INTEGRATED CHROMATOGRAPHY
Two or Three Steps. One Run. 2D/3D Integrated Batch.
Your batch method is already step one. ChromaCraft™ adds the next — orchestrating multi-step purification on the Contichrom® CUBE in a single integrated run, with automated transfer, in-line dilution, and full method control across every dimension.
One System. Two or Three Purification Steps.
The moment you run your first batch method on the Contichrom® CUBE, you have the foundation for a 2D purification process. The same hardware, columns, and ChromIQ® software that ran your Protein A capture can route the eluate directly onto a second column — IEX polishing, HIC, desalting — without breaking the run.
The CUBE handles the handoff automatically:
- In-line dilution between steps
- No hold tank
- No manual intervention
- No separate method file per column
That’s 2D integrated batch chromatography. Add a third column step and it becomes 3D. The CUBE’s twin-column valve architecture supports both natively, and ChromaCraft™ designs the complete method in the same visual Gantt chart editor you already use for single-column batch.
The result is an automated, end-to-end purification train — capture through polishing to desalting — completed in a single unattended run. Collect one product pool or fractionate as desired. Time from load to final purified fraction drops from days to hours.
How It Works
The CUBE’s valve network connects the outlet of the first column directly to the inlet of the second. When the Dimension 1 UV trace meets the Product Transfer Window you set in ChromaCraft™, ChromIQ® diverts the eluate to Dimension 2 and applies in-line dilution at the ratio you specify.
The transfer window can be triggered two ways:
- Absolute mAU threshold — fires at a fixed UV value (peak front marker)
- Relative percentage of peak maximum — fires at a fraction of the observed peak height (peak tail marker)
The pumps adjust automatically. No manual action between steps.
Dimension 2 then runs its own equilibration, bind, wash, and elution sequence, governed by the method parameters defined for that column. Both steps run within the same ChromIQ® method.
For 3D methods, add a third column position using the Column Selection Valve Kit — a full capture → polishing → desalting train in one automated run.
Supported step combinations on the Contichrom® CUBE:
| Format | Step 1 | Step 2 | Step 3 | Required accessories |
|---|---|---|---|---|
| 2D | Isocratic (e.g. Protein A, IMAC) | Isocratic (e.g. SEC, desalting) | — | Column Bypass Valve Kit |
| 2D | Isocratic (e.g. Protein A) | Gradient (e.g. CIEX, AEX, HIC) | — | Column Bypass Valve Kit |
| 2D | Gradient (e.g. RP) | Gradient (e.g. AIEX) | — | Column Bypass Valve Kit + Buffer Selection Valve Kit |
| 3D | Isocratic | Gradient | Isocratic (e.g. desalting) | Column Bypass + Column Selection Valve Kits |
| 3D | Isocratic | Gradient | Gradient | Column Bypass + Buffer Selection + Column Selection Valve Kits |
Analysing Results: The Evaluation Center
Both dimensions of a 2D or 3D run are captured in a single, continuous run record in the Evaluation Center. The UV trace spans the complete method — you see the Dimension 1 elution, the transfer point, and the Dimension 2 (and Dimension 3) chromatogram as a single timeline.
- Peak integration — automatic or manual, applied independently to each dimension’s elution profile
- Fraction analysis — final collected fractions mapped against the full run trace; purity and yield assessed in one view
- Run comparison — overlay multiple 2D/3D runs to confirm reproducibility of both the transfer timing and the final product peak
- PDF report export — full structured report spanning all dimensions, transfer parameters included
- Excel / CSV export — complete signal data and integration results across the entire multi-step run
The ChromIQ® logbook records every system event — including the Product Transfer Window trigger — in an unalterable audit trail with data integrity checksums and multi-level user rights management.
Platform Advantages at a Glance
| Advantage | What it means in practice |
|---|---|
| No hold tanks between steps | Eluate transfers column-to-column automatically — no intermediate container, no manual handling, no wait |
| In-line dilution built in | Ionic strength or pH adjustment between dimensions is handled by the pump network — no separate dilution step |
| Single product pool | Fraction collection happens once, at the end of the final dimension — not after every step |
| Reduced QC burden | One run record, one chromatogram, one report — instead of three per downstream step |
| Same hardware as batch | No additional system purchase — 2D/3D runs on the CUBE you already have, with accessory valve kits |
| Direct scale-up path | 2D methods transfer directly to the Contichrom® PILOT 300X and TWIN systems |
Applications
| Molecule class | Typical 2D/3D configuration |
|---|---|
| Monoclonal antibodies (mAbs) | 2D: Protein A capture → CIEX polishing; 3D: Protein A → CIEX → desalting — full downstream train, single run |
| ADCs | 2D: Protein A capture → HIC (DAR fractionation); or HIC → IEX polishing |
| Recombinant proteins / hormones | 2D: His-Tag IMAC → IEX polishing; 3D: Protein L → IEX → SEC |
| Peptides | 2D: RP polishing (Dim 1) → AIEX polishing (Dim 2) — orthogonal gradient-gradient; or RP → desalting |
| Oligonucleotides | 2D: AEX gradient → RP polishing; orthogonal selectivity, single automated run |
| AAV / gene therapy | 2D: Affinity capture → IEX polishing |
| mRNA / LNP | 2D: Affinity → IEX at appropriate scale |
| Nutraceuticals / small molecules | 2D: RP → mixed-mode or normal-phase polishing |
One System. Two or Three Purification Steps.