ProGet does not support the deprecate command, but you could accomplish the same thing by adding a Manual Vulnerability. We can't seem to figure out what the deprecate command actually does, or how it's supposed to work. It's pretty poorly documented, and since there is no deprecated flag in npm package metadata, the client must be doing some strange things to check. Who knows... Anyways, I'd stick with Manual Vulnerability, since at least that's documented a lot better and won't change from client version to client version.