Application of BiopharmaLynx Software in Protein Peptide Mapping

Application of BiopharmaLynx Software in Protein Peptide Mapping

Zhou Chunxi

Waters Technology (Shanghai) Co., Ltd. Experimental Center

In the development of new drugs, protein drugs are occupying a larger and larger proportion, and the complexity of protein molecular structure requires comprehensive characterization of protein drugs to meet the requirements of new drug approval, process improvement and patent protection. At present, the development and characterization of protein drugs still face many challenges, especially in the sequence confirmation of recombinant proteins, the detection and quantification of trace impurity proteins, the comparison of products between batches and quality control. Mass spectrometry plays a crucial role in the characterization of proteins. It not only determines the molecular weight of protein drugs and the heterogeneity of products, but also confirms the primary structure of protein molecules, including amino acid sequences, mutations and modifications, by peptide mapping. , disulfide bond positioning and other information.

But without the help of powerful software, analysis, comparison, annotation, extraction of valid information, and analysis of mass spectrometry data can be a complex process that is time consuming and labor intensive. If you do manual analysis, even experienced analysts will feel a headache, and it is difficult to ensure that errors will not be made in such a complicated analysis process. Once errors occur, it will not only seriously affect the development process, but also make some wrong judgments. It may also lead to the failure of the entire project. Therefore, analysis software is essential. Ideal software not only automates the analysis process in accordance with standard processes, but also allows analysts to examine and correct error results based on experience and knowledge. Waters' BiopharmaLynxTM software is the ideal tool to automate the analysis of protein molecular weight and peptide maps, compare samples from batch to batch and confirm for differences, and has the following features:

First, the peptide map analysis coverage is high

Peptide mapping can confirm the primary structure of protein molecules, including amino acid sequences, mutations and modifications, and disulfide bond localization. The peptide map is very complicated because the fully enzymatic peptide, incompletely cleaved peptide, non-specific peptide, modified peptide and heteroprotein peptide are present in the sample after enzymatic hydrolysis. All of the parent ions and their fragment ion information in the sample can be simultaneously recorded by full information tandem mass spectrometry (MS ^E ). Based on comprehensive information, BiopharmaLynx software will automatically perform retention time alignment, intensity normalization, trace impurity analysis, and sequence confirmation. Figure 1 shows the results of the analysis of the coverage of the peptide mapping of the two interferon products by BiopharmaLynx software, and its sequence alignment interface.

Second, BiopharmaLynx has a variety of enzyme digestion functions

In calculating the theoretical peptide map, BiopharmaLynx can perform theoretical digestion in a variety of ways, including half-enzyme digestion, multi-enzyme digestion, non-specific digestion, and self-edited digestion. Fully meet the various enzyme digestion analysis needs in the experiment.

Third, BiopharmaLynx has a variety of post-translational modifications available

BiopharmaLynx can also consider a variety of post-translational modifications when calculating theoretical peptide maps. With 90 common modifications to choose from, analysts can also edit the special modifications they need for analysis.

4. Comparison of the content of modified peptides between different samples

BiopharmaLynx software can compare the difference in the content of a peptide (including mutated peptides and specific modified peptides) between different samples, and find the nuances between the samples and display them in an intuitive way.

5. Comparison of peptide mapping between samples of BiopharmaLynx

BiopharmaLynx software automatically compares the peptide maps of individual batch samples to the peptide plots of the reference samples, helping us to quickly and sensitively identify nuances between batches of samples.

6. Positioning of disulfide bonds

Disulfide bonds play an important role in the formation of high-protein structures and maintenance of functions. The location of disulfide bonds is also an important aspect of protein structure analysis. However, the positioning of disulfide bonds has been a time consuming and very challenging task, especially for proteins containing multiple pairs of disulfide bonds, such as immunoglobulins. Waters' Complete Peptide Mapping Analysis Solution Quickly automate the localization of disulfide bonds using the unique UPLC/MS ^E data acquisition method and the powerful BiopharmaLynx software (see Figure 6).

In the field of biopharmaceuticals, BiopharmaLynx software has been widely used as the most professional software for liquid crystal data analysis. Currently, the world's top ten biopharmaceutical companies have become users of Waters biopharmaceutical solutions.

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For more than 50 years, Waters Corporation (NYSE: WAT) has made significant advances in medical services, environmental management, food safety and global water quality monitoring by providing practical and sustainable innovations that have created business for laboratory-related organizations. Advantage.

As a pioneer in a range of separation science, laboratory information management, mass spectrometry and thermal analysis technologies, Waters technology's breakthroughs and laboratory solutions create a lasting platform for customer success.

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