That's a lovely question. As there are no sampoles beyond our own DNA-RNA-protein biopsphere, no-one knows.
Some things can be stated though.
1.) it almost certain that the genetic code almost universally employed by the Terran biosphere is not dictated by the laws of chmeistry alone but contingent upon its history of formation. While a (say) Glycin-coding tRNA works because its chemical affinity to Glycin is orders of magnitude higher than for any other amino acid, it is quite conceivable that totally different tRNA (or whatever NA) could exist that display a similar preponderance towards glycin. Thus, a different molecular basis for genetics (different sugars, different nucleotides...), a different genetic code, and a different set of biogenic amino acids are all conceivable.
2.) Short of being toxic, an alien could simply be non-digestible - an alien amino acid could simply be immune to enteric proteases or pass by the transport proteins embedded in the gut wall. Also, they could be non-nourishing. Many Terran organisms (among them, humans) have deficiencies in amino acid synthesis, thus depending on their food containing those amino acids (which are called essential amino acids). If your alien beef does not contain all essential amino acids, you die of malourishment no matter how many alien calories your diet contains.
3. And yes, the foreign proteins culd happen to be toxic - the proteins or their constituent amino acids (or a foreigns nuclei acid, nucleoside or nucleotide, for that matter).
The subject got some treatment in a "hard science fiction" novel,
Encounter With Tiber, to which Buzz Aldrin lent his name. The rather humanoid aliens that dicover humanity around 7200 B.C. find, to their chagrin, that Earth's biosphere can't support them because (only) a few amino acids don't fit and accumulate in their body, causing some organ failure over time.