Applications of targeted proteomics in metabolic engineering: advances and opportunities

Biofuels for a sustainable future

(2021) Yuzhong Liu et al.   CELL

Proteome analysis of response to different spectral light irradiation in Synechocystis sp. PCC 6803

(2021) Masakazu Toyoshima et al.   Journal of Proteomics

Microbial production of advanced biofuels

(2021) Jay Keasling et al.   NATURE REVIEWS MICROBIOLOGY

Protein expression in the obligate hydrocarbon‐degrading psychrophile Oleispira antarctica RB‐8 during alkane degradation and cold tolerance

(2020) Benjamin H. Gregson et al.   ENVIRONMENTAL MICROBIOLOGY

Production of ent-kaurene from lignocellulosic hydrolysate in Rhodosporidium toruloides

(2020) Gina M. Geiselman et al.   Microbial Cell Factories

The production of isoprene from cellulose using recombinant Clostridium cellulolyticum strains expressing isoprene synthase

(2020) Christian Janke et al.   MicrobiologyOpen

Recent Development of Extremophilic Bacteria and Their Application in Biorefinery

(2020) Daochen Zhu et al.   Frontiers in Bioengineering and Biotechnology

Quantitative and targeted proteomics-based identification and validation of drug efficacy biomarkers

(2020) Takeshi Masuda et al.   Drug Metabolism and Pharmacokinetics

Reconstructing organisms in silico: genome-scale models and their emerging applications

(2020) Xin Fang et al.   NATURE REVIEWS MICROBIOLOGY

A machine learning Automated Recommendation Tool for synthetic biology

(2020) Tijana Radivojević et al.   Nature Communications

Machine learning for metabolic engineering: A review

(2020) Christopher E. Lawson et al.   METABOLIC ENGINEERING

High-Throughput Large-Scale Targeted Proteomics Assays for Quantifying Pathway Proteins in Pseudomonas putida KT2440

(2020) Yuqian Gao et al.   Frontiers in Bioengineering and Biotechnology

Predicting proteome allocation, overflow metabolism, and metal requirements in a model acetogen

(2019) Joanne K. Liu et al.   PLoS Computational Biology

Systems Metabolic Engineering Strategies: Integrating Systems and Synthetic Biology with Metabolic Engineering

(2019) Kyeong Rok Choi et al.   TRENDS IN BIOTECHNOLOGY

Trends in the Design of New Isobaric Labeling Reagents for Quantitative Proteomics

(2019) Remigiusz Bąchor et al.   MOLECULES

Transomics data-driven, ensemble kinetic modeling for system-level understanding and engineering of the cyanobacteria central metabolism

(2019) Hiroki Nishiguchi et al.   METABOLIC ENGINEERING

Engineering Corynebacterium glutamicum to produce the biogasoline isopentenol from plant biomass hydrolysates

(2019) Yusuke Sasaki et al.   Biotechnology for Biofuels

Development of a metabolic pathway transfer and genomic integration system for the syngas-fermenting bacterium Clostridium ljungdahlii

(2019) Gabriele Philipps et al.   Biotechnology for Biofuels

Multi-omics analysis unravels a segregated metabolic flux network that tunes co-utilization of sugar and aromatic carbons in Pseudomonas putida

(2019) Matthew A. Kukurugya et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

De novo production of benzyl glucosinolate in Escherichia coli

(2019) Annette Petersen et al.   METABOLIC ENGINEERING

Targeted Proteomics for Studying Pathogenic Bacteria

(2019) Sara Saleh et al.   PROTEOMICS

The effect of modulating the quantity of enzymes in a model ethanol pathway on metabolic flux in Synechocystis sp. PCC 6803

(2019) Paulina Bartasun et al.   PeerJ

Extreme thermophiles as emerging metabolic engineering platforms

(2019) James R Crosby et al.   CURRENT OPINION IN BIOTECHNOLOGY

Investigation of the methylerythritol 4-phosphate pathway for microbial terpenoid production through metabolic control analysis

(2019) Daniel Christoph Volke et al.   Microbial Cell Factories

Methanol-free biosynthesis of fatty acid methyl ester (FAME) in Synechocystis sp. PCC 6803

(2019) Ian Sofian Yunus et al.   METABOLIC ENGINEERING

Application of targeted mass spectrometry in bottom-up proteomics for systems biology research

(2018) Nathan P. Manes et al.   Journal of Proteomics

Pseudomonas putida as a functional chassis for industrial biocatalysis: From native biochemistry to trans -metabolism

(2018) Pablo I. Nikel et al.   METABOLIC ENGINEERING

Comparative Targeted Proteomics of the Central Metabolism and Photosystems in SigE Mutant Strains of Synechocystis sp. PCC 6803

(2018) Yuma Tokumaru et al.   MOLECULES

A GFP-fusion coupling FACS platform for advancing the metabolic engineering of filamentous fungi

(2018) Guokun Wang et al.   Biotechnology for Biofuels

Photosynthesis-dependent biosynthesis of medium chain-length fatty acids and alcohols

(2018) Ian Sofian Yunus et al.   METABOLIC ENGINEERING

Modular Metabolic Engineering for Biobased Chemical Production

(2018) Hongyuan Lu et al.   TRENDS IN BIOTECHNOLOGY

Absolute Quantification of Major Photosynthetic Protein Complexes in Chlamydomonas reinhardtii Using Quantification Concatamers (QconCATs)

(2018) Alexander Hammel et al.   Frontiers in Plant Science

Machine Learning of Designed Translational Control Allows Predictive Pathway Optimization in Escherichia coli

(2018) Adrian J. Jervis et al.   ACS Synthetic Biology

Improving the phenotype predictions of a yeast genome‐scale metabolic model by incorporating enzymatic constraints

(2017) Benjamín J Sánchez et al.   Molecular Systems Biology

Targeted proteome analysis of single-gene deletion strains of Saccharomyces cerevisiae lacking enzymes in the central carbon metabolism

(2017) Fumio Matsuda et al.   PLoS One

Heterologous Biosynthesis of Spinosad: An Omics-Guided Large Polyketide Synthase Gene Cluster Reconstitution in Streptomyces

(2017) Gao-Yi Tan et al.   ACS Synthetic Biology

Engineering Cellular Metabolism

(2016) Jens Nielsen et al.   CELL

Metabolic engineering of Clostridium cellulolyticum for the production of n-butanol from crystalline cellulose

(2016) Stefan Marcus Gaida et al.   Microbial Cell Factories

Advances in targeted proteomics and applications to biomedical research

(2016) Tujin Shi et al.   PROTEOMICS

A strategy for absolute proteome quantification with mass spectrometry by hierarchical use of peptide-concatenated standards

(2016) Keiji Kito et al.   PROTEOMICS

Characterizing Strain Variation in Engineered E. coli Using a Multi-Omics-Based Workflow

(2016) Elizabeth Brunk et al.   Cell Systems

Nano-scale liquid chromatography coupled to tandem mass spectrometry using the multiple reaction monitoring mode based quantitative platform for analyzing multiple enzymes associated with central metabolic pathways of Saccharomyces cerevisiae using ultra fast mass spectrometry

(2015) Fumio Matsuda et al.   JOURNAL OF BIOSCIENCE AND BIOENGINEERING

Development of a Quantitative SRM-Based Proteomics Method to Study Iron Metabolism of Synechocystis sp. PCC 6803

(2015) Linda Vuorijoki et al.   JOURNAL OF PROTEOME RESEARCH

Absolute quantification of Corynebacterium glutamicum glycolytic and anaplerotic enzymes by QconCAT

(2015) Raphael Voges et al.   Journal of Proteomics

Targeted quantitative proteomic investigation employing multiple reaction monitoring on quantitative changes in proteins that regulate volatile biosynthesis of strawberry fruit at different ripening stages

(2015) Jun Song et al.   Journal of Proteomics

Quantitative changes in proteins responsible for flavonoid and anthocyanin biosynthesis in strawberry fruit at different ripening stages: A targeted quantitative proteomic investigation employing multiple reaction monitoring

(2015) Jun Song et al.   Journal of Proteomics

Quantitative prediction of genome-wide resource allocation in bacteria

(2015) Anne Goelzer et al.   METABOLIC ENGINEERING

Principal component analysis of proteomics (PCAP) as a tool to direct metabolic engineering

(2015) Jorge Alonso-Gutierrez et al.   METABOLIC ENGINEERING

Engineering an iterative polyketide pathway in Escherichia coli results in single-form alkene and alkane overproduction

(2015) Qian Liu et al.   METABOLIC ENGINEERING

Targeted engineering and scale up of lycopene overproduction in Escherichia coli

(2015) Fayin Zhu et al.   PROCESS BIOCHEMISTRY

Quantitative proteomics using SILAC: Principles, applications, and developments

(2015) Xiulan Chen et al.   PROTEOMICS

Applications of targeted proteomics in systems biology and translational medicine

(2015) H. Alexander Ebhardt et al.   PROTEOMICS

Metabolic engineering for the high-yield production of isoprenoid-based C5 alcohols in E. coli

(2015) Kevin W. George et al.   Scientific Reports

A kinetic-based approach to understanding heterologous mevalonate pathway function inE. coli

(2014) Lane J. Weaver et al.   BIOTECHNOLOGY AND BIOENGINEERING

Correlation analysis of targeted proteins and metabolites to assess and engineer microbial isopentenol production

(2014) Kevin W. George et al.   BIOTECHNOLOGY AND BIOENGINEERING

In vitro reconstitution of mevalonate pathway and targeted engineering of farnesene overproduction inEscherichia coli

(2014) Fayin Zhu et al.   BIOTECHNOLOGY AND BIOENGINEERING

Adaptation ofBacillus subtiliscarbon core metabolism to simultaneous nutrient limitation and osmotic challenge: a multi-omics perspective

(2014) Michael Kohlstedt et al.   ENVIRONMENTAL MICROBIOLOGY

A targeted proteomics toolkit for high-throughput absolute quantification of Escherichia coli proteins

(2014) Tanveer S. Batth et al.   METABOLIC ENGINEERING

Mass Spectrometry-based Workflow for Accurate Quantification ofEscherichia coliEnzymes: How Proteomics Can Play a Key Role in Metabolic Engineering

(2014) Mathieu Trauchessec et al.   MOLECULAR & CELLULAR PROTEOMICS

Highly Precise Quantification of Protein Molecules per Cell During Stress and Starvation Responses inBacillus subtilis

(2014) Sandra Maaβ et al.   MOLECULAR & CELLULAR PROTEOMICS

Comparison of targeted peptide quantification assays for reductive dehalogenases by selective reaction monitoring (SRM) and precursor reaction monitoring (PRM)

(2013) Christian Schiffmann et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

Metabolic pathway optimization using ribosome binding site variants and combinatorial gene assembly

(2013) Farnaz F. Nowroozi et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

A model of yeast glycolysis based on a consistent kinetic characterisation of all its enzymes

(2013) Kieran Smallbone et al.   FEBS LETTERS

Stable isotope labeling of mammals (SILAM) for in vivo quantitative proteomic analysis

(2013) Navin Rauniyar et al.   METHODS

Engineering dynamic pathway regulation using stress-response promoters

(2013) Robert H Dahl et al.   NATURE BIOTECHNOLOGY

QconCATs: design and expression of concatenated protein standards for multiplexed protein quantification

(2012) Deborah M. Simpson et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

An insight into iTRAQ: where do we stand now?

(2012) Caroline Evans et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

PSAQ™ standards for accurate MS-based quantification of proteins: from the concept to biomedical applications

(2012) Guillaume Picard et al.   JOURNAL OF MASS SPECTROMETRY

Quantification of proteome dynamics in Corynebacterium glutamicum by 15N-labeling and selected reaction monitoring

(2012) Raphael Voges et al.   Journal of Proteomics

Enhancing fatty acid production by the expression of the regulatory transcription factor FadR

(2012) Fuzhong Zhang et al.   METABOLIC ENGINEERING

Selected reaction monitoring–based proteomics: workflows, potential, pitfalls and future directions

(2012) Paola Picotti et al.   NATURE METHODS

Quantitative analysis of peptides and proteins in biomedicine by targeted mass spectrometry

(2012) Michael A Gillette et al.   NATURE METHODS

Application of targeted proteomics to metabolically engineeredEscherichia coli

(2012) Pragya Singh et al.   PROTEOMICS

Modular Engineering of l-Tyrosine Production in Escherichia coli

(2011) Darmawi Juminaga et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Proteomics of extremophiles

(2011) Dominic Burg et al.   ENVIRONMENTAL MICROBIOLOGY

Optimization of a heterologous mevalonate pathway through the use of variant HMG-CoA reductases

(2011) Suzanne M. Ma et al.   METABOLIC ENGINEERING

Targeted proteomics for metabolic pathway optimization: Application to terpene production

(2011) Alyssa M. Redding-Johanson et al.   METABOLIC ENGINEERING

Absolute Quantification of the Glycolytic Pathway in Yeast:

(2011) Kathleen M. Carroll et al.   MOLECULAR & CELLULAR PROTEOMICS

Comprehensive quantitative analysis of central carbon and amino-acid metabolism in Saccharomyces cerevisiae under multiple conditions by targeted proteomics

(2011) R. Costenoble et al.   Molecular Systems Biology

Monitoring protein expression in whole-cell extracts by targeted label- and standard-free LC-MS/MS

(2011) Katharina Bluemlein et al.   Nature Protocols

Absolute quantification of protein and post-translational modification abundance with stable isotope–labeled synthetic peptides

(2011) Arminja N Kettenbach et al.   Nature Protocols

Targeted proteomics for Chlamydomonas reinhardtii combined with rapid subcellular protein fractionation, metabolomics and metabolic flux analyses

(2010) Stefanie Wienkoop et al.   Molecular BioSystems

Full Dynamic Range Proteome Analysis of S. cerevisiae by Targeted Proteomics

(2009) Paola Picotti et al.   CELL

Targeted proteomics using selected reaction monitoring reveals the induction of specific terpene synthases in a multi-level study of methyl jasmonate-treated Norway spruce (Picea abies)

(2009) Katherine G. Zulak et al.   PLANT JOURNAL

Absolute quantification of Medicago truncatula sucrose synthase isoforms and N-metabolism enzymes in symbiotic root nodules and the detection of novel nodule phosphoproteins by mass spectrometry

(2008) S. Wienkoop et al.   JOURNAL OF EXPERIMENTAL BOTANY

Halobacterium salinarum NRC-1PeptideAtlas: Toward Strategies for Targeted Proteomics and Improved Proteome Coverage

(2008) Phu T. Van et al.   JOURNAL OF PROTEOME RESEARCH

Selected reaction monitoring for quantitative proteomics: a tutorial

(2008) Vinzenz Lange et al.   Molecular Systems Biology