The amount of tax that you say the IRS is asking for strongly implies that you are at a financial level where you should be working with a tax professional who specializes in high-net-worth individuals, not doing it yourself.
If you choose to try to handle this yourself, follow the instructions in the IRS letter for how to respond if you disagree with the amount owed. Read the entire letter carefully. Be sure to respond by the deadline in the letter. Send your response by a service that provides tracking and confirmation of delivery, such as certified mail with a return receipt. Keep a copy of everything you send.
If you prepare an amended return (which seems likely), follow the instructions in the IRS letter for where to send it, which is probably different from where you would send it if you were filing it on your own initiative.
