A Top 20 global pharmaceutical company came to Dotmatics with a problem familiar to nearly every large research organization: thousands of instruments, generating data every day, with no way to see it as a whole. Here's how they started fixing that, and why they didn't try to fix all of it at once.
The problem: powerful instruments, disconnected data
Walk into almost any large pharma company's discovery or early development labs and you'll find the same thing: rows of high-performing instruments, each one working exactly as designed, each one quietly generating its own island of data.
That was the reality at this organization. Thousands of standalone instruments were running across labs in discovery research, early development, and manufacturing. Every instrument generated data independently. Every instrument stored that data in isolation.
The instruments themselves spanned multiple vendors and multiple modalities — LCMS systems from Waters, Agilent, Thermo Fisher, and SCIEX, sitting alongside multimode readers, liquid handlers, and flow cytometers. Each vendor used its own proprietary data format. Several vendors went a step further, locking chromatography results inside vendor-specific chromatography data systems (CDS) — Empower, OpenLab, and Chromeleon — which made the data even harder to extract, let alone combine.
The result: tens of thousands of files generated daily, scattered across instrument PCs, shared directories, therapeutic areas, functional groups, and divisions. A scientist in one group had no visibility into data generated by another. Nobody had a unified view of instrument performance, utilization, or output across the organization.
Starting with LCMS, not all 5,000 instruments at once
The company's goal was ambitious and clearly stated: integrate and harmonize data from more than 5,000 instruments across their campus. But they also knew that trying to connect everything on day one wasn't realistic. What they needed was a phased entry point — a place to start that would deliver value quickly while building the foundation for broader connectivity over time.
They chose to start with their LCMS fleet.
It was a logical first move. LCMS instruments were among the organization's highest-volume data sources, and also among the most fragmented. Multiple vendors, multiple CDS systems, and no way to merge chromatography data across any of them. Instrument performance couldn't be trended across vendors. Results couldn't be compared across sites or groups. AI couldn't be applied to a data set that had never been unified. Even basic operational questions — about instrument utilization, service history, or capital planning — required manual effort to piece together from disconnected sources.
The solution: Luma, without disrupting the lab
Dotmatics deployed Luma to begin connecting the LCMS fleet. Luma ingests chromatography data, converts proprietary vendor formats into a harmonized, FAIR-aligned structure, and makes that data available inside Luma for deeper processing, AI, and more.
Importantly, none of this required disrupting the lab. The instruments kept running. The CDS systems kept operating. Scientists continued working exactly as they had before. What changed wasn't the lab — it was where the data stopped. It no longer stopped at the boundary of each vendor's system.
The rollout happened in phases:
Phase 1 brought approximately 1,000 LCMS instruments online across Waters, Agilent, Thermo Fisher, and SCIEX, alongside roughly 500 additional instruments — multimode readers, liquid handlers, and flow cytometers.
Phase 2 and beyond set a clear path toward connecting more than 5,000 instruments total across the organization's campus, with the goal of eventually capturing, harmonizing, and making every instrument's data available for real-time insight and decision-making.
What became possible once the data was unified
Once LCMS data was flowing into Luma, the organization gained capabilities it had never had before:
A single view across all four vendor CDS systems — chromatography data from Waters, Agilent, Thermo Fisher, and SCIEX visible in one place for the first time.
Trending without manual work — across instruments, methods, and sites, with no manual data exports or reformatting.
Purity analysis across instruments and projects, from a single, unified view.
Instrument utilization and uptime data, sitting alongside scientific results — enabling conversations about service contracts, capital equipment planning, and lab layout that used to require guesswork.
A clean, structured, historically complete data set, ready for AI and machine learning, including Luma's own Luma Agent capability.
The ability to push harmonized data back out to connected systems — including ELNs, LIMS, and asset management — so downstream tools could benefit from the unified record too.
Why this matters beyond the numbers
The people involved in the implementation described something simple but striking: having all of that disparate data accessible in one place created insight — scientific and operational — that the organization had never had before. For the first time, they could draw insight from a combined data set spanning instruments, therapeutic areas, modalities, and stages of the research pipeline.
“Having access to all of that disparate data in a single location creates insight, scientifically and operationally, that their organization has never had before.” - Dotmatics implementation team on customer response
But maybe the more useful takeaway is how they got there. This organization didn't attempt to connect 5,000 instruments on day one. They started with a focused, high-value application — LCMS chromatography harmonization — proved the value, and used that as the foundation for an orchestration path forward.
That phased approach is repeatable, and it's how Dotmatics recommends organizations enter the orchestration story: start where the pain is most acute, deliver value quickly, and expand from a foundation that already works.
Curious what chromatography harmonization could look like for your own lab? Talk to Dotmatics about connecting your instrument fleet to Luma.