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sneumannHi, 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 <a href="https://mastodon.online/tags/Metabolomics2025" class="mention hashtag" rel="nofollow noopener" target="_blank">#Metabolomics2025</a>, featuring <a href="https://mastodon.online/tags/xcms" class="mention hashtag" rel="nofollow noopener" target="_blank">#xcms</a>, <a href="https://mastodon.online/tags/massbank" class="mention hashtag" rel="nofollow noopener" target="_blank">#massbank</a>, not <a href="https://mastodon.online/tags/metfrag" class="mention hashtag" rel="nofollow noopener" target="_blank">#metfrag</a> but <a href="https://mastodon.online/tags/CASMI" class="mention hashtag" rel="nofollow noopener" target="_blank">#CASMI</a> and <a href="https://mastodon.online/tags/MetFamily" class="mention hashtag" rel="nofollow noopener" target="_blank">#MetFamily</a>, please find them at <a href="https://doi.org/10.5281/zenodo.15719512" rel="nofollow noopener" translate="no" target="_blank">https://doi.org/10.5281/zenodo.15719512</a>

Johannes RainerWe just added a <a href="https://fediscience.org/tags/reproducible" class="mention hashtag" rel="nofollow noopener" target="_blank">#reproducible</a> example for large-scale <a href="https://fediscience.org/tags/metabolomics" class="mention hashtag" rel="nofollow noopener" target="_blank">#metabolomics</a> data preprocessing using the <a href="https://genomic.social/@bioconductor" class="u-url mention" rel="nofollow noopener" target="_blank">@bioconductor</a> <a href="https://fediscience.org/tags/xcms" class="mention hashtag" rel="nofollow noopener" target="_blank">#xcms</a> package to <a href="https://genomic.social/@phili" class="u-url mention" rel="nofollow noopener" target="_blank">@phili</a> 's <a href="https://fediscience.org/tags/Metabonaut" class="mention hashtag" rel="nofollow noopener" target="_blank">#Metabonaut</a> tutorials resource! 💪<a href="https://rformassspectrometry.github.io/Metabonaut/articles/large-scale-analysis.html" rel="nofollow noopener" translate="no" target="_blank">https://rformassspectrometry.github.io/Metabonaut/articles/large-scale-analysis.html</a>runs also on a standard 💻 - thanks to the new memory-saving processing in <a href="https://fediscience.org/tags/xcms" class="mention hashtag" rel="nofollow noopener" target="_blank">#xcms</a> using the largest (n=4000) data set from MetaboLights<a href="https://fediscience.org/tags/rstats" class="mention hashtag" rel="nofollow noopener" target="_blank">#rstats</a> <a href="https://fediscience.org/tags/teammassspec" class="mention hashtag" rel="nofollow noopener" target="_blank">#teammassspec</a>

Johannes RainerUpdates from our continuous development of the <a href="https://fosstodon.org/tags/xcms" class="mention hashtag" rel="nofollow noopener" target="_blank">#xcms</a> <a href="https://fosstodon.org/tags/rstats" class="mention hashtag" rel="nofollow noopener" target="_blank">#rstats</a> :rstats: <a href="https://fosstodon.org/tags/metabolomics" class="mention hashtag" rel="nofollow noopener" target="_blank">#metabolomics</a> package:👉 retention time alignment against external data set 👉 chromatographic peak quality metrics 👉 preformance improvementsAll available in current version in <a href="https://genomic.social/@bioconductor" class="u-url mention" rel="nofollow noopener" target="_blank">@bioconductor</a> release 3.21 🚀 Up next: memory-saving analysis of very large data sets!<a href="https://fosstodon.org/tags/TeamMassSpec" class="mention hashtag" rel="nofollow noopener" target="_blank">#TeamMassSpec</a>

Johannes RainerSharing our 🚀 Metabonaut resource:A collection of comprehensive tutorials for LC-MS/MS <a href="https://fosstodon.org/tags/metabolomics" class="mention hashtag" rel="nofollow noopener" target="_blank">#metabolomics</a> data analysis in :rstats: by <a href="https://genomic.social/@phili" class="u-url mention" rel="nofollow noopener" target="_blank">@phili</a> et al.Learn raw data processing, annotation & stats with <a href="https://fosstodon.org/tags/xcms" class="mention hashtag" rel="nofollow noopener" target="_blank">#xcms</a>, <a href="https://fosstodon.org/tags/RforMassSpectrometry" class="mention hashtag" rel="nofollow noopener" target="_blank">#RforMassSpectrometry</a> & <a href="https://genomic.social/@bioconductor" class="u-url mention" rel="nofollow noopener" target="_blank">@bioconductor</a> - all reproducible & community-driven! <a href="https://fosstodon.org/tags/rstats" class="mention hashtag" rel="nofollow noopener" target="_blank">#rstats</a><a href="https://fosstodon.org/tags/CompMS" class="mention hashtag" rel="nofollow noopener" target="_blank">#CompMS</a> <a href="https://fosstodon.org/tags/teammassspec" class="mention hashtag" rel="nofollow noopener" target="_blank">#teammassspec</a> <a href="https://rformassspectrometry.github.io/Metabonaut/" rel="nofollow noopener" translate="no" target="_blank">https://rformassspectrometry.github.io/Metabonaut/</a>

Johannes RainerAnd <a href="https://genomic.social/@phili" class="u-url mention" rel="nofollow noopener" target="_blank">@phili</a> with her poster on a complete end-to-end workflow for untargeted <a href="https://fosstodon.org/tags/metabolomics" class="mention hashtag" rel="nofollow noopener" target="_blank">#metabolomics</a> data analysis in <a href="https://fosstodon.org/tags/rstats" class="mention hashtag" rel="nofollow noopener" target="_blank">#rstats</a> with <a href="https://genomic.social/@bioconductor" class="u-url mention" rel="nofollow noopener" target="_blank">@bioconductor</a> and <a href="https://fosstodon.org/tags/RforMassSpectrometry" class="mention hashtag" rel="nofollow noopener" target="_blank">#RforMassSpectrometry</a> <a href="https://fosstodon.org/tags/xcms" class="mention hashtag" rel="nofollow noopener" target="_blank">#xcms</a> etc<a href="https://fosstodon.org/tags/MetSoc2024" class="mention hashtag" rel="nofollow noopener" target="_blank">#MetSoc2024</a> poster # 1008 👉 <a href="https://doi.org/10.5281/zenodo.11370612" rel="nofollow noopener" translate="no" target="_blank">https://doi.org/10.5281/zenodo.11370612</a> 👀

Johannes RainerOn my way 🚞 to Vienna 🇦🇹for the MassSpec Forum 2024 <a href="https://bit.ly/3T3LFEm" rel="nofollow noopener" translate="no" target="_blank">https://bit.ly/3T3LFEm</a> !Will have a workshop on how to handle and preprocess LC-MS data with our <a href="https://genomic.social/@bioconductor" class="u-url mention" rel="nofollow noopener" target="_blank">@bioconductor</a> :rstats: packages <a href="https://fosstodon.org/tags/Spectra" class="mention hashtag" rel="nofollow noopener" target="_blank">#Spectra</a> and <a href="https://fosstodon.org/tags/xcms" class="mention hashtag" rel="nofollow noopener" target="_blank">#xcms</a> !<a href="https://fosstodon.org/tags/metabolomics" class="mention hashtag" rel="nofollow noopener" target="_blank">#metabolomics</a> <a href="https://fosstodon.org/tags/massspectrometry" class="mention hashtag" rel="nofollow noopener" target="_blank">#massspectrometry</a>

Johannes RainerYes, we're still working on improving the <a href="https://fosstodon.org/tags/xcms" class="mention hashtag" rel="nofollow noopener" target="_blank">#xcms</a> <a href="https://genomic.social/@bioconductor" class="u-url mention" rel="nofollow noopener" target="_blank">@bioconductor</a> :rstats: package for LC-MS <a href="https://fosstodon.org/tags/metabolomics" class="mention hashtag" rel="nofollow noopener" target="_blank">#metabolomics</a> data preprocessing!This time: filter features based on quality criteria from <a href="https://mastodon.social/@davidbroadhurst" class="u-url mention" rel="nofollow noopener" target="_blank">@davidbroadhurst</a> et al. (<a href="https://doi.org/10.1007/s11306-018-1367-3" rel="nofollow noopener" translate="no" target="_blank">https://doi.org/10.1007/s11306-018-1367-3</a>).great contribution from <a href="https://genomic.social/@phili" class="u-url mention" rel="nofollow noopener" target="_blank">@phili</a> !More info: <a href="https://bit.ly/3UqmfSx" rel="nofollow noopener" translate="no" target="_blank">https://bit.ly/3UqmfSx</a>Next on the list: mzTab-M export.

Johannes Rainer<a href="https://fosstodon.org/tags/xcms" class="mention hashtag" rel="nofollow noopener" target="_blank">#xcms</a> version 4 is here! Now we use the full power of the <a href="https://fosstodon.org/tags/Bioconductor" class="mention hashtag" rel="nofollow noopener" target="_blank">#Bioconductor</a> <a href="https://fosstodon.org/tags/Spectra" class="mention hashtag" rel="nofollow noopener" target="_blank">#Spectra</a> :rstats: package and the <a href="https://fosstodon.org/tags/RforMassSpectrometry" class="mention hashtag" rel="nofollow noopener" target="_blank">#RforMassSpectrometry</a> package ecosystem 🥳 <a href="https://fosstodon.org/tags/MassSpectrometry" class="mention hashtag" rel="nofollow noopener" target="_blank">#MassSpectrometry</a> <a href="https://fosstodon.org/tags/Metabolomics" class="mention hashtag" rel="nofollow noopener" target="_blank">#Metabolomics</a>Available through <a href="https://genomic.social/@bioconductor" class="u-url mention" rel="nofollow noopener" target="_blank">@bioconductor</a> release 3.18A small tutorial (incl :docker:) showcasing this update: <a href="https://bit.ly/3QxVxFf" rel="nofollow noopener" translate="no" target="_blank">https://bit.ly/3QxVxFf</a>

Johannes RainerMy view during my workshop on <a href="https://fosstodon.org/tags/LC" class="mention hashtag" rel="nofollow noopener" target="_blank">#LC</a>-MS <a href="https://fosstodon.org/tags/Metabolomics" class="mention hashtag" rel="nofollow noopener" target="_blank">#Metabolomics</a> data analysis with the <a href="https://genomic.social/@bioconductor" class="u-url mention" rel="nofollow noopener" target="_blank">@bioconductor</a> <a href="https://fosstodon.org/tags/xcms" class="mention hashtag" rel="nofollow noopener" target="_blank">#xcms</a> :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 😂

Eric R. ScottI 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! <a href="https://www.biorxiv.org/content/10.1101/2023.07.28.551024v1" rel="nofollow noopener" target="_blank">https://www.biorxiv.org/content/10.1101/2023.07.28.551024v1</a><a href="https://fosstodon.org/tags/GCMS" class="mention hashtag" rel="nofollow noopener" target="_blank">#GCMS</a> <a href="https://fosstodon.org/tags/LCMS" class="mention hashtag" rel="nofollow noopener" target="_blank">#LCMS</a> <a href="https://fosstodon.org/tags/XCMS" class="mention hashtag" rel="nofollow noopener" target="_blank">#XCMS</a> <a href="https://fosstodon.org/tags/AnalyticalChemistry" class="mention hashtag" rel="nofollow noopener" target="_blank">#AnalyticalChemistry</a> <a href="https://fosstodon.org/tags/Chromatography" class="mention hashtag" rel="nofollow noopener" target="_blank">#Chromatography</a> <a href="https://fosstodon.org/tags/Metabolomics" class="mention hashtag" rel="nofollow noopener" target="_blank">#Metabolomics</a>

Johannes Rainer<a href="https://fosstodon.org/@lgatto" class="u-url mention" rel="nofollow noopener" target="_blank">@lgatto</a> <a href="https://genomic.social/@translational_proteomics" class="u-url mention" rel="nofollow noopener" target="_blank">@translational_proteomics</a> You could use <a href="https://fosstodon.org/tags/xcms" class="mention hashtag" rel="nofollow noopener" target="_blank">#xcms</a> in combination with all other <a href="https://fosstodon.org/tags/RforMassSpectrometry" class="mention hashtag" rel="nofollow noopener" target="_blank">#RforMassSpectrometry</a> package. Maybe more info here: <a href="https://jorainer.github.io/xcmsTutorials/" rel="nofollow noopener" target="_blank">https://jorainer.github.io/xcmsTutorials/</a>

Johannes RainerMy recent PR to the <a href="https://genomic.social/@bioconductor" class="u-url mention" rel="nofollow noopener" target="_blank">@bioconductor</a> <a href="https://fosstodon.org/tags/xcms" class="mention hashtag" rel="nofollow noopener" target="_blank">#xcms</a> package has the ID 666 👹 well - no surprise, it comes with some devilishly good new functionality: - fully based on the <a href="https://fosstodon.org/tags/Spectra" class="mention hashtag" rel="nofollow noopener" target="_blank">#Spectra</a> and MsExperiment :rstats: packages - code refactoring to increase performance - ...<a href="https://github.com/sneumann/xcms/pull/666" rel="nofollow noopener" target="_blank">https://github.com/sneumann/xcms/pull/666</a>

Johannes Rainer<a href="https://fosstodon.org/@lgatto" class="u-url mention" rel="nofollow noopener" target="_blank">@lgatto</a> <a href="https://fosstodon.org/@toschber" class="u-url mention" rel="nofollow noopener" target="_blank">@toschber</a> excellent idea - could go into <a href="https://fosstodon.org/tags/Chromatograms" class="mention hashtag" rel="nofollow noopener" target="_blank">#Chromatograms</a> or <a href="https://fosstodon.org/tags/xcms" class="mention hashtag" rel="nofollow noopener" target="_blank">#xcms</a> (maybe along with the peak detection method?).As Laurent said, we at <a href="https://fosstodon.org/tags/RforMassSpectrometry" class="mention hashtag" rel="nofollow noopener" target="_blank">#RforMassSpectrometry</a> are always open for contributions from the community

Johannes RainerCurrently working on a major update of the <a href="https://fosstodon.org/tags/xcms" class="mention hashtag" rel="nofollow noopener" target="_blank">#xcms</a> <a href="https://fosstodon.org/tags/rstats" class="mention hashtag" rel="nofollow noopener" target="_blank">#rstats</a> <a href="https://fosstodon.org/tags/Bioconductor" class="mention hashtag" rel="nofollow noopener" target="_blank">#Bioconductor</a> package: switch to our new, more powerful <a href="https://fosstodon.org/tags/MS" class="mention hashtag" rel="nofollow noopener" target="_blank">#MS</a> infrastructure: the <a href="https://fosstodon.org/tags/Spectra" class="mention hashtag" rel="nofollow noopener" target="_blank">#Spectra</a> package <a href="https://github.com/RforMassSpectrometry/Spectra" rel="nofollow noopener" target="_blank">https://github.com/RforMassSpectrometry/Spectra</a>

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