The ACQUITY UPLC H-Class System provides the accuracy and reproducibility of extended batch peptide mapping.
aims
Analytical reproducibility of the ACQUITY UPLC ® H-Class system in long-light elution gradient applications to resolve complex mixtures such as peptide mapping.
background
Peptide mapping is used to identify the primary structure of a protein, identify post-translational modifications (PTM), and analyze potential impurities. Any difference in protein structure should be reflected in the change in retention time of the peptide containing the modification. The relative amount of peptides with and without specific modifications is used to determine the proportion or amount of protein in a particular sample containing the modification.
The change in area ratio corresponds to the amount of protein molecules in the sample containing the particular modification. To meet these application requirements, long and shallow gradient elution is required. These separation conditions have been a challenge in the past for single pump gradient systems. In this study, we tested a typical peptide mapping protocol on the ACQUITY UPLC H-Class system. 
Figure 1. Peptide mapping sample list starts on Friday and runs automatically throughout the weekend. When the staff returns to work on Monday, the data is ready for review. The figure shows every three separations, showing excellent reproducibility, resolution and retention time. As summarized in Table 1, the five labeled peaks, from A to E, were selected as representatives of the quantitative analysis.
Solution
The ACQUITY UPLC H-Class system consists of a Quaternary Solvent Manager (QSM) that flows through a Needle Sample Manager (SM-FTN), a column heater, and a Photodiode Array (PDA) detector. An optional 250μL mixer is installed. The standard peptide solution in the MassPREPTM BSA reagent was separated on an ACQUITY UPLC BEH 300 C 18 reverse phase column. The elution gradient increased by 1.0% for each additional bed volume elution volume and the gradient increased by approximately 0.6% per minute. This gradient was selected as a typical polypeptide mapping gradient.
The program takes full advantage of the instrument's automatic mixing capabilities. Pure solvent reservoirs and concentrated modifier stocks are used to replace binary, pretreated solvents. In this example, the gradient is formed in pure water in line A and pure acetonitrile in line B, and a portion of the stream is drawn from a water reservoir D containing 1% TFA. In the gradient, the ratio of line D is reduced from 5% to 4%, which corresponds to a decrease in TFA concentration from 0.05% to 0.04%, thus minimizing baseline drift.
The peptide map is shown in Figure 1, and the parameters such as retention time and peak area are statistically analyzed in Table 1. Relative retention and resolution remain constant during long series runs. The retention time is fully reproducible to ensure that the peaks are always correctly identified. Taking the area of ​​peak A as a reference, compare peaks B, C, D, and E and calculate the corresponding proportions in each test sample. The ratios of these areas are highly consistent in each test sample (see Table 1), and such accuracy is consistent with our requirement to measure the proportion of modified protein in a series of samples.
Table 1. Summary of chromatographic peak retention time and area ratios. The five peaks selected for quantitative comparison were evenly spaced for 10 min throughout the elution gradient.
to sum up
Mapping for meaningful peptides requires both quantitative and qualitative reproducibility. The ACQUITY UPLC H-Class system provides precise control of peptide separation for large samples, giving analysts confidence in the instrument. It is believed that any retention time deviation indicates a change in sample composition, not due to instrument variability. of. The observed separation meets this goal when utilizing this multi-solvent mixing capability. The design of this system ensures that both quantitative and qualitative results meet the requirements of modern analytical biochemistry.
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