Estimating the statistical significance of the difference between two spectra or series is challenging. Multivariate significance tests exist but the limitations preclude their use in many common cases; e.g., one-sided testing, unequal variance and when few repetitions are acquired all of which are required in magnetic spectroscopy of nanoparticle Brownian motion (MSB). We introduce a test, termed the T-S test, that is powerful, exact (type I error is the selected significance threshold when the null hypothesis is true) and flexible. It is flexible enough to be one or two sided and the one sided version can specify arbitrary regions where each spectra should be larger. The T-S test takes the one or two sided p-value at each frequency and combines them using Stouffer’s method. We evaluated it using simulated spectra and measured MSB spectra. For the single sided version, mean of the spectrum, A-T, was used as a reference; the T-S test is as powerful when the variance at each frequency is uniform and outperforms when the noise power is not uniform. For the two sided version, the Hotelling T2 two-sided multivariate test was used as a reference; the two-sided T-S test is only slightly less powerful for large numbers of repetitions and outperforms rather dramatically for small numbers of repetitions. The T-S test was used to estimate the sensitivity of our current MSB spectrometer showing 1 nanogram sensitivity. Using eight repetitions the T-S test allowed 15 pM concentrations of mouse IL-6 to be identified while the mean of the spectra only identified 76 pM.