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

Robust, reproducible and quantitative analysis of thousands of proteomes by micro-flow LC–MS/MS

(2020) Yangyang Bian et al.   Nature Communications

Engineering glucose metabolism for enhanced muconic acid production in Pseudomonas putida KT2440

(2020) Gayle J. Bentley et al.   METABOLIC ENGINEERING

Detection of Head and Neck Cancer Based on Longitudinal Changes in Serum Protein Abundance

(2020) Ju Yeon Lee et al.   CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION

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

Pathway Tools version 23.0 update: software for pathway/genome informatics and systems biology

(2019) Peter D Karp et al.   BRIEFINGS IN BIOINFORMATICS

Rapidly Assessing the Quality of Targeted Proteomics Experiments through Monitoring Stable-Isotope Labeled Standards

(2018) Bryson C. Gibbons et al.   JOURNAL OF PROTEOME RESEARCH

The Omics Dashboard for interactive exploration of gene-expression data

(2017) Suzanne Paley et al.   NUCLEIC ACIDS RESEARCH

From dirt to industrial applications: Pseudomonas putida as a Synthetic Biology chassis for hosting harsh biochemical reactions

(2016) Pablo I Nikel et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

MPLEx: a Robust and Universal Protocol for Single-Sample Integrative Proteomic, Metabolomic, and Lipidomic Analyses

(2016) Ernesto S. Nakayasu et al.   mSystems

A Metabolic Widget Adjusts the Phosphoenolpyruvate-Dependent Fructose Influx in Pseudomonas putida

(2016) Max Chavarría et al.   mSystems

Pseudomonas putida—a versatile host for the production of natural products

(2015) Anita Loeschcke et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Pseudomonas putidaKT2440 Strain Metabolizes Glucose through a Cycle Formed by Enzymes of the Entner-Doudoroff, Embden-Meyerhof-Parnas, and Pentose Phosphate Pathways

(2015) Pablo I. Nikel et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Using Data Independent Acquisition (DIA) to Model High-responding Peptides for Targeted Proteomics Experiments

(2015) Brian C. Searle et al.   MOLECULAR & CELLULAR PROTEOMICS

Applications of targeted proteomics in systems biology and translational medicine

(2015) H. Alexander Ebhardt et al.   PROTEOMICS

The Functional Structure of Central Carbon Metabolism in Pseudomonas putida KT2440

(2014) Suresh Sudarsan et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

MSstats: an R package for statistical analysis of quantitative mass spectrometry-based proteomic experiments

(2014) Meena Choi et al.   BIOINFORMATICS

Expediting SRM Assay Development for Large-Scale Targeted Proteomics Experiments

(2014) Chaochao Wu et al.   JOURNAL OF PROTEOME RESEARCH

Lignin valorization through integrated biological funneling and chemical catalysis

(2014) J. G. Linger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The challenge of constructing, classifying, and representing metabolic pathways

(2013) Ron Caspi et al.   FEMS MICROBIOLOGY LETTERS

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

(2012) Paola Picotti et al.   NATURE METHODS

A comparative analysis of computational approaches to relative protein quantification using peptide peak intensities in label-free LC-MS proteomics experiments

(2012) Melissa M. Matzke et al.   PROTEOMICS

Reproducible Quantification of Cancer-Associated Proteins in Body Fluids Using Targeted Proteomics

(2012) R. Huttenhain et al.   Science Translational Medicine

Regulatory Tasks of the Phosphoenolpyruvate-Phosphotransferase System of Pseudomonas putida in Central Carbon Metabolism

(2012) M. Chavarria et al.   mBio

CONSeQuence: Prediction of Reference Peptides for Absolute Quantitative Proteomics Using Consensus Machine Learning Approaches

(2011) Claire E. Eyers et al.   MOLECULAR & CELLULAR PROTEOMICS

A statistical selection strategy for normalization procedures in LC-MS proteomics experiments through dataset-dependent ranking of normalization scaling factors

(2011) Bobbie-Jo M. Webb-Robertson et al.   PROTEOMICS

Skyline: an open source document editor for creating and analyzing targeted proteomics experiments

(2010) Brendan MacLean et al.   BIOINFORMATICS

Combined Statistical Analyses of Peptide Intensities and Peptide Occurrences Improves Identification of Significant Peptides from MS-Based Proteomics Data

(2010) Bobbie-Jo M. Webb-Robertson et al.   JOURNAL OF PROTEOME RESEARCH

Central Carbon Metabolism as a Minimal Biochemical Walk between Precursors for Biomass and Energy

(2010) Elad Noor et al.   MOLECULAR CELL

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

(2009) Paola Picotti et al.   CELL

DAnTE: a statistical tool for quantitative analysis of -omics data

(2008) A. D. Polpitiya et al.   BIOINFORMATICS