Sequence Variant Analysis by LC-MS/MS
Sequence variants can be the result of a cell line contaminated with a subpopulation having a mutation, suboptimal codon usage in the product protein’s gene, or conditions in the bioreactor that stress the cells. We have worked on sequence variant projects in microbial and mammalian expression systems and have seen variants that range from ppm levels up to 10% at a particular site. Sequence variant analysis (SVA) is more challenging than standard peptide mapping because we are looking for low-abundance peptides and careful data analysis is required. We design SVA experiments to maximize coverage of proteins at the MS/MS fragment ion level, so multiple digests are usually required. We search the data for all possible single-base variants, and we manually confirm the search engine results to ensure you get accurate results. For each sequence variant, we report the %SV (or ppm) relative to the native/wildtype peptide.
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