Peptide Storage: Are You Getting the Best Return on Your Investment? Defining Optimal Storage Conditions for Proteomics Samples

Abstract

To comply with current proteomics guidelines, it is often necessary to analyze the same peptide samples several times. Between analyses, the sample must be stored in such a way as to conserve its intrinsic properties, without losing either peptides or signal intensity. This article describes two studies designed to define the optimal storage conditions for peptide samples between analyses. With the use of a label-free strategy, peptide conservation was compared over a 28-day period in three different recipients: standard plastic tubes, glass tubes, and low-adsorption plastic tubes. The results of this study showed that standard plastic tubes are unsuitable for peptide storage over the period studied. Glass tubes were found to perform better than standard plastic, but optimal peptide recovery was achieved using low-adsorption plastic tubes. The peptides showing poor recovery following storage were mainly hydrophobic in nature. The differences in peptide recovery between glass and low-adsorption plastic tubes were further studied using isotopically labeled proteins. This study allowed accurate comparison of peptide recovery between the two tube types within the same LC-MS run. The results of the label-free study were confirmed. Further, it was possible to demonstrate that peptide recovery in low-adsorption plastic tubes was optimal whatever the peptide concentration stored.

Improved sensitivity of the nano ultra-high performance liquid chromatography-tandem mass spectrometric analysis of low-concentrated neuropeptides by reducing aspecific adsorption and optimizing the injection solvent

“…However, when adding 40 g mL −1 of BSA to the optimal dilution solvent (water/FA 95/5 V/V) aspecific adsorption of NT, NMB and NMN is not influenced in a regular Eppendorf tube (data not shown). Since differences in the extent of peptide adsorption as a function of time are reported [40,41], we incubated regular Eppendorf tubes, UHPLC vials and pipette tips for 24 h with 40 g mL −1 of BSA. In this way, we increased the probability of a complete saturation of the nonspecific binding sites of the material.…”

The Impact of Delayed Storage on the Measured Proteome and Metabolome of Human Cerebrospinal Fluid

“…To detect reliable molecular biomarkers, it is imperative to handle biological fluids according to standardized procedures and to evaluate the effects of preanalytical parameters on the final result to avoid artifacts (1,2 ). Earlier studies on urine, plasma, and cerebrospinal fluid (CSF) 9 have shown that sample handling can affect the stability of proteins as well as metabolites (3)(4)(5)(6)(7)(8)(9)(10)(11). Standardized sample handling is also important when trying to compare results between different laboratories (12)(13)(14).…”

Identification of a plant gene encoding glutamate/aspartate‐prephenate aminotransferase: The last homeless enzyme of aromatic amino acids biosynthesis

“…The 43 kDa band was cut from the gel and proteins and peptides were prepared as described in [26]. Nanoliquid chromatography, LTQ-Orbitrap and bioinformatics analyses were performed as described in [27].…”