We have updated our preprint with a benchmark of 17 methods for structural annotation of MS/MS spectra: www.biorxiv.org/content/10.6...

Confronting spurious evaluations of computational methods in small molecule mass spectrometry

Mass spectrometry-based metabolomics detects thousands of small molecule-associated signals in biological samples, but the vast majority cannot be structurally identified. Mounting interest in this me...

biorxiv.org

Michael Skinnider@skinnider.bsky.social · 3mo ago

We have identified what we believe to be a critical issue in the way that computational methods for structural annotation of small molecule MS/MS spectra have historically been evaluated. Fortunately, there is a solution: www.biorxiv.org/content/10.6...

We have identified what we believe to be a critical issue in the way that computational methods for structural annotation of small molecule MS/MS spectra have historically been evaluated. Fortunately, there is a solution: www.biorxiv.org/content/10.6...

Very happy to share our latest efforts to map the mammalian metabolome, in which we combine large-scale in vivo isotope tracing with biochemical AI to discover several structurally unprecedented and biologically fascinating metabolites: www.biorxiv.org/content/10.6...

Comparative whole-brain and single-cell analyses are identifying neurons orchestrating neurological functions. Learn more in a new #SciencePerspective: https://scim.ag/3JOh0co

Unbiased discovery of neuronal architectures

Comparative whole-brain and single-cell analyses identify neurons orchestrating neurological functions

scim.ag

Thrilled to share our approach for language model-guided discovery of unknown mammalian metabolites: DeepMet. We’ve now used this approach to discover ~50 new human and mouse metabolites! www.biorxiv.org/content/10.1...

Language model-guided anticipation and discovery of unknown metabolites

Despite decades of study, large parts of the mammalian metabolome remain unexplored. Mass spectrometry-based metabolomics routinely detects thousands of small molecule-associated peaks within human ti...

biorxiv.org

Very happy to share this work testing a widespread assumption in chemical AI and showing that invalid SMILES are a feature, not a bug: www.nature.com/articles/s42...

Very happy to share our latest work on harmonizing raw mass spectrometry data from >21,000 proteomic experiments to enable meta-analyses of protein interactions and phosphorylation at the largest scale yet: www.nature.com/articles/s41...