A rapid methods development workflow for high-throughput quantitative proteomic applications

Conventional-Flow Liquid Chromatography–Mass Spectrometry for Exploratory Bottom-Up Proteomic Analyses

(2018) Juraj Lenčo et al.   ANALYTICAL CHEMISTRY

Increased glutarate production by blocking the glutaryl-CoA dehydrogenation pathway and a catabolic pathway involving l-2-hydroxyglutarate

(2018) Manman Zhang et al.   Nature Communications

A multicentric study to evaluate the use of relative retention times in targeted proteomics

(2017) Vital Vialas et al.   Journal of Proteomics

Quantitative proteomics: challenges and opportunities in basic and applied research

(2017) Olga T Schubert et al.   Nature Protocols

Multi-laboratory assessment of reproducibility, qualitative and quantitative performance of SWATH-mass spectrometry

(2017) Ben C. Collins et al.   Nature Communications

Application of an Acyl-CoA Ligase from Streptomyces aizunensis for Lactam Biosynthesis

(2017) Jingwei Zhang et al.   ACS Synthetic Biology

Human SRMAtlas: A Resource of Targeted Assays to Quantify the Complete Human Proteome

(2016) Ulrike Kusebauch et al.   CELL

A Skyline Plugin for Pathway-Centric Data Browsing

(2016) Michael G. Degan et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

Quantification and Classification of E. coli Proteome Utilization and Unused Protein Costs across Environments

(2016) Edward J. O’Brien et al.   PLoS Computational Biology

Multiplexed, Scheduled, High-Resolution Parallel Reaction Monitoring on a Full Scan QqTOF Instrument with Integrated Data-Dependent and Targeted Mass Spectrometric Workflows

(2015) Birgit Schilling et al.   ANALYTICAL CHEMISTRY

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

Precise quantitation of 136 urinary proteins by LC/MRM-MS using stable isotope labeled peptides as internal standards for biomarker discovery and/or verification studies

(2015) Andrew J. Percy et al.   METHODS

2016 update of the PRIDE database and its related tools

(2015) Juan Antonio Vizcaíno et al.   NUCLEIC ACIDS RESEARCH

Label-free quantification reveals major proteomic changes inPseudomonas putidaF1 during the exponential growth phase

(2015) Florian-Alexander Herbst et al.   PROTEOMICS

The Pacific Northwest National Laboratory library of bacterial and archaeal proteomic biodiversity

(2015) Samuel H. Payne et al.   Scientific Data

Panorama: A Targeted Proteomics Knowledge Base

(2014) Vagisha Sharma et al.   JOURNAL OF PROTEOME RESEARCH

PeptidePicker: A scientific workflow with web interface for selecting appropriate peptides for targeted proteomics experiments

(2014) Yassene Mohammed et al.   Journal of Proteomics

Targeted Peptide Measurements in Biology and Medicine: Best Practices for Mass Spectrometry-based Assay Development Using a Fit-for-Purpose Approach

(2014) Steven A. Carr et al.   MOLECULAR & CELLULAR PROTEOMICS

Current topics in the biotechnological production of essential amino acids, functional amino acids, and dipeptides

(2013) Satoshi Mitsuhashi   CURRENT OPINION IN BIOTECHNOLOGY

Performance Comparisons of Nano-LC Systems, Electrospray Sources and LC–MS-MS Platforms

(2013) Qian Liu et al.   JOURNAL OF CHROMATOGRAPHIC SCIENCE

The One Hour Yeast Proteome

(2013) Alexander S. Hebert et al.   MOLECULAR & CELLULAR PROTEOMICS

Comparison of standard- and nano-flow liquid chromatography platforms for MRM-based quantitation of putative plasma biomarker proteins

(2012) Andrew J. Percy et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

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

(2012) Paola Picotti et al.   NATURE METHODS

Using iRT, a normalized retention time for more targeted measurement of peptides

(2012) Claudia Escher et al.   PROTEOMICS

PASSEL: The PeptideAtlas SRMexperiment library

(2012) Terry Farrah et al.   PROTEOMICS

Recommendations for Mass Spectrometry Data Quality Metrics for Open Access Data (Corollary to the Amsterdam Principles)

(2011) Christopher R. Kinsinger et al.   JOURNAL OF PROTEOME RESEARCH

Expediting the Development of Targeted SRM Assays: Using Data from Shotgun Proteomics to Automate Method Development

(2009) Amol Prakash et al.   JOURNAL OF PROTEOME RESEARCH

Repeatability and Reproducibility in Proteomic Identifications by Liquid Chromatography−Tandem Mass Spectrometry

(2009) David L. Tabb et al.   JOURNAL OF PROTEOME RESEARCH

Prediction of high-responding peptides for targeted protein assays by mass spectrometry

(2009) Vincent A Fusaro et al.   NATURE BIOTECHNOLOGY

Multi-site assessment of the precision and reproducibility of multiple reaction monitoring–based measurements of proteins in plasma

(2009) Terri A Addona et al.   NATURE BIOTECHNOLOGY