AAT Bioquest

What are the differences between magnetic-activated cell sorting and FACS?

Posted May 9, 2023


Magnetic-activated cell sorting (MACS) and FACS (fluorescence-activated cell sorting) are two different types of cell sorting techniques. There are a few significant differences between the two methods. 

Magnetic-activated cell sorting 

MACS works by using magnetic particles that are coated with antibodies that bind to specific cell surface markers. These magnetic particles attach to targeted cells in a mixed cell population, allowing them to be separated from the rest of the cells using a magnetic field. 

The biggest advantage of magnetic-activated cell sorting is its speed. This cell sorting method is about 4 to 6 times faster than fluorescence-activated cell sorting, allowing researchers to run a higher volume of samples in a shorter time. 

The disadvantage of MACS is that the magnetic nature of the process can be very harsh on fragile cells and can damage the target cell membrane. This can make it especially challenging to isolate a sufficient quantity of the desired cell when working with cells of higher rarity. 


FACS uses fluorescent labeling to target and isolate groups of cells based on their physical and biological characteristics such as size, morphological parameters, and granularity. The desired cells are isolated from the rest of the population on the basis of their fluorescent signal. 

The biggest advantage of FACS is its versatility. This method enables researchers to separate cells based on size and granularity as well as their surface markers, allowing for more in-depth isolations. 

The disadvantage is that it takes around 2 to 3 hours to run a single sample, which is much longer than other cell sorting methods. Moreover, the larger sample sizes increase the likelihood of contamination in the sample. 

Flow cytometers, which are required to perform FACS, are very expensive. Moreover, learning to operate the equipment can involve many hours of training. 

Additional resources

Fluorescence- and magnetic-activated cell sorting strategies to isolate and enrich human spermatogonial stem cells

Fluorescence Activated Cell Sorting (FACS)

Flow Cytometry Reagents

ReadiUse™ CFSE [5-(and 6)-Carboxyfluorescein diacetate, succinimidyl ester] *CAS 150347-59-4*