Identification and Quantification of Host Cell Proteins in Biopharmaceuticals using a Novel Data-Independent Acquisition Mode and MS/MS Spectral Library Search

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Catalin Doneanu, Sarah Lennon, Malcolm Anderson, Ian Reah, Mal Ross, Steven Anderson, Ian Morns, Robert Tonge, Ying Qing Yu, Asish Chakraborty, Laetitia Denbigh and Weibin Chen
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Host cell proteins (HCPs) are process-related impurities sometimes present in trace level amounts (1-100 ppm) in biopharmaceuticals.

Here we describe an LC/MS assay that is capable to identify and quantify HCPs found in high-purity monoclonal antibodies (mAbs). The assay relies on a novel data-independent acquisition mode recently implemented on a quadrupole/time-of-flight mass spectrometer, namely SONAR data acquisition. Instead of transmitting all peptide ions produced by the electrospray source, in SONAR mode the quadrupole is continuously scanned for isolating specific m/z regions prior to TOF analysis. As with an MSE acquisition, MS scans alternate between precursor (low energy) and collisionally induced product ions scans (high energy). SONAR offers additional selectivity, by producing clean MS/MS fragmentation spectra with minimal interferences.

The utility of the LC/MS assay was demonstrated using a high-purity mAb produced in a murine cell line (NIST mAb). Forty two high-resolution (> 30,000) SONAR MS/MS spectra originating from 27 HCP peptides identified in the NIST mAb were assembled in a spectral library using Progenesis QI for proteomics software. Compared to the traditional workflow of LC/MS HCP assay based relying on a protein database search, the LLOQ of the HCP assay was improved 10-fold when using the spectral library search.

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