From Discovery Proteomics to Process-Informed Monitoring in Biomanufacturing Chassis Development.
- 1Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, U.K.
- 2Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, U.K.
Abstract
Gaining control of existing biomanufacturing chassis organisms, such as Escherichia coli K12, and novel isolates, such as the salt-tolerant Halomonas bluephagenesis sp TD01 studied here, may be facilitated by the investigation and monitoring of their metabolic and regulatory processes, particularly through proteomics. Here, we consider the performance of a range of typically available proteomics platforms across a range of price points to map chassis organisms' metabolic pathways. A set of model bacterial samples was prepared from E. coli and H. bluephagenesis sp. TD01 in 1:1, 1:2, and 2:1 ratios and analyzed using five LC-MS systems. Of the 8222 proteins identified across all samples analyzed (4401 proteins from E. coli; 3821 from Halomonas sp. TD01), the TimsTOF and Exploris were able to achieve extensive proteome coverage, quantifying 5.5k and 5k proteins, respectively, with the ZenoTOF, Waters MRT, and the legacy Waters Vion, respectively, quantifying 3.5k, 1.3k, and ∼850 proteins at 1% FDR. Proteins comprising core metabolic pathways critical to biomanufacturing in these chassis' organisms can be quantified with all instruments. We characterize metabolic adaptation in H. bluephagenesis by showing that replacement of glucose with a carboxylic acid feedstock directs carbon flux toward potential butane precursors, as well as how the acquired data permits monitoring of the cobalamin (vitamin B₁₂) production pathway.
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BibTeX
@article{russell2026from,
title = {{From Discovery Proteomics to Process-Informed Monitoring in Biomanufacturing Chassis Development.}},
author = {Matthew R Russell and Philip J Brownridge and Joseph Windo and Nigel S Scrutton and Claire E Eyers and Perdita Barran},
journal = {ACS measurement science au},
year = {2026},
month = sep,
doi = {10.1021/acsmeasuresciau.6c00194},
url = {https://europepmc.org/article/MED/42921447},
note = {CC BY-NC-ND},
}
RIS
TY - JOUR
TI - From Discovery Proteomics to Process-Informed Monitoring in Biomanufacturing Chassis Development.
AU - Matthew R Russell
AU - Philip J Brownridge
AU - Joseph Windo
AU - Nigel S Scrutton
AU - Claire E Eyers
AU - Perdita Barran
PY - 2026
DA - 2026/09/23
JO - ACS measurement science au
DO - 10.1021/acsmeasuresciau.6c00194
UR - https://europepmc.org/article/MED/42921447
AB - Gaining control of existing biomanufacturing chassis organisms, such as Escherichia coli K12, and novel isolates, such as the salt-tolerant Halomonas bluephagenesis sp TD01 studied here, may be facilitated by the investigation and monitoring of their metabolic and regulatory processes, particularly through proteomics. Here, we consider the performance of a range of typically available proteomics platforms across a range of price points to map chassis organisms' metabolic pathways. A set of model bacterial samples was prepared from E. coli and H. bluephagenesis sp. TD01 in 1:1, 1:2, and 2:1 ratios and analyzed using five LC-MS systems. Of the 8222 proteins identified across all samples analyzed (4401 proteins from E. coli; 3821 from Halomonas sp. TD01), the TimsTOF and Exploris were able to achieve extensive proteome coverage, quantifying 5.5k and 5k proteins, respectively, with the ZenoTOF, Waters MRT, and the legacy Waters Vion, respectively, quantifying 3.5k, 1.3k, and ∼850 proteins at 1% FDR. Proteins comprising core metabolic pathways critical to biomanufacturing in these chassis' organisms can be quantified with all instruments. We characterize metabolic adaptation in H. bluephagenesis by showing that replacement of glucose with a carboxylic acid feedstock directs carbon flux toward potential butane precursors, as well as how the acquired data permits monitoring of the cobalamin (vitamin B₁₂) production pathway.
SN - 2694-250X
ER -