How do I compare measured ratios to calculated ratios in peptide mass spectrometry?
From a statistical perspective ratios are icky because the variance of the sampling distribution of a ratio decreases with the size of the numerator and denominator being sampled to create the ratio. If you can get at the numerator and denominator separately, then you should absolutely do that and look at count based tests like the Chi-square test, Fisher's exact test, or Poisson regression. 

That said, a t-test would be appropriate in the two-sample case if its assumptions are met.  You need to check that both samples are normally distributed, ideally via a qq-plot. You also need to check the variance of both samples and choose a variant of the t-test that does or does not assume equal variances.

If the samples are not normally distributed, then the next approach would be a Mann-Whitney U test.