Welcome to PULSE, our monthly round-up of what's new in Mass Dynamics. It's your discoveries compounding in practice: the same connected platform, doing more with your data each month, with nothing for you to rebuild.
We've laid this edition out the way you work - from getting your data in, to interpreting and comparing it, to driving it your way. Something moved in every part this month. The biggest is modifications: post-translational modifications now run end to end.
Here's what's new, across your workflow.
01 · Get your data in
Your data lands ready to work, whatever pipeline it comes from.
Modifications, end to end
A modification is often where the signal is - the difference between a protein being present and a protein being active. Post-translational modifications now run the full length of the platform: bring them in, prep them like any other data, and read them with modules built for the job.
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Bring PTMs in from your pipeline. Full Spectronaut support with site localization probabilities, plus the existing PTM support across DIA-NN and MD Format.
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Build a PTM table from your peptide data. Turn an existing peptide dataset into a PTM-level table, filtering by modification type and localization probability, and choosing how sites are summarized.
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PTMs flow through your prep. Filtering, normalization and imputation now work on PTM datasets, the same way they do on other entities
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More modifications. Added support and visualizations for four more: Deamidation, Pyro-glu, Met-loss, and TMTpro on top of the existing support for Oxidation, Phosphorylation, Acetylation, and Carbamidomethylation.
Two plots to read your modifications at a glance: a new PTM intensity barplot joins the PTM identification barplot, so you can see how much and how many, side by side.
Co-expression networks are easier to trust when you can see what's driving each module. Two additions this month give you exactly that.
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Module membership table. For every entity, see the module it's assigned to, its hub score (how central it is within that module), and how closely its expression tracks the module's overall pattern.
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Variance filter. A new option in the dataset form to keep the most variable entities, so your network is built on the signals that vary most across your data.
Explore it, ask an agent, or script it - the same pipeline runs underneath.
Science doesn't happen in one mode.
Some days you need a thousand different analyses, once. Some days you need one analysis, a thousand times. Mass Dynamics is built for both - three ways to drive the same platform:
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In the app. Click through it and explore, visually.
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With an agent. Ask in plain language - the Agent Pack is in beta now.
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Through the API. Script it, at scale.
Underneath, the same versioned pipeline runs every time - so the analysis you explore today becomes the workflow you scale tomorrow, across proteomics, transcriptomics and beyond. Flexible enough to discover, standard enough to scale. Same rigor, either way.
Whether this month moved the part of the workflow you live in or a part you'll grow into, it all lands on one connected platform. A modification you find today sits next to the proteins, peptides and transcripts you've already run, in the same workspace, with the same record of how you got there. Nothing to re-import, nothing to reconcile. That's what we mean when we say your discoveries compound - each layer you add makes the last one worth more.
Feedback on any of this - or want early access to what's next - just reply to this email. We read every one.
- Team Mass Dynamics
Mass Dynamics, Level 3, 31 Queen St, Melbourne, Victoria 3000, Australia
