title: Host Cell Protein Profiling by Targeted and Untargeted Analysis of Data Independent Acquisition Mass Spectrometry Data with Parallel Reaction Monitoring Verification.
abstract: Host cell proteins (HCPs) are process-related impurities of biopharmaceuticals that remain at trace levels despite multiple stages of downstream purification. Currently, there is interest in implementing LC-MS in biopharmaceutical HCP profiling alongside conventional ELISA, because individual species can be identified and quantitated. Conventional data dependent LC-MS is hampered by the low concentration of HCP-derived peptides, which are 5-6 orders of magnitude less abundant than the biopharmaceutical-derived peptides. In this paper, we present a novel data independent acquisition (DIA)-MS workflow to identify HCP peptides using automatically combined targeted and untargeted data processing, followed by verification and quantitation using parallel reaction monitoring (PRM). Untargeted data processing with DIA-Umpire provided a means of identifying HCPs not represented in the assay library used for targeted, peptide-centric, data analysis. An IgG1 monoclonal antibody (mAb) purified by Protein A column elution, cation exchange chromatography, and ultrafiltration was analyzed using the workflow with 1D-LC. Five protein standards added at 0.5 to 100 ppm concentrations were detected in the background of the purified mAb, demonstrating sensitivity to low ppm levels. A calibration curve was constructed on the basis of the summed peak areas of the three highest intensity fragment ions from the highest intensity peptide of each protein standard. Sixteen HCPs were identified and quantitated on the basis of the calibration curve over the range of low ppm to over 100 ppm in the purified mAb sample. The developed approach achieves rapid HCP profiling using 1D-LC and specific identification exploiting the high mass accuracy and resolution of the mass spectrometer.
authors.affiliation: Barnett Institute and Department of Chemistry and Chemical Biology, Northeastern University , Boston, Massachusetts 02115, United States.
authors.forename: Simion
authors.initials: S
authors.lastname: Kreimer
authors.affiliation: Barnett Institute and Department of Chemistry and Chemical Biology, Northeastern University , Boston, Massachusetts 02115, United States.
authors.forename: Yuanwei
authors.initials: Y
authors.lastname: Gao
authors.affiliation: Barnett Institute and Department of Chemistry and Chemical Biology, Northeastern University , Boston, Massachusetts 02115, United States.
authors.forename: Somak
authors.initials: S
authors.lastname: Ray
authors.affiliation: Bristol-Myers Squibb , Biologics Process and Product Development, 38 Jackson Road, Devens, Massachusetts 01434, United States.
authors.forename: Mi
authors.initials: M
authors.lastname: Jin
authors.affiliation: Bristol-Myers Squibb , Biologics Process and Product Development, 38 Jackson Road, Devens, Massachusetts 01434, United States.
authors.forename: Zhijun
authors.initials: Z
authors.lastname: Tan
authors.affiliation: Bristol-Myers Squibb , Biologics Process and Product Development, 38 Jackson Road, Devens, Massachusetts 01434, United States.
authors.forename: Nesredin A
authors.initials: NA
authors.lastname: Mussa
authors.affiliation: Bristol-Myers Squibb , Biologics Process and Product Development, 38 Jackson Road, Devens, Massachusetts 01434, United States.
authors.forename: Li
authors.initials: L
authors.lastname: Tao
authors.affiliation: Bristol-Myers Squibb , Biologics Process and Product Development, 38 Jackson Road, Devens, Massachusetts 01434, United States.
authors.forename: Zhengjian
authors.initials: Z
authors.lastname: Li
authors.affiliation: Barnett Institute and Department of Chemistry and Chemical Biology, Northeastern University , Boston, Massachusetts 02115, United States.
authors.forename: Alexander R
authors.initials: AR
authors.lastname: Ivanov
authors.affiliation: Barnett Institute and Department of Chemistry and Chemical Biology, Northeastern University , Boston, Massachusetts 02115, United States.
authors.forename: Barry L
authors.identifier: 0000-0002-9786-0036
authors.initials: BL
authors.lastname: Karger
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D000911:Antibodies, Monoclonal / Q000235:genetics / Q000378:metabolism*; D016466:CHO Cells; D002851:Chromatography, High Pressure Liquid; D006224:Cricetinae; D003412:Cricetulus; D030562:Databases, Protein; D013058:Mass Spectrometry; D010455:Peptides / Q000032:analysis / Q000302:isolation & purification; D011506:Proteins / Q000032:analysis* / Q000378:metabolism; D011994:Recombinant Proteins / Q000032:analysis / Q000096:biosynthesis / Q000302:isolation & purification
chemical_list: D000911:Antibodies, Monoclonal; D010455:Peptides; D011506:Proteins; D011994:Recombinant Proteins