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Tobias Kroniger @kronigert.bsky.social · 18/03/2026

Hey Luke! Happy to hear that you like timsCompare and find it useful! Yes, it's exactly that. 0 means the polygon is disabled in the method. The setting is just for the interface though. It should not affect acquired data

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Tobias Kroniger @kronigert.bsky.social · 10/03/2026

Cool! I was also successful in using LLMs to make some customization to the visual basic Da scripts! Can be very handy!

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Tobias Kroniger @kronigert.bsky.social · 10/03/2026

Sounds interesting. What differences in the methods did it apply? What did you use as instructions for the aim of the method development?

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Tobias Kroniger @kronigert.bsky.social · 31/10/2025

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...

github.com

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...

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Tobias Kroniger @kronigert.bsky.social · 15/10/2025

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

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Tobias Kroniger @kronigert.bsky.social · 15/10/2025

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

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Tobias Kroniger @kronigert.bsky.social · 15/10/2025

Yes, that should be unnecessary now!

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Tobias Kroniger @kronigert.bsky.social · 15/10/2025

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

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Tobias Kroniger @kronigert.bsky.social · 15/10/2025

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.

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Tobias Kroniger @kronigert.bsky.social · 15/10/2025

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.

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Tobias Kroniger @kronigert.bsky.social · 15/10/2025

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.

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Tobias Kroniger @kronigert.bsky.social · 15/10/2025

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.

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Tobias Kroniger @kronigert.bsky.social · 15/10/2025

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 🧵)

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Tobias Kroniger @kronigert.bsky.social · 14/06/2025

Will send you a document via DM! :)

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Tobias Kroniger @kronigert.bsky.social · 13/06/2025

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?

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Tobias Kroniger @kronigert.bsky.social · 27/05/2025

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

bruker.com

ASMS 2025

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

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Tobias Kroniger @kronigert.bsky.social · 04/04/2025

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

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Reposted by Tobias Kroniger

Andrea Sinz 🧪 @sinzandrea.bsky.social · 07/02/2025

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!

personal.verwaltung.uni-halle.de

Externe Stellenausschreibungen- Wissenschaftliche Mitarbeiterinnen und Mitarbeiter, Ärzte und Lehrkräfte für besondere Aufgaben

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Andrea Sinz 🧪 @sinzandrea.bsky.social · 13/02/2025

🧪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

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Patricia Skowronek @patiskowronek.bsky.social · 20/01/2025

🚀 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/🧵

doi.org

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Andrea Sinz 🧪 @sinzandrea.bsky.social · 15/12/2024

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

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Tobias Kroniger @kronigert.bsky.social · 02/12/2024

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

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Tobias Kroniger @kronigert.bsky.social · 30/11/2024

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

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Tobias Kroniger @kronigert.bsky.social · 29/11/2024

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

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Tobias Kroniger @kronigert.bsky.social · 29/11/2024

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

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Witold Szymański @witek-teammassspec.bsky.social · 26/11/2024

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

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Michael Sinden @mdsinden.bsky.social · 25/11/2024

@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

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Alejandro Brenes @ajbrenes.com · 10/11/2024

#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

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Jan Schejbal @schejbaljlab.bsky.social · 13/11/2024

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.

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PastelBio @pastelbio.bsky.social · 30/05/2024

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

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PastelBio @pastelbio.bsky.social · 11/05/2024

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

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PastelBio @pastelbio.bsky.social · 23/04/2024

Ultra-sensitive metaproteomics (uMetaP) redefines the dark field of metaproteome, enables single-bacterium resolution, and discovers hidden functions in the gut microbiome www.biorxiv.org/cont... --- #proteomics #prot-preprint

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PastelBio @pastelbio.bsky.social · 16/03/2024

News in Proteomics Research blog post | THUNDER-PASEF - Get those real immunopeptides! proteomicsnews.blogs... --- #proteomics #prot-other

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PastelBio @pastelbio.bsky.social · 12/03/2024

News in Proteomics Research blog post | Need more surfactants for proteomics? Here is a big table! proteomicsnews.blogs... --- #proteomics #prot-other

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Tobias Kroniger @kronigert.bsky.social · 01/12/2023

I am afraid that's not gonna work. The data analysis of iRT peptides (RT, 1/k0, FWHM etc) is done with Proteoscape and is only stored in TwinScape cloud. There will be other data stored that may be useful to monitor. Here is a demo: twinscape.bruker.com

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Tobias Kroniger @kronigert.bsky.social · 01/12/2023

I don't think that there will be license costs for TwinScape as you already need iRTs and Bruker Proteoscape to use the QuiC-like feature of it.

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Tobias Kroniger @kronigert.bsky.social · 28/11/2023

Maybe this paper is interesting for you: www.biorxiv.org/content/10.1...

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PastelBio @pastelbio.bsky.social · 15/11/2023

Comprehensive Overview of Bottom-up Proteomics using Mass Spectrometry arxiv.org/abs/2311.0... --- #proteomics #prot-preprint

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Witold Szymański @witek-teammassspec.bsky.social · 01/11/2023

JOB ALERT! We are looking for technical support in our lab! Permanent position! No BS time-limited contracts! Have a look and apply! stellenangebote.uni-marburg.de/jobposting/e... #marburg #germany #proteomics #laboratory

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Alejandro Brenes @ajbrenes.com · 12/10/2023

Our new preprint optimising search parameters in DIA is out. We show DIA can suffer effects similar to match-between runs in DDA, with false positives being detected across runs. But we offer simple solution that dramatically reduces them while maintaining proteome depth. #proteomics

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Tobias Kroniger @kronigert.bsky.social · 10/10/2023

Are you interested in the Bruker timsTOF Ultra? Then I am happy to inform you that the Webinar with our Application Development Specialist Christoph Krisp about “Setting and maintaining the single cell proteomics benchmark” is now available on-demand: www.bruker.com/de/news-and-...

bruker.com

Setting and maintaining the single cell proteomics benchmark - Meet the timsTOF Ultra

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