You cannot easily do it by FACS. Firstly, specific surface markers of chondrogenic differentiation are not defined. Secondly, if the cells have differentiated properly, they will have elaborated extracellular matrix that you will need to digest to reach the cells for FACS. However, the digestion can also digest any markers you might look for from the cell surface. Better and easier to extract RNA and do RT-PCR for known markers, which must include collagen II and aggrecan. Also do histology/immunohistochemistry to show actual matrix elaboration of these molecules. Matrix digestion and measurement of glycosaminoglycans by assay, collagen II by ELISA etc will also give some quantification of the matrix elaborated and thus the differentiation.

I agree with Dr. Johnstone. You also might try a marker for type-IX collagen, the bridge molecules between type-II collagen and non-collagenous ECMs.

Full text in my researchgate page; 

Cells were detached with trypsin-EDTA (0.25 %), and then centrifuged at +4 °C three times, 5 min at 1200 rpm, washing with fresh medium each time. The pellets were resuspended in freshly prepared cell culture medium and transferred into falcon tubes. After cell counting (between 103 and 106), the cells were incubated with fluorescein isothiocyanate (FITC)- and phycoerythrin (PE)-conjugated monoclonal antibodies against cell surface markers (CD29, CD44, CD90, CD166, HLA-DR, CD10, CD11b, CD14, CD34, CD45, CD117), with appropriate controls, at 4 °C for 50 min, protected from the light. The cells were washed by the addition of PBS containing 0.1 % sodium azide, followed by centrifugation for 5 min at 1200 rpm. The supernatant was removed and the cells were resuspended in assay buffer and analyzed with a flow cytometer. Results were evaluated using the native software of the flow cytometer (Beckman Coulter Navious Software) (Are biological agents toxic to human chondrocytes and osteocytes? Isyar M, Bilir B, Yilmaz I, Cakmak S, Sirin DY, Guzelant AY, Mahirogullari M. J Orthop Surg Res. 2015 Jul 30;10:118. doi: 10.1186/s13018-015-0264-y.).

For a number of reason I believe there is not a good marker for chondrogenic differentiation.  

The most reliable way is to stain micromass pellets with  toluidine blue and safranin O , which complexes with sulfured proteoglycan and glycoanimoglncans, the product of mature chondrocytes.  

 Another is  [35S] Incorporation Assay which is based on the incorporated  radioactive sulphate into the ends of glycoaminoglycans during chondrogensis. 

If you would like protocols or links to the papers I published send me a message. 

Why do you ask since you know the answer? :)))

You know its not immunflow cytometric methods (The most reliable way is to stain micromass pellets with  toluidine blue and safranin O , which complexes with sulfured proteoglycan and glycoanimoglncans, the product of mature chondrocytes.)

Is it possible to make the hMSC differentiation in 2D? I mean NOT IN PELLETS.... because what I am testing is a bioactive material(film) that I prepare... therefore I want to see the if in my bioactive surface differentiation is enhanced or something like this.... and my control will be differentiation in a normal culture plate... but still not in pellets... is it possible? thanks

Ah, that's a trickier question, and the answer depends on what your goal is for the use of your bioactive film. If you are thinking it will be the basis of building a cartilage implant, a 2D film is perhaps the hardest way to start. You might get some stimulation of some genes that you can detect by RT-PCR even at lower cell densities if you have something that stimulates differentiation attached to your bioactive film, or see it when you add a chondrogenic medium. However, cartilage is a tissue defined by elaboration of an extensive 3D extracellular matrix, not by gene expression. Once you get cells to differentiate into chondrocytes they tend to stop proliferating, so its not easy to build a 3D construct that is relevant to in vivo needs from a 2D system. 

Consider also that cell density is important, but at the point where they pile up and become chondrocytes e.g. in micromass, one would start to ask how relevant the bioactive film is if the cells that differentiate aren't in contact with it. Careful controls needed.

One other comment in response to the suggestion of histological staining (toluidine blue/safranin O) or 35S-labeling to define chondrogenesis. I applaud the use of anything that examines actual matrix production, not just gene expression. At a minimum, the histological staining should be done. However, even undifferentiated MSCs can make large proteoglycans, as do other cell types, so these aren't necessarily specific. The reliable marker of a chondrocyte is collagen type II, detected at both the gene (e.g. RT-PCR) and protein (e.g. immunohistochemistry, ELISA, Western blots) level. Even that won't define the type of chondrocyte you have created but its a basic requirement to define chondrogenic differentiation.