Welcome to PULSE, our monthly round-up of what's new in Mass Dynamics.
The big news this month: the AI tool you already use, whether that's Claude, ChatGPT or Codex, can now connect to your Mass Dynamics workspace.
Three new capabilities are ready for you:
01 Connect your AI tool to Mass Dynamics
02 Bring your own analysis sets to GSEA
03 Run GSEA and ORA on your PTM data
01 · Connect your AI tool
Your AI tool, now integrated with Mass Dynamics.
Ask in plain language and it gets your data in and your analyses running, right where your existing data already is.
Your AI tool, such as Claude or Codex, is now a third way to work with your Mass Dynamics workspaces, alongside the browser and the API.
A dataset your AI tool builds today is one you can open in the browser tomorrow, or run a thousand times through the API.
Why connect it
✓
Less setup, more science. Hand over the fiddly parts, like uploads, sample names and metadata, by asking in plain language.
✓
Work in the tool you already use. Claude, ChatGPT, Codex, Copilot Studio or any other MCP-compatible tool. No new app to learn, nothing to install.
How it connects: through our MCP server. MCP (Model Context Protocol) is the open standard AI tools use to plug into other software, so any AI tool that lets you add an MCP server can connect to Mass Dynamics.
Everything you need to get set up is on the next page. Rather do it together? Just reply.
02 · Interpret the biology
Bring your own analysis sets to GSEA
Your GSEA analysis is no longer limited to the gene sets we support. CAMERA GSEA now runs against your own target lists, panels or signatures from earlier work, alongside the knowledge bases already built in.
Add your analysis set. After choosing your input dataset and species, click Add analysis set, name it and pick the lists to test against.
Adding more flexibility, a new Modify Selection option on the GSEA dot plot lets you switch between saving only the entities measured in your data and saving the entire pathway.
A modification is often where the biology actually happens. Like a switch, it can redefine a protein's function and reshape an entire pathway.
GSEA and ORA now run on PTM datasets, and you can ask the question two ways:
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At the site. Test your modified sites directly against OmniPath kinase-substrate signatures.
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At the protein. Roll your sites up to their proteins and test against the same pathway knowledge bases you already use for proteins.
From the ORA dot plot, new selection options let you take the entities measured in your dataset, or only those that overlap the pathway.
Also new: the PTM intensity barplot, under your control. Sort and color the x-axis, group by as many metadata layers as your design needs, and filter samples and groups out of the view. It now works on peptide-level data too.
