"Pressure makes diamonds"
— George S. Patton Jr.
ChromTroller (Chromatogram Acquisition Controller) is an automated control‑and‑analysis package that triggers an Agilent 1290 Infinity II UPLC‑MS via an Arduino and automatically analyzes the resulting chromatographic data.
It integrates LC/MS hardware (valves, sensors) with a remoteable client–server app and a robust analysis pipeline (MOCCA‑based), making it easy to slot an Agilent UPLC into automated workflows.
ChromTroller was developed to bridge OpenLab CDS v2.8 (which lacks macro automation) with external experiment controllers (e.g., RoboChem) by providing hardware control, data analysis, and TCP/IP communication between PCs.
- Installation
- Usage
- HPLC System Details
- Automation & Connectivity
- Project Structure
- Architecture
- Troubleshooting
- Contributing
- License
- Acknowledgements
- Author
Before proceeding, make sure you have:
- Python 3.8+ (Recommended: Python 3.13)
- Conda (Recommended: install via Anaconda)
- Git
- Arduino IDE from arduino.cc
- Agilent OpenLab CDS v2.8 (instrument control)
- (Optional) A Python IDE (e.g. PyCharm Community Edition)
Conda helps isolate project dependencies to avoid version conflicts across Python projects.
Git enables version control and easy updates to the codebase.
Create and activate the Conda environment from the provided spec:
conda env create -f .config/ChromTroller_env.yml
conda activate ChromTroller-
Assemble & wire hardware
Follow the control box assembly guide inassembly_readme.md. -
Upload the Arduino sketch
- Board: Arduino Uno R3
- Connect via USB and select the correct COM port in the Arduino IDE.
- Upload the firmware from
src/arduino_sketches/.
-
Supported peripherals
- VICI two‑position six‑port switch valve (with micro‑electric actuator & controller)
- OCB350 phase sensor board
- Agilent 1290 Infinity II UPLC‑MS
- Ensure OpenLab CDS v2.8 is installed and the instrument is available on the instrument PC.
- Connect the Arduino Uno R3 over USB; note the assigned COM port.
- Verify valves and sensors are wired and powered.
- Confirm file paths (raw data, results) are accessible by the account running ChromTroller.
Launch the ChromTroller server on the instrument PC:
python ChromTroller.pyThis exposes a TCP/IP socket for remote clients (e.g., RoboChem) while handling low‑level device control and data analysis.
Copy the example settings and customize for your setup:
src/settings_files/example_settings.json → src/settings_files/settings.json
Key fields to adjust:
- Hardware: Arduino COM port, valve positions, timeouts
- Analysis: Peak detection/integration parameters, baseline correction, wavelength ranges
- Paths: Project directories, file naming, raw data / results locations
- Targets: Retention times and tolerances for peak assignment
Instrument: Agilent 1290 Infinity II series with:
- High Speed Binary Pump (G7120A)
- Vial Sampler (G7129B)
- Thermostated Column Compartment (G7116B)
- Diode Array Detector (G7117B, DAD)
- InfinityLab LC/MSD XT Single Quadrupole detector (G6135C)
Injection hardware: External VICI two‑position six‑port valve with a 1.0 µL stainless‑steel loop (≈ 90 mm × 0.12 mm). Effective injected volume ≈ 1.4 µL due to additional valve dead volume.
OpenLab CDS v2.8 controls the UPLC but lacks a macro language for automation. ChromTroller fills this gap by providing:
- Hardware control (valve actuation, ERI digital I/O, phase sensor).
- Data analysis (see next section).
- Intersystem communication (TCP/IP sockets).
- A VICI valve is installed between the vial sampler and column.
- Position “load” fills the loop from the external process at low pressure; position “inject” places the loop inline for analysis.
- The VICI actuator is driven from the control box; the UPLC acquisition is triggered via Agilent ERI digital input.
- In OpenLab, a Sample Prep method is configured to wait for an external trigger (e.g., “pin 1”). Runs can be queued and started only when the START REQUEST signal is received from ChromTroller/Arduino.
This ensures tight timing between valve switching and acquisition start, improving retention‑time reproducibility and peak shapes.
Commands are human‑readable:
- Set:
Sx=y(no response unless specified) - Read:
Rx(always returns value)
Key variables include: valve position (5, 0=A / 1=B), START REQUEST (6), STOP (7), READY (8), phase sensor (9–10), and ERI state lines (11–13). See assembly_readme.md for the full table.
ChromTroller includes a processing pipeline based on the MOCCA package from the BAYER group. This analysis system parses the raw files, automatically processes the chromatograms contained within , and returns tidy results (e.g., a pandas DataFrame). Operations include:
- file parsing and dimensional reduction
- baselining and peak picking
- deconvolution, integration, and quantification
- identity assignment and error analysis
This enables multi‑wavelength chromatograms to be consumed by external platforms (e.g., RoboChem) as simple peak integrals.
ChromTroller/
├── .config/ # Conda environment specs
├── docs/ # Documentation & diagrams
├── reference_spectra/ # Reference spectra for analysis
├── reference_spectra_db/ # Spectra database
├── results/ # Latest analysis results
├── run_logs/ # Runtime logs
├── saved_results/ # Archived analysis runs
├── src/ # Source code
│ ├── ct_components/ # Core components
│ │ ├── devices/ # Device interfaces
│ │ └── mocca2/ # MOCCA-based analysis
│ ├── arduino_sketches/ # Arduino firmware
│ └── settings_files/ # JSON configuration
├── ChromTroller.py # Entry point (server)
├── assembly_readme.md # Control box build guide
└── README.md
graph TD;
Client[Client Application] <-->|TCP/IP Socket| Server[ChromTroller Server]
Server <--> Controller[LCMS Controller]
Controller <-->|Serial| Arduino[Control Box]
Arduino -->|I/O| LCMS[Agilent LC/MS]
Arduino -->|I/O| Valve[VICI Switch Valve]
Controller --> Monitor[System Monitor]
Controller --> Analyzer[Data Analyzer]
Connection issues
- Confirm the COM port in
settings.jsonmatches Device Manager. - Ensure Arduino drivers are installed and the board is detected.
- Close any program using the serial port (Arduino Serial Monitor, etc.).
Acquisition/trigger issues
- Verify the OpenLab Sample Prep method waits for the correct ERI pin.
- Check grounds/common reference between ERI and control box.
- Confirm valve position changes acknowledge back to the host.
Analysis errors
- Verify raw data paths and filenames match LC/MS export settings.
- Check analysis parameters (peak detection, baselining) against your method.
- Ensure reference spectra exist and are correctly formatted.
Contributions are welcome—please open a Pull Request with a clear description of your changes.
This project is licensed under the GNU General Public License (GPL). See the LICENSE file for details.
The GPL License is a copyleft license, that requires any derivative work to also be released under the GPL License.
This means any derivative software that uses this code remains open-source and freely available to the public.
- Bayer Group for the MOCCA package
- Agilent Technologies for instrument support
Olly Bayley — Noël Research Group, 2024 — o.m.bayley@uva.nl