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
@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?
@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.
@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
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🧵
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
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
@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.
@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.