Comparing Label-Free Quantitative Peptidomics Approaches to Characterize Diurnal Variation of Peptides in the Rat Suprachiasmatic Nucleus

Mammalian
circadian rhythm is maintained by the suprachiasmatic nucleus (SCN)
via an intricate set of neuropeptides and other signaling molecules.
In this work, peptidomic analyses from two times of day were examined
to characterize variation in SCN peptides using three different label-free
quantitation approaches: spectral count, spectra index and SIEVE.
Of the 448 identified peptides, 207 peptides were analyzed by two
label-free methods, spectral count and spectral index. There were
24 peptides with significant (adjusted p-value <
0.01) differential peptide abundances between daytime and nighttime,
including multiple peptides derived from secretogranin II, cocaine
and amphetamine regulated transcript, and proprotein convertase subtilisin/kexin
type 1 inhibitor. Interestingly, more peptides were analyzable and
had significantly different abundances between the two time points
using the spectral count and spectral index methods than with a prior
analysis using the SIEVE method with the same data. The results of
this study reveal the importance of using the appropriate data analysis
approaches for label-free relative quantitation of peptides. The detection
of significant changes in so rich a set of neuropeptides reflects
the dynamic nature of the SCN and the number of influences such as
feeding behavior on circadian rhythm. Using spectral count and spectral
index, peptide level changes are correlated to time of day, suggesting
their key role in circadian function.