Mass spectrometry based metabolomics for in vitro systems pharmacology: pitfalls, challenges, and computational solutions

LC–MS-based metabolome analysis on steroid metabolites from the starfish Patiria (=Asterina) pectinifera in conditions of active feeding and stresses

(2016) Roman S. Popov et al.   Metabolomics

Large-scale untargeted LC-MS metabolomics data correction using between-batch feature alignment and cluster-based within-batch signal intensity drift correction

(2016) Carl Brunius et al.   Metabolomics

Untangling the wine metabolome by combining untargeted SPME–GCxGC-TOF-MS and sensory analysis to profile Sauvignon blanc co-fermented with seven different yeasts

(2016) Margaret E. Beckner Whitener et al.   Metabolomics

Analytical pitfalls and challenges in clinical metabolomics

(2016) Isabelle Kohler et al.   Bioanalysis

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

Workflow4Metabolomics: a collaborative research infrastructure for computational metabolomics

(2014) F. Giacomoni et al.   BIOINFORMATICS

NMR Spectroscopy-Based Metabolic Profiling of Drug-Induced Changes In Vitro Can Discriminate between Pharmacological Classes

(2014) Obaid Aftab et al.   Journal of Chemical Information and Modeling

Partial least squares discriminant analysis: taking the magic away

(2014) Richard G. Brereton et al.   JOURNAL OF CHEMOMETRICS

Large-scale Metabolomic Profiling Identifies Novel Biomarkers for Incident Coronary Heart Disease

(2014) Andrea Ganna et al.   PLoS Genetics

Characterising and correcting batch variation in an automated direct infusion mass spectrometry (DIMS) metabolomics workflow

(2013) J. A. Kirwan et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

An Automated Pipeline for High-Throughput Label-Free Quantitative Proteomics

(2013) Hendrik Weisser et al.   JOURNAL OF PROTEOME RESEARCH

Automated Label-free Quantification of Metabolites from Liquid Chromatography–Mass Spectrometry Data

(2013) Erhan Kenar et al.   MOLECULAR & CELLULAR PROTEOMICS

Targeted metabolomics identifies perturbations in amino acid metabolism that sub-classify patients with COPD

(2012) Baljit K. Ubhi et al.   Molecular BioSystems

A cross-platform toolkit for mass spectrometry and proteomics

(2012) Matthew C Chambers et al.   NATURE BIOTECHNOLOGY

ProteinSeq: High-Performance Proteomic Analyses by Proximity Ligation and Next Generation Sequencing

(2011) Spyros Darmanis et al.   PLoS One

Metabolomic high-content nuclear magnetic resonance-based drug screening of a kinase inhibitor library

(2011) Stefano Tiziani et al.   Nature Communications

Some common misunderstandings in chemometrics

(2010) Karin Kjeldahl et al.   JOURNAL OF CHEMOMETRICS

Analytical Error Reduction Using Single Point Calibration for Accurate and Precise Metabolomic Phenotyping

(2009) Frans M. van der Kloet et al.   JOURNAL OF PROTEOME RESEARCH

Effect of the Histone Deacetylase Inhibitor Trichostatin A on the Metabolome of Cultured Primary Hepatocytes

(2009) James K. Ellis et al.   JOURNAL OF PROTEOME RESEARCH

OpenMS – An open-source software framework for mass spectrometry

(2008) Marc Sturm et al.   BMC BIOINFORMATICS