Cytometry and Antibody Technology

NovoCyte Penteon

Traditional benchtop analyzer

Home » Benchtop Analyzers » NovoCyte Penteon


The NovoCyte Penteon is both very nimble and easy to use. Compared to other traditional benchtop analyzers in the CAT Facility, the Penteon has the highest number of detectors.  Features include:

  • 5 lasers (349nm, 405nm, 488nm, 561nm and 637nm) and 30 detectors
  • NovoSampler Q loads tubes and plates
  • Intuitive software
  • High sensitivity and resolution 
  • Wide, 7-log dynamic range eliminates the need for routine detector adjustments (learn more about SiPM detectors here)
  • Equipped with automation features for for walk-away operation
  • Volumetric acquisition – provides true count of the cells in each sample
NovoCyte Penteon 5-30
Model : NovoCyte Penteon
Manufacturer: Agilent
Optical configuration
Located in BSLC room R022

Software Tutorial

Sample Preparation Tips

Accepted Tubes

The Penteon accepts 5mL round bottom tubes (FACS tubes) and a variety of 96- and 384- well plates including deep-well.

Sample Volume/Concentration

Many users will not need to make any instrument adjustments to the Penteon instrument settings, so samples can be concentrated depending on how fast the sample wants to be run. Samples can be run between 5 to 120 μL/min. Regardless of the volume used, it’s important to know the value so that it can be entered into the software.

  • 200-500 μL is a typical volume, but may vary depending on the experiment and samples
  • It’s better to bring concentrated samples, once you are at the cytometer you can easily dilute your tubes if they are running to quickly
  • In general, run samples at less than 35,000 events/sec
Dead Volume

Dead Volume is the volume of the sample remaining inside the sample tube or plate well that cannot be aspirated into sample injection probe after each sample acquisition.  NovoSampler Q User Manual p.27-29.

Sample Overhead and Minimal Sample Volume

Sampling Overhead Volume is the volume of extra sample aspirated into the SIP during each sample acquisition. Sampling Volume is the volume of the sample user defined in the Stop Condition. Sample Volume is the volume of the sample user prepared and placed inside the sample rube or plate well before each sample run.  NovoSampler Q User Manual pp 27-29


In development

Startup - First user in the day
  1. Check on the Fluidics tank: everything full, waste empty. NOTE - remove the tanks from the fluidic station before filling them up, spills may damage the electronic balance at the bottom of the unit.
  2. Power on the instrument - it will take ~6 minutes before the instrument is ready to go.
  3. Open your Windows session and the software.
  4. Run the QC Test protocol, from the instrument menu (see below for instructions).

If the instrument has already been started by another user, you do not have to repeat these steps.

How and when should I run the QC Test

Run the QC Test whenever you turn the instrument ON. The test should take ~6 minutes.

1 - Prepare the beads: vortex the tube, add 1 drop to 0.5ml of diH2O
2 - Make sure the correct plate or rack is selected
3 - From the Instrument menu, check QC Test
3 (optional) - save the file when prompted
4 - Check the bead lot and location of the bead sample on the plate, press Run
5 - The software runs 3 tests: Electronic Noise, Optical Noise, and the QC Test
6 - Everything should pass. Contact the CAT Facility if anything fails.

How do I use the Compensation Wizard / The Compensation Wizard is acting funny

Below is a training video on the NovoExpress Auto Compensation tool. There's a few hiccups with the tool: 1 - the software decides the location and order of the controls on the plate, which may not fit what you decided when you loaded your plate. We suggest adding your compensation controls in tubes so you can re-arrange the order on the rack. 2 - Once the compensation matrix is calculated, you won't be allowed to run samples on any other platform then the one that you used for your controls. One way around that is to create an experiment template containing your compensation matrix. See video for details.

No data is showing
  • It is possible to open multiple instances of the NovoExpress software, having one of them connected to the instrument, while looking at previously saved experiments. So make sure that you are looking at the one that should be connecting to the instrument.
  • Reboot the computer re-open the session and software.
  • If that fails, power cycle both the instrument and the computer. This may trigger the instrument to do its 20 minutes clean-up protocol, followed by the 6 minutes startup. Sorry.
'Collision of SIP' error message
The probe hit something it wasn't expecting. This could be because:
1 - you have not selected the proper plate or tube rack in the Plate Manage Window, make the appropriate modification.
2 - you are using a whole new type of plate on the instrument and it has not been calibrated for it (contact the staff for assistance)
3 - the NovoSampler Q needs to be recalibrated (go to Instrument -> Calibrate)
End of session
  • From the Template menu, open the 3-tubes clean SIP protocol, and load tubes of 3ml of NovoClean, NovoRinse and water in position A1, A2, and A3 respectively on the rack. Let the instrument complete the protocol
  • Close the software and close your windows session

If you are the user in the day, turn off the instrument by pushing the power button. This will trigger a 20 minutes flow cell cleaning protocol. You are not required to stay during the protocol.

Data will not upload to the server
  • The data should upload automatically every 30 minutes, so be sure that you gave enough time for the transfer to occur.
  • Data should b exported to D:/NovoExpress Data. Make sure that you did not export your files in another location - either somewhere else on the disk, or a sub-folder of NovoExpress data.
  • In some case communication gets lost, contact the staff and we will alert our IT manager.