Use an apostrophe to pluralize abbreviations composed of both upper and lower case letters. For example, "Mary had two PhD's and an MA to her name." Notice that the abbreviation 'PhD's' has been pluralized with an apostrophe.
Note that abbreviations that include two or more periods can be pluralized using an apostrophe. For example, "The C.O.D.'s have been paid for," is acceptable.
Use an apostrophe to pluralize abbreviations when the meaning would be confusing or ambiguous without the apostrophe. "The sailor sent out two SOS's," is correct, as the sentence is clarified by using an apostrophe.
Avoid ambiguity by omitting the apostrophe when it can cause confusion. The use of an apostrophe here confuses the reader: "FDA's paper flawed." This sentence could mean the FDA has actual paper that is in some way flawed, or it could mean that they have written a paper that is flawed. Omitting the apostrophe here pluralizes the word without seeming to make it possessive.
Notice the use of capital letter abbreviations such as URL, CMS or P and Q. To pluralize these abbreviations you would not use an apostrophe, so they would become URLs, CMSs and Ps and Qs.
Note that abbreviations that do not include periods are not pluralized with an apostrophe. For example, "The CODs have been paid for."