#MassSpec #TeamMassSpec #Proteomics #timsTOF #diaPASEF #diagonalPASEF

(Disclaimer: This is an independent project, not an official Bruker tool.)

Need to document your method for a publication or lab notebook? timsCompare generates professional, multi-page PDF reports with high-quality plots and neatly organized parameter tables. CSV export is also supported for easy data handling.

Visualize acquisition schemes for PASEF, dia-PASEF, and diagonal-PASEF methods. You can easily export these window schemes directly from your raw data into a simple text file for documentation. The exported text file can also be read directly by timsControl.

Simply drag & drop your .d or .m folders. timsCompare instantly gives you a side-by-side parameter comparison. Any differences between methods are automatically highlighted, so you can spot changes at a glance.

Struggling to compare Bruker timsTOF methods or extract window schemes from raw .d files? I developed a free desktop tool to solve this: timsCompare! 🚀

It automates the manual work of extracting method parameters, presenting them in a structured and comparable view.

(A thread 🧵)

Will send you a document via DM! :)

Hi Dorothy, do you mean the valve plumbing or the method setup? I guess you plan to make a calibration segment at the start of each run for external calibration?

ASMS 2025 Join Bruker at ASMS 2025. Experience cutting-edge advancements in mass spectrometry technology as the innovation superheroes come to ASMS 2025.

If you're not attending ASMS but are interested in updates from Bruker, you can still take part in the eXceed symposia via livestream.

Register here to join the livestream:
www.bruker.com/en/landingpa...

#ASMS2025 #Bruker #MassSpectrometry #eXceedSymposia

Do you want to do m/z or IM calibration?

Job alert 🧪 ‼️ Hi #teammassspec: In our #RTG2467 @unihalle.bsky.social we have a job opening for a PhD student in my group! 🎉 If you want to do cool stuff in cross-linking mass spectrometry of the tumor suppressor p53, please take a look:
personal.verwaltung.uni-halle.de/jobs/wissmi/
Please RT!

🧪If you join our lab you will be able to use our three timsTOF mass spectrometers….and we also got a new microwave oven for our lab kitchen today!😜
#ChemSky
#AcademicSky

🚀 Robust and high sensitivity #proteomics: Our Nature protocol demystifies #PASEF workflows and provides ready-to-use dia-PASEF & synchro-PASEF methods. Find out how to achieve 7,000 protein groups or 29,000 phosphosites in 21min. Let's explore! #TeamMassSpec #Bruker doi.org/10.1038/s415... 1/🧵

TimsTOF ultra 2 cookies for the group.🍪😋🎄🎄🎄 #teammassspec @brukercorporation.bsky.social

There is a disclaimer when you scan the QR-Code. They are built from biodegradable, food-contact-safe-plastic. Please hand-wash only!

Both options are usable. For SN only directDIA is available, while TIMS DIANN uses a library-based approach

I think it's very hard to make a fair comparison between instruments. There are just too many variables

Happy to hear that everything was working out in the end! Crossing fingers for your measurements!

Just got my TimsTof Ultra cookie form 😏 a nice touch from #bruker

@brukercorporation.bsky.social‘s latest app note highlights that ultra-high-throughput proteomics doesn’t have to compromise depth or quality.

Pairing a timsTOF HT with an Aurora Rapid 5x75 column, researchers ID over 7,200 protein groups & 85,658 precursors in 5 mins.

Read: bit.ly/3YWZk27

#teamMassSpec here is a starting pack in case you just moved over, or in case you've been absent for a while. This is #proteomics or #massspec related. The pack is not comprehensive but it's a start.

go.bsky.app/HH7kqEh

Hi #TeamMassSpec, 👋 good to see everyone on 🦋 side. I am still looking for a PhD-level immunopeptidomics intern for summer 2025 with expected graduation by summer 2026. If you know of any good labs to check with, please let me know! Bruker timsTOF experience is a big plus.

diaTracer enables spectrum-centric analysis of diaPASEF proteomics data www.biorxiv.org/cont...

---
#proteomics #prot-preprint

Fragment ion intensity prediction improves the identification rate of non-tryptic peptides in timsTOF - Nature Communications www.nature.com/artic...



---
#proteomics #prot-paper