Discrepancies between High-Resolution Native and Glycopeptide-Centric Mass Spectrometric Approaches: A Case Study into the Glycosylation of Erythropoietin Variants

Glycosylation represents
a critical quality attribute modulating
a myriad of physiochemical properties and effector functions of biotherapeutics.
Furthermore, a rising landscape of glycosylated biotherapeutics including
biosimilars, biobetters, and fusion proteins harboring complicated
and dynamic glycosylation profiles requires tailored analytical approaches
capable of characterizing their heterogeneous nature. In this work,
we perform in-depth evaluation of the glycosylation profiles of three
glycoengineered variants of the widely used biotherapeutic erythropoietin.
We analyzed these samples in parallel using a glycopeptide-centric
liquid chromatography/mass spectrometry approach and high-resolution
native mass spectrometry. Although for all of the studied variants
the glycopeptide and native mass spectrometry data were in good qualitative
agreement, we observed substantial quantitative differences arising
from ionization deficiencies and unwanted neutral losses, in particular,
for sialylated glycopeptides in the glycoproteomics approach. However,
the latter provides direct information about glycosite localization.
We conclude that the combined parallel use of native mass spectrometry
and bottom-up glycoproteomics offers superior characterization of
glycosylated biotherapeutics and thus provides a valuable attribute
in the characterization of glycoengineered proteins and other complex
biotherapeutics.