Hello !
My task is to sort out endothelial cells from mouse lungs. Im using antibodies against CD31 and VEGFR-2. The problem is, that VEGFR-2 seems not to work in lungs case, but in MS1 cell culture it works. Where can be the problem ? Is it good idea to sort cells stained only with one antibody ?

I have no experience with that particular cell source, but there is no reason that you can't sort with as many antibodies (colors) as your instrument can handle. My guess is that either cells that express VEGFR2 are not there or your not seeing them. In the later case, it may be that VEGFR2 is poorly expressed and you are just not detecting it. Titrate you antibodies to make sure everything is optimal. Try the antibody in PE and APC, to see which is better. The other possiblity is that all those other lung cells have a high autofluorescence and that you are not seeing your endothelial cells because they are lost in the mess. You may need aditional antibodies that help you identify and eliminate the cell populations you don't want to help you find the ones that you want. Using the forward and side light-scatter channels may also help you to gate-out the large cells you don't want and reduce the autofluorescence whne looking at your two markers.

Happy hunting.