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J Biomol Tech. 2010 September; 21(3 Suppl): S63.
PMCID: PMC2918049

Towards 100% Sequence Coverage in Protein QC: In-depth Sequence Characterization of Monoclonal Antibodies

U. Schweiger-Hufnagel, P. Hufnagel, R. Hebeler, M. Witt, P.O. Schmit, and M. Macht
Bruker Daltonik GmbH, Bremen, Germany

Abstract

RP-132

Quality control of biotherapeutic proteins requires access to the full protein sequence to account for every single aminoacid and its modification status. This is typically not achieved in a single LC-MS/MS analysis, but requires combined analytical strategies. However, this complicates the downstream data analysis due to distribution of relevant information in multiple datasets. A new bioinformatics platform, ProteinScape, is described here, which facilitates in-depth protein characterization tasks at an unparalleled level of efficiency. The analysis of a monoclonal antibody (mAB) described here utilized digestion by multiple enzymes (trypsin, chymotrypsin, LysC, GluC), with and without upfront SDS-PAGE separation, followed by LC-MALDI-TOF/TOF. LC-MALDI analysis of these digests yielded individual sequence coverages between 64 and 88%. A significant increase in sequence coverage was achieved when compiling the four individual digest analyses into one overall sequencing result. This rather demanding compilation step is easily performed using ProteinExtractor, a unique software algorithm implemented in ProteinScape. ProteinExtractor compilation of the LC-MALDI data yielded 100% coverage for the mAB light chain, and 98% for the heavy chain (HC). Additional electrospray measurements were performed to obtain information on the mAB HĆs sequence range [177-184] which was not accessible by MALDI. Again, ProteinExtractor was used to compile ESI and MALDI data resulting in a further increased sequence coverage of 99% for the HC. ESI measurements added 2 unique MS/MS spectra covering 3 aminoacid residues [range 182-184] that had not been detected by MALDI. In addition to the aminoacid sequence, the HĆs N-terminal modification status was characterized. Evaluation of the respective MS/MS spectra, which are directly accessible in ProteinScape, confirmed N-terminal conversion Glu to pyroGlu based on consistent ESI and MALDI data.


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