Creation and filtering of a recurrent spectral library of CHO cell metabolites and media components

• Published in: Biotechnology and bioengineering Vol. 118; no. 4; pp. 1491 - 1510
• Main Authors: Telu, Kelly H., Marupaka, Ramesh, Andriamaharavo, Nirina R., Simón‐Manso, Yamil, Liang, Yuxue, Mirokhin, Yuri A., Bukhari, Tallat H., Preston, Renae J., Kashi, Lila, Kelman, Zvi, Stein, Stephen E.
• Format: Journal Article
• Language: English
• Published: United States Wiley Subscription Services, Inc 01.04.2021; John Wiley and Sons Inc
• Subjects: Animals; Annotations; Chinese hamster ovary cells; CHO Cells; Conditional probability; Cricetulus; Culture Media - chemistry; global metabolite profiling; Libraries; Liquid chromatography; liquid chromatography‐tandem mass spectrometry; Mass spectrometry; Mass spectroscopy; Metabolites; Metabolome; Metabolomics; nontargeted metabolomics; recurrent unidentified spectra; Scientific imaging; Small Molecule Libraries; Spectra; Spectroscopy; Toxicity; Workflow; liquid chromatography-tandem mass spectrometry; nontargeted metabolomics; global metabolite profiling; recurrent unidentified spectra; Chinese hamster ovary cells
• ISSN: 0006-3592; 1097-0290
• DOI: 10.1002/bit.27661

This paper reports the first implementation of a new type of mass spectral library for the analysis of Chinese hamster ovary (CHO) cell metabolites that allows users to quickly identify most compounds in any complex metabolite sample. We also describe an annotation methodology developed to filter out artifacts and low‐quality spectra from recurrent unidentified spectra of metabolites. CHO cells are commonly used to produce biological therapeutics. Metabolic profiles of CHO cells and media can be used to monitor process variability and look for markers that discriminate between batches of product. We have created a comprehensive library of both identified and unidentified metabolites derived from CHO cells that can be used in conjunction with tandem mass spectrometry to identify metabolites. In addition, we present a workflow that can be used for assigning confidence to a NIST MS/MS Library search match based on prior probability of general utility. The goal of our work is to annotate and identify (when possible), all liquid chromatography‐mass spectrometry generated metabolite ions as well as create automatable library building and identification pipelines for use by others in the field. A freely available mass spectral library composed of identified and unidentified recurrent spectra from the analysis of Chinese hamster ovary (CHO) cell metabolites has been created. The comprehensive library of metabolites can be used in conjunction with tandem mass spectrometry to quickly identify compounds in a complex metabolite sample. An annotation strategy to filter out background, artifacts, and low‐quality spectra from recurrent unidentified spectra of metabolites was also developed.