#xcms — Public Fediverse posts

Hi, in case your phone didn't pick up the QR code to the slides of my Hitch-Hikers Guide to Computational Metabolomics talk this morning at #Metabolomics2025, featuring #xcms, #massbank, not #metfrag but #CASMI and #MetFamily, please find them at https://doi.org/10.5281/zenodo.15719512

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!

#TeamMassSpec

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

#CompMS #teammassspec

https://rformassspectrometry.github.io/Metabonaut/

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

👉 https://doi.org/10.5281/zenodo.11370612 👀

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 !

#metabolomics #massspectrometry

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 @[email protected] 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
- ...

https://github.com/sneumann/xcms/pull/666

@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