Frontiers in Bioengineering and Biotechnology (Dec 2020)
High-Throughput Large-Scale Targeted Proteomics Assays for Quantifying Pathway Proteins in Pseudomonas putida KT2440
- Yuqian Gao,
- Yuqian Gao,
- Thomas L. Fillmore,
- Nathalie Munoz,
- Nathalie Munoz,
- Gayle J. Bentley,
- Gayle J. Bentley,
- Christopher W. Johnson,
- Christopher W. Johnson,
- Joonhoon Kim,
- Joonhoon Kim,
- Jamie A. Meadows,
- Jamie A. Meadows,
- Jeremy D. Zucker,
- Jeremy D. Zucker,
- Meagan C. Burnet,
- Meagan C. Burnet,
- Anna K. Lipton,
- Anna K. Lipton,
- Aivett Bilbao,
- Aivett Bilbao,
- Daniel J. Orton,
- Young-Mo Kim,
- Young-Mo Kim,
- Ronald J. Moore,
- Errol W. Robinson,
- Errol W. Robinson,
- Scott E. Baker,
- Scott E. Baker,
- Bobbie-Jo M. Webb-Robertson,
- Bobbie-Jo M. Webb-Robertson,
- Adam M. Guss,
- Adam M. Guss,
- John M. Gladden,
- John M. Gladden,
- Gregg T. Beckham,
- Gregg T. Beckham,
- Jon K. Magnuson,
- Jon K. Magnuson,
- Kristin E. Burnum-Johnson,
- Kristin E. Burnum-Johnson
Affiliations
- Yuqian Gao
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States
- Yuqian Gao
- Pacific Northwest National Laboratory, Richland, WA, United States
- Thomas L. Fillmore
- Pacific Northwest National Laboratory, Richland, WA, United States
- Nathalie Munoz
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States
- Nathalie Munoz
- Pacific Northwest National Laboratory, Richland, WA, United States
- Gayle J. Bentley
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States
- Gayle J. Bentley
- National Renewable Energy Laboratory, Golden, CO, United States
- Christopher W. Johnson
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States
- Christopher W. Johnson
- National Renewable Energy Laboratory, Golden, CO, United States
- Joonhoon Kim
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States
- Joonhoon Kim
- Pacific Northwest National Laboratory, Richland, WA, United States
- Jamie A. Meadows
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States
- Jamie A. Meadows
- Sandia National Laboratories, Livermore, CA, United States
- Jeremy D. Zucker
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States
- Jeremy D. Zucker
- Pacific Northwest National Laboratory, Richland, WA, United States
- Meagan C. Burnet
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States
- Meagan C. Burnet
- Pacific Northwest National Laboratory, Richland, WA, United States
- Anna K. Lipton
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States
- Anna K. Lipton
- Pacific Northwest National Laboratory, Richland, WA, United States
- Aivett Bilbao
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States
- Aivett Bilbao
- Pacific Northwest National Laboratory, Richland, WA, United States
- Daniel J. Orton
- Pacific Northwest National Laboratory, Richland, WA, United States
- Young-Mo Kim
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States
- Young-Mo Kim
- Pacific Northwest National Laboratory, Richland, WA, United States
- Ronald J. Moore
- Pacific Northwest National Laboratory, Richland, WA, United States
- Errol W. Robinson
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States
- Errol W. Robinson
- Pacific Northwest National Laboratory, Richland, WA, United States
- Scott E. Baker
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States
- Scott E. Baker
- Pacific Northwest National Laboratory, Richland, WA, United States
- Bobbie-Jo M. Webb-Robertson
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States
- Bobbie-Jo M. Webb-Robertson
- Pacific Northwest National Laboratory, Richland, WA, United States
- Adam M. Guss
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States
- Adam M. Guss
- Oak Ridge National Laboratory, Oak Ridge, TN, United States
- John M. Gladden
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States
- John M. Gladden
- Sandia National Laboratories, Livermore, CA, United States
- Gregg T. Beckham
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States
- Gregg T. Beckham
- National Renewable Energy Laboratory, Golden, CO, United States
- Jon K. Magnuson
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States
- Jon K. Magnuson
- Pacific Northwest National Laboratory, Richland, WA, United States
- Kristin E. Burnum-Johnson
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States
- Kristin E. Burnum-Johnson
- Pacific Northwest National Laboratory, Richland, WA, United States
- DOI
- https://doi.org/10.3389/fbioe.2020.603488
- Journal volume & issue
-
Vol. 8
Abstract
Targeted proteomics is a mass spectrometry-based protein quantification technique with high sensitivity, accuracy, and reproducibility. As a key component in the multi-omics toolbox of systems biology, targeted liquid chromatography-selected reaction monitoring (LC-SRM) measurements are critical for enzyme and pathway identification and design in metabolic engineering. To fulfill the increasing need for analyzing large sample sets with faster turnaround time in systems biology, high-throughput LC-SRM is greatly needed. Even though nanoflow LC-SRM has better sensitivity, it lacks the speed offered by microflow LC-SRM. Recent advancements in mass spectrometry instrumentation significantly enhance the scan speed and sensitivity of LC-SRM, thereby creating opportunities for applying the high speed of microflow LC-SRM without losing peptide multiplexing power or sacrificing sensitivity. Here, we studied the performance of microflow LC-SRM relative to nanoflow LC-SRM by monitoring 339 peptides representing 132 enzymes in Pseudomonas putida KT2440 grown on various carbon sources. The results from the two LC-SRM platforms are highly correlated. In addition, the response curve study of 248 peptides demonstrates that microflow LC-SRM has comparable sensitivity for the majority of detected peptides and better mass spectrometry signal and chromatography stability than nanoflow LC-SRM.
Keywords
- targeted proteomics
- Pseudomonas putida KT2440
- mass spectrometry
- selected reaction monitoring
- central carbon metabolism