Earlier today Microsoft announced that it has filed a formal lawsuit against Barnes & Noble because of a patent infringement related to its Android-based Nook e-reader. Related to that, Microsoft is also taking legal action against Inventec and Foxconn, who manufacture the Nook e-reader.

The cause over this issue resides over certain aspects of the Android user experience. Microsoft was reluctant on certain issues but only mentioned “natural ways of interacting with devices by tabbing through various screens to find the information they need, surfing the Web more quickly, and interacting with documents and e-books” were owned and patented by Microsoft.

Usually instead of going after everybody and their mother, Microsoft typically lets them sign a patent licensing agreement. This brings us back to about this time last year when Microsoft and HTC entered a licensing deal that covers its Android devices. In return, HTC agreed to pay Microsoft royalty fees yearly.

The special deal with Barnes & Noble’s e-reader has to do with the custom version of Android that it runs. The custom operating system is manufactured by Inventec and Foxconn, who build the complete device. Reports say that Barnes & Noble, Foxconn, and Inventec haven’t signed a licensing deal and negotiations with the companies have come to a grinding halt. Apparently Microsoft has gotten fed up with the companies and decided legal action is the right choice.

Microsoft Corporate Vice President Horacio Gutierrez said: “We have tried for over a year to reach licensing agreements with Barnes & Noble, Foxconn and Inventec. Their refusals to take licenses leave us no choice but to bring legal action to defend our innovations and fulfill our responsibility to our customers, partners, and shareholders to safeguard the billions of dollars we invest each year to bring great software products and services to market.”

This is not the first and certainly not the last time Microsoft is suing a device manufacturer over the Android operating system. It is a very strict deal between Microsoft and Android and it doesn’t want to lose what gives it the upper hand in the mobile market.