MGH Pathology: Flow and Mass Cytometry Core (CNY)

The core facilities at MGH Pathology provide flow cytometric cell sorting and analysis and mass cytometry with the most sophisticated instruments currently available. The core is located at the Charlestown Navy Yard (CNY) in building 149. 

Flow Cytometry: The core is able to analyze and physically separate cells based upon features detectable with fluorescently labeled monoclonal antibodies. We are able to sort unfixed specimens in our BSL2+ FACSAria Fusion sorter.

Mass Cytometry: Helios, which is a CyTOF (cytometry by Time-Of-Flight) system, permits single-cell analysis using stable heavy metal-tagged antibodies (~45) rather than fluorescent antibodies.

CNY Site

13th Street, Building 149, Room 5.226, Charlestown Navy Yard, Charlestown, MA 02129

Flow Cytometry Equipment:


  • SORP 4 Laser BD Fortessa (OUT-OF-SERVICE)
  • SORP 5 Laser BD Fortessa X-20
  • SORP 5 Laser Cytek Aurora with Plate Loader
    • Chart of Aurora configuration


  • SORP 4 Laser BD FACSAria II Cell Sorter
  • SORP 5 Laser BD FACSAria Fusion Cell Sorter, BSL2+
  • 3 Laser BD FACSMelody Cell Sorter, BSL2+

Chart of BD FACS configuration

Mass Cytometry Equipment: Helios (a CyTOF system)

For inquiries on the CyTOF, please contact

First-time Users

To get started please email flow core staff and include both emails: and

Returning Users

Sort Appointments (FACS):

Sort Request Form

  • All sort times will be scheduled on a "first come, first served" basis and users who fill out the request form will get preference over users who just email.

Analyzer Appointments:

For independent analysis please use the “Schedule” link to book analyzer time.

  • NOTE: The first user of the day should turn the machine on 15 minutes before running to allow the lasers sufficient time to warm up. The last user of the day is responsible for shutting down the computer and machine, to avoid leaving the lasers on overnight – double check on the schedule whether you are the last user before you leave! Instruments left on overnight will have the time charged to the last user as if they ran the whole time.

Cancellation Policy: 

Sorting and CyTOF appointments must be cancelled at least five business days in advance to avoid incurring the full fee, unless the user can find someone to replace the booking.

Tardiness Policy: 

If you are running late for sorting, you must contact the Flow Core Staff Members. If you are beyond 15 minutes late, your appointment may be subject to cancellation with charge. 

Sort Time Extension Policy: 

The Flow Core Staff will not be extending sort times beyond their scheduled bookings. Sorts will end at the designated time, regardless of whether the sort is "finished". Please plan accordingly. 

Data Storage Policy: 

All users are responsible for their own data and it is highly recommended that files are backed up after every run. The core is not responsible for lost data due to a computer crash or other issue. All files and experiment templates older than one month will be deleted and removed from the computers. Very large files (containing over a million events) should be deleted after every run, as their storage fills up the program slows down. All files for users who have been inactive for over a year will be deleted.