title: Comparing label-free quantitative peptidomics approaches to characterize diurnal variation of peptides in the rat suprachiasmatic nucleus.
abstract: 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.
authors: Department of Animal Sciences, ‡Department of Chemistry, §Institute for Genomic Biology, ∥Neuroscience Program, ⊥Department of Cell and Developmental Biology, and ¶Beckman Institute, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States.
authors: Bruce R
authors: BR
authors: Southey
authors: Ji Eun
authors: JE
authors: Lee
authors: Leonid
authors: L
authors: Zamdborg
authors: Norman
authors: N
authors: Atkins
authors: Jennifer W
authors: JW
authors: Mitchell
authors: Mingxi
authors: M
authors: Li
authors: Martha U
authors: MU
authors: Gillette
authors: Neil L
authors: NL
authors: Kelleher
authors: Jonathan V
authors: JV
authors: Sweedler
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D002940:Circadian Rhythm / Q000502:physiology; D008297:Male; D013058:Mass Spectrometry / Q000379:methods*; D008969:Molecular Sequence Data; D009479:Neuropeptides / Q000032:analysis* / Q000235:genetics*; D051381:Rats; D020318:Rats, Long-Evans; D013493:Suprachiasmatic Nucleus / Q000737:chemistry* / Q000502:physiology*
chemical_list: D009479:Neuropeptides