Updates from our continuous development of the #xcms #rstats :rstats: #metabolomics package:
👉 retention time alignment against external data set
👉 chromatographic peak quality metrics
👉 preformance improvements
All available in current version in @bioconductor release 3.21 🚀
Up next: memory-saving analysis of very large data sets!
Sharing our 🚀 Metabonaut resource:
A collection of comprehensive tutorials for LC-MS/MS #metabolomics data analysis in :rstats: by @phili et al.
Learn raw data processing, annotation & stats with #xcms, #RforMassSpectrometry & @bioconductor - all reproducible & community-driven! #rstats
And @phili with her poster on a complete end-to-end workflow for untargeted #metabolomics data analysis in #rstats with @bioconductor and #RforMassSpectrometry #xcms etc
#MetSoc2024 poster # 1008
On my way 🚞 to Vienna 🇦🇹for the MassSpec Forum 2024 https://bit.ly/3T3LFEm !
Will have a workshop on how to handle and preprocess LC-MS data with our @bioconductor :rstats: packages #Spectra and #xcms !
Yes, we're still working on improving the #xcms @bioconductor :rstats: package for LC-MS #metabolomics data preprocessing!
This time: filter features based on quality criteria from @davidbroadhurst et al. (https://doi.org/10.1007/s11306-018-1367-3).
great contribution from @phili !
More info: https://bit.ly/3UqmfSx
Next on the list: mzTab-M export.
#xcms version 4 is here!
Now we use the full power of the #Bioconductor #Spectra :rstats: package and the #RforMassSpectrometry package ecosystem 🥳
#MassSpectrometry #Metabolomics
Available through @bioconductor release 3.18
A small tutorial (incl :docker:) showcasing this update: https://bit.ly/3QxVxFf
My view during my workshop on #LC-MS #Metabolomics data analysis with the @bioconductor #xcms :rstats: package during the Munich Metabolomics Meeting 😳
Reason: HDMI connection was only available next to the audio system at the back of the lecture hall 😂
I spent SO MANY HOURS in grad school manually adjusting peak baselines and deciding what should or shouldn't count as a peak and then going back and doing it all again because I called it a peak in one sample but not the other. I'm SO happy that progress is being made on this problem and very excited to read this preprint!
https://www.biorxiv.org/content/10.1101/2023.07.28.551024v1
#GCMS #LCMS #XCMS #AnalyticalChemistry #Chromatography
#Metabolomics
@lgatto @translational_proteomics
You could use #xcms in combination with all other #RforMassSpectrometry package. Maybe more info here: https://jorainer.github.io/xcmsTutorials/
My recent PR to the @bioconductor #xcms package has the ID 666 👹
well - no surprise, it comes with some devilishly good new functionality:
- fully based on the #Spectra and MsExperiment :rstats: packages
- code refactoring to increase performance
- ...
@lgatto @toschber excellent idea - could go into #Chromatograms or #xcms (maybe along with the peak detection method?).
As Laurent said, we at #RforMassSpectrometry are always open for contributions from the community
Currently working on a major update of the #xcms #rstats #Bioconductor package: switch to our new, more powerful #MS infrastructure: the #Spectra package https://github.com/RforMassSpectrometry/Spectra
