Abstract
Over the past decade, the study of proteomics has been rapidly evolving and so too have the technologies that accompany it. One branch of proteomics in particular— bottom-up proteomics— has become a cornerstone of many studies. Extracting and storing peptides over long periods of time for bottom-up analysis can prove to be a cumbersome task, requiring specific storage conditions that do not result in the degradation of the sample of interest. To date, there are no studies that analyze the effects of various storage conditions on the stability of peptides over an extended period. In this study, tryptic digests were performed on human breast milk and the resulting peptides were subject to varying storage temperatures and buffers. Four storage temperatures—room temperature, 4°C, −20°C, and −80°C— and three storage conditions—dried, re-suspended in ultra-pure water, and re-suspended in 0.1% trifluoroacetic acid (TFA)—were compared over an eight week time frame. Peptide degradation was analyzed using spectral counting on the protein level. In addition, five proteins were tracked in the milk digest and were analyzed using assigned spectra. Each condition consisted of four replicates and statistical analysis was done to test for variations between samples. Preliminary data suggests that there is a degradation of peptides over extended periods of time and that certain storage temperatures and buffers may impede such losses. A solution of 0.1% TFA at temperatures between 4°C and −80°C appear to slow down the degradation of peptides.