Tobias Kroniger

tidyplots Time to say goodbye to ggplot2?🫡 "a significant reduction of code complexity" vs ggplot2 cran.r-project.org/web/packages/t… @JanBroderEngler bioRxiv 2024 biorxiv.org/content/10.110…

@lgamon That's odd. Using a method like this for in-batch calibrating for example a blank in between runs (same IM slope) should work. The signal is definitely enough. Let me get back to you tomorrow.

@kronigert It is visible with >10^5 signal. Made a method specifically to catch all three ions. I only have a picture from one of the heavily spiked filters:

For those keeping track… had to pause the run Saturday night at 184/432. Mobility was drifting too much. Back at it tomorrow 🤞

@lgamon There has been a change in the software. Now all three masses have to be visible for a successful calibration. Often, the 1222 is not visible as it requires at least 1.45 1/k0 on the upper IM range. Is this maybe the issue?

@kronigert Thanks Tobias. I’ve had great success with it a couple of years ago but I’m having the in-batch calibration fail both with ‘low’ spiked signal and ‘high’ spiked signal. Any ideas? The IM and m/z calibration are otherwise perfect.

@rbharathkumar91 @ItsBiniR Yes. There are three different libraries available via ProteoScape at help.proteoscape.io

@ItsBiniR May they provide as part of their Proteoscope software?? 🤔🤔

Spectra for 1536 single cells acquired over 40 SPD Slice-PASEF workflow.. ~40 days of acquisition! Btw Bruker provides a spectra library? 'Analyses were performed using a library-based approach (spectral library provided by BRUKER containing 67686 proteins and 13827 genes)' 🤔

@DavidGomezZep Thanks for this tool! Just tried it last week and it works like a charm :)

Dear #proteomicscommunity and #TeamMassSpec, I am happy to share HowDirty, an R package that facilitates evaluating and reporting molecular contaminants in LC-MS experiments. authorea.com/users/643346/a…

@DavidGomezVar Congrats David! 🎉

I'm excited to share that I'll lead a new Center of Excellence for Metaproteomics, a joint venture between the University of Vienna and Bruker. This initiative will leverage cutting-edge mass spectrometry and AI to unravel the mysteries of the microbiome. medienportal.univie.ac.at/en/media/recen…

Proteomics goes viral! We present vPro-MS to identify human-pathogenic viruses in patient samples from diaPASEF/DIA data. We developed a peptide library covering the human virome from 20,000 genomes, which enables highly specific detection (>99,9%) using vProID scoring.

@UCDProteomics @neely615 @JeremyBalsbaugh @lgamon For full functionality in DataAnalysis a licence is necessary that's true. If no floating licence is present it can be operated in Viewer mode. In viewer mode you cannot create traces, but if traces are already saved within the .d (e.g. by a script), you could have a look at them

@kronigert @neely615 @JeremyBalsbaugh @lgamon Wait have they finally changed this policy ? Last I checked you needed a stupid license even for the data viewer .

@JeremyBalsbaugh @lgamon @neely615 My DMs are open if you need assistance. I can also share a DA script with you that does TICs, BPC and EICs that are set in a .csv. You can edit the respective peptide masses in the .csv to get your desired output.

@kronigert @lgamon @neely615 I agree - quick data viewer is helpful for a quick “squinty eyes” glance at the chromatogram pattern. Have played with the DA script a bit ages ago for QC runs, probably worth exploring again. Thanks

@lgamon @JeremyBalsbaugh @neely615 If you have certain traces (TIC MS, TICMSMS, BPC, EICs of your favorite peptides) that you monitor all the time, you can set them up in a DA script and let it run after finished acquisition using the "Automated Processing" Function in HyStar. Traces are then shown instantly in DA

@JeremyBalsbaugh @neely615 TIC MS1, MS2 and BPC plotting in the ‘Quick Data Viewer’ in Hystar (eg if using chromeleon/Dionex LC) is essentially instant. I’m guessing this info is extracted during the run and saved in the the hystar info? Really nice solution

The #mdcBerlin and @bruker are proud to announce the launch of the MDC – Bruker Center of Excellence for #SingleCellOmics! 🎉 Join us on July 8th at @BIMSB_MDC to learn more about the center's mission and goals. Full program and registration 👉 mdc-berlin.de/MDC_Bruker_Cen…

Thrilled to finally see µPhos published in @MolSystBiol! A big thank you to @fmeierX, @SeanJHumphrey and all other coauthors for this exciting journey! Check out our greatly improved and extended story on how to unlock the true power of phosphoproteomics: embopress.org/doi/full/10.10…

Excited to announce DIA-NN version 1.9, our software suite for proteomics data processing! A range of cool new features and general performance improvements. We consider it the most significant update in the history of DIA-NN. github.com/vdemichev/DiaN…

High-throughput proteome profiling with low variation in a multi-center study using dia-PASEF biorxiv.org/cgi/content/sh… #biorxiv_sysbio

To get there was quite a journey, but finally it is out: Our massive High-Throughput #Proteomics study on sepsis with >4500 LCMS runs using #Evosep, #Bruker #TimsTOF and #Fragpipe: science.org/doi/10.1126/sc…

A new resource to assist with scalable & multiplied single-cell proteomics. It describes a workflow using nPOP and plexDIA on timsTOF systems. #resources" target="_blank" rel="nofollow noopener">scp.slavovlab.net/protocols#reso… bruker.com/en/products-an…

On average, >7k PG and >99k peptides were identified with 200 ng K562 digest with low variation. Also, differences between regularly used QC-standards were assessed (K562, HeLa, and HEK (in-house digest). The SOP provided to the laboratories is available in the supplement

Check out our newest preprint where the same instrument setup (nanoElute2 + timsTOF HT) was used in 11 laboratories to evaluate the performance and reproducibility using short 5-min gradients. biorxiv.org/content/10.110…