1. Prepare the Instrument

1. Switch on the MACS Sampler first, then the MACS Matchmaker.
2. Ensure the waste bottles are empty and the running buffer bottle is full and connected.
3. Check that the MilliQ wash bottle on the MACS Sampler is filled to prevent air bubbles.

For full details, see the Instrument Setup Workflow.

2. Select and Assemble the Chip

1. Choose the appropriate chip type for your assay. Use DDI chips (oligo-based) for regenerable assays or Click Chemistry chips (Tz/MeTz) for covalent immobilization. Refer to the Chip Selection Guide for help choosing.
2. Insert the chip into the flow chamber with the Lino logo facing up and toward the triangle marker.
3. Secure the lid with finger-tight screws.

Step-by-step assembly instructions are in the Chip Assembly section.

3. Prepare Samples and Buffer

• Use a running buffer supplied with Tween20 (0.05%) to minimize nonspecific binding and prevent air bubbles. For serum/plasma, 0.1% BSA can be added to the buffer to further reduce nonspecific interactions.
• Prepare analyte dilutions according to your experiment plan (e.g., titration series for SCK).
• For complex media (serum, plasma), centrifuge samples and use only the supernatant to avoid clogging.
• Place samples in the autosampler and buffer in the buffer position.

See Experiment Design for buffer recommendations and flow parameters.

4. Design Your Experiment

Use the Injection Manager in the software to set up your experiment phases:

• Immobilization: Functionalize the chip with your ligand. Recommended flow rate: 20 µL/min. Pickup volume: 30 µL to compensate for tail diffusion.
• Kinetics (SCK/MCK): Set up a titration series or single cycle kinetics phase. Recommended flow rate: 50 µL/min for both association and dissociation. Pickup volume: 30 µL.
• Regeneration: If using DDI chips, add regeneration steps (e.g., 50 mM NaOH, 30 s at 400 µL/min).

The flow rates above are the typical defaults — for the full per-phase table, see Recommended Flow Parameters. For detailed protocols, see Experiment Design and Surface Functionalization.

5. Prime and Prepare the Reader

1. Go to the Perform Tab and select the corresponding experiment.
2. Select the flow channel in the software.
3. Run Prepare Reader. If the flow chamber selected on the Prepare page differs from the saved experiment plan, review the warning before measuring. When all status indicators show "Success", you are ready to measure.
4. If preparation fails, use "Reoptimize" or manually check:
   • Coupling should be symmetrical across all 8 channels.
   • The Fourier Aperture should show symmetric intensity distribution.
5. Validate the preparation by clicking on Check Molograms. If the molograms are not recognized, repeat Prepare Reader.
6. Check for air bubbles on the chip surface. If present, prime the chip once or twice. If bubbles persist, reassemble the chip.

Manual coupling and XY-stage adjustment are described in Manual Chip Preparation.

6. Run the Measurement

1. Review your injection plan and verify vial placement on the well plate.
2. Press Start Measurement. The sensogram will begin recording in real time.
3. Monitor the live trace for expected binding behavior. If no signal increase appears during association, check the Troubleshooting guide.

7. Analyze Your Data

1. Open your measurement in Insights.
2. Use Clean Up Data to remove offsets, cut irrelevant parts, and smooth the signal. Start by removing the offset so all traces begin at zero.
3. Select the SCK or MCK phase and click Use for Evaluation.
4. Choose a binding model (start with Langmuir 1:1 for simple interactions) and run the evaluation.
5. Review the fitted curves and extracted parameters (k_on, k_off, K_D).

For model selection guidance, see Binding Models. For background on the theory, see Biomolecular Interaction Analysis.

8. Shut Down

1. Flush the fluidics system with ultrapure water using the Flush Fluidic System protocol.
2. If you used complex samples (blood, lysate), run the full cleaning protocol with Clean 1 and Clean 2 solutions.
3. For storage beyond 24 hours, run 20% ethanol through the system.

See Maintenance for detailed cleaning and storage procedures.