Georg Wallmann

PhD student at the Mann lab

[Georg Wallmann @GeorgWa]

We just release alphaDIA 1.8.2 including some new step-by-step guides for #Proteomics.

Learn how to:
• Run DIA searches from the GUI
• Create custom PTM models with DIA transfer learning
• Evaluate model performance with detailed metrics

https://t.co/R99QYxLDRe
#TeamMasSpec

[Georg Wallmann @GeorgWa]

@wfondrie @nesvilab @i000 @bruker @jspaezp1 To my knowledge we are still lacking some additional proprietary calibration with timsrust/alphatims on Unix when Bruker DLLs are not available. What’s your experience?

[Georg Wallmann @GeorgWa]

@DemichevLab Ah okay, I see 👍🏻thanks

[Georg Wallmann @GeorgWa]

@ucdmrt @michaellazear @fcyucn @animesh1977 @chrashwood @maxquant @github @JimmyEng Yes sure! Best is if you reach out on GitHub discussions: https://t.co/686WTJAFJz

[Georg Wallmann @GeorgWa]

@ucdmrt @michaellazear @fcyucn @animesh1977 @chrashwood @maxquant @github @JimmyEng I can only speak for alphaDIA but we are actively developing it and get very competetive performance for all Thermo or Sciex instruments as well as library based TimsTOF searches. Feel free to reach out if you want to discuss some use case.

[Georg Wallmann @GeorgWa]

@jalew188 @Westlake_Uni @labs_mann Well deserved! It was a great pleasure working with you and I'm looking forward to future collaborations 😀.

[Georg Wallmann @GeorgWa]

@ItsBiniR No need for libraries. This is a perfect application for end-to-end transfer learning. It allows you to train your own instrument and modification specific model right from your DIA data:
https://t.co/uvZzKRi6GG

[Georg Wallmann @GeorgWa]

@chrashwood I know another feature free DIA tool ;). Sounds like this is hot at the moment.

[Jason Derks @_JasonDerks]

Cellular states prior to stimulation will be predictively associated to outcomes. By linking variable proteomes to responses, we may identify regulators.
https://t.co/PmS5zB6Azu
Here, we use single-nucleus proteomics to identify regulators of LPS-induced protein transport🧵

[Georg Wallmann @GeorgWa]

@Hamish_Stewart @mjmaccoss @DemichevLab Isn't this already somewhat accessible by looking at SNR ratios and fill times?

[biorxiv_biochem @biorxiv_biochem]

A novel hybrid high speed mass spectrometer allows rapid translation from biomarker candidates to targeted clinical tests using 15N ... https://t.co/BQuoMA6G64 #biorxiv_biochem

[Matthias Mann Lab @labs_mann]

1/7 @labs_mann and Georg Wallmann @GeorgWa are proud to announce alphaDIA, our open source, next generation DIA search engine. Check out the preprint @biorxivpreprint

https://t.co/2HuOd1AJMy

[bioRxiv Bioinfo @biorxiv_bioinfo]

AlphaDIA enables End-to-End Transfer Learning for Feature-Free Proteomics https://t.co/J4MM6w9mzH #biorxiv_bioinfo

[Georg Wallmann @GeorgWa]

@OliverMBernhar1 @labs_mann I think Spectronaut should qualify you 🤔

[Matthias Mann Lab @labs_mann]

We've got something exciting to share before #ASMS2024! But first, how confident do you feel about your DIA search? #TeamMassSpec

[Georg Wallmann @GeorgWa]

@MartinFrejno @msaid_de What external benchmarking would you like to see to feel confident about an identification from MS1 only?

[Georg Wallmann @GeorgWa]

@mjmaccoss @MartinFrejno @msaid_de @SciFiRobitaille I very much agree with this notion. I think confident identifications with few or even none fragments are well possible if there is enough evidence. The real challenge is quantification and giving good estimates of quant certainty.

[Georg Wallmann @GeorgWa]

@MartinFrejno @msaid_de I mean, it's just idea :D. I'm thinking of something like an AMT Tag. Just not with a proteome specific library but a whole proteome library. You wouldn't get the same performance in complex bulk proteomes, but maybe it's something for single cell.