See what your letter says and compare it to your net gain for that account for 2015. If the IRS has it right, then you really don't have an argument except to pay the tax they are demanding. If they want to charge you tax on something other than the net gain - for instance, if some of your entries on the Morgan Stanley form are missing the basis, or the basis is incorrect - then it would be worth your while to do your own calculations by entering this form in 2015 software and correcting the basis. You do that by clicking on one of the buttons to "add additional information," and put the corrected basis there. Boxes 1a through 1e should contain the info printed on the 1099-B.
Generally, the IRS does not ask you to amend your return if you agree with their assessment. If you don't agree, though, you will need to submit documents to prove your case. Either way, you are not submitting a new 1040 or 1040X - but if you don't agree with their assessment, you will need to submit a revised Schedule D and Form 8949.
