How do you pronounce “MS” when it’s the abbreviation for “manuscript?”
According to both the online Oxford and Merriam-Webster dictionaries, it’s pronounced “em ess,” making it an initialism rather than an abbreviation. (It’s also shown in capital letters, MS, in keeping with it being an initialism.)
My own experience styles it lower case, ms, and I’ve never heard anyone say “em ess.” However, that’s exactly what both sources give as the US pronunciation. (Perhaps my colleagues and I were all quite sheltered. I don’t know.)
To me it makes sense to use the article that matches the reading you intend as a result. If you expect the readers to say “em ess” in their heads, use “an MS.” For the result “manuscript,” use “a MS.” Give the readers a clue about your intention, and they’ll follow.
And whatever you do, do not style it “Ms.” That’s an entirely different issue (and it’s pronounced “mizz”).
ETA: After a year and a half, and no small amount of discussion among my peers and colleagues, I’ve come to the conclusion that no one who understands the abbreviation would ever say “em ess” (despite what the dictionaries tell us); they’d say “manuscript.” However, I’m not going to tell you never to use “an MS.” If that’s what you want to do, it’s certainly correct from a mechanical standpoint; someone reading that will either say “an em ess” (because they don’t know any better, and you’ve led them to that conclusion with the “an”) or think “WTF are they doing? It’s a manuscript.”
Have at it, folks. And thank you to @Mededitor and @LisaPoisso for the thoughtful discussion today, which poked me enough that I came here and wrote this.