A Longitudinal Proteomic Assessment of Peptide Degradation and Loss Under Acidic Storage Conditions

Sample preparation prior to analysis by liquid chromatography electrospray ionisation mass spectrometry (LC-ESI-MS) usually involves the storage of frozen peptide samples in an acidic environment for variable time periods. Questions arose in our laboratory regarding the stability of peptides in acid under medium to long-term storage. Thus, a 10 month longitudinal study was designed to assess the effect on storage of tryptic peptides at -20°C and -80°C under acidic conditions. Our conclusion and proposal from this evaluation is that the optimal storage conditions of peptide samples in acid for proteomic experiments is at -80°C, and ideally, as separate aliquots. Abbreviations: 6BM, bovine 6 protein tryptic digest equimolar mixture; AGC, automatic gain control; BSA, bovine serum albumin; CID, collision-induced dissociation; FT, freeze-thaw; IQR, interquartile range; MS, mass spectrometry; LC-ESI-MS, liquid chromatography electrospray ionisation mass spectrometry; LCMS, liquid chromatography mass spectrometry; RT, room temperature; SU, single use.