A sentinel protein assay for simultaneously quantifying cellular processes

Reproducibility of combinatorial peptide ligand libraries for proteome capture evaluated by selected reaction monitoring

(2013) Francesco Di Girolamo et al.   Journal of Proteomics

Response to Hyperosmotic Stress

(2012) H. Saito et al.   GENETICS

Phosphorylation of Yeast Hexokinase 2 Regulates Its Nucleocytoplasmic Shuttling

(2012) Paula Fernández-García et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Comprehensive profiling of proteome changes upon sequential deletion of deubiquitylating enzymes

(2012) Jon W. Poulsen et al.   Journal of Proteomics

Quantitative Analysis of Energy Metabolic Pathways in MCF-7 Breast Cancer Cells by Selected Reaction Monitoring Assay

(2012) Andrei P. Drabovich et al.   MOLECULAR & CELLULAR PROTEOMICS

Tools for Label-free Peptide Quantification

(2012) Sven Nahnsen et al.   MOLECULAR & CELLULAR PROTEOMICS

Secretomic Analysis Identifies Alpha-1 Antitrypsin (A1AT) as a Required Protein in Cancer Cell Migration, Invasion, and Pericellular Fibronectin Assembly for Facilitating Lung Colonization of Lung Adenocarcinoma Cells

(2012) Ying-Hua Chang et al.   MOLECULAR & CELLULAR PROTEOMICS

PaxDb, a Database of Protein Abundance Averages Across All Three Domains of Life

(2012) M. Wang et al.   MOLECULAR & CELLULAR PROTEOMICS

Targeted Data Extraction of the MS/MS Spectra Generated by Data-independent Acquisition: A New Concept for Consistent and Accurate Proteome Analysis

(2012) Ludovic C. Gillet et al.   MOLECULAR & CELLULAR PROTEOMICS

Targeted proteomics reveals compositional dynamics of 60S pre-ribosomes after nuclear export

(2012) Martin Altvater et al.   Molecular Systems Biology

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

(2012) Paola Picotti et al.   NATURE METHODS

Update on activities at the Universal Protein Resource (UniProt) in 2013

(2012)   NUCLEIC ACIDS RESEARCH

STRING v9.1: protein-protein interaction networks, with increased coverage and integration

(2012) Andrea Franceschini et al.   NUCLEIC ACIDS RESEARCH

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

(2012) Claudia Escher et al.   PROTEOMICS

Hyperplexing: A Method for Higher-Order Multiplexed Quantitative Proteomics Provides a Map of the Dynamic Response to Rapamycin in Yeast

(2012) N. Dephoure et al.   Science Signaling

The Response to Heat Shock and Oxidative Stress in Saccharomyces cerevisiae

(2011) K. A. Morano et al.   GENETICS

Protein Expression Regulation under Oxidative Stress

(2011) Christine Vogel et al.   MOLECULAR & CELLULAR PROTEOMICS

System-wide Perturbation Analysis with Nearly Complete Coverage of the Yeast Proteome by Single-shot Ultra HPLC Runs on a Bench Top Orbitrap

(2011) Nagarjuna Nagaraj 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

Selected reaction monitoring mass spectrometry reveals the dynamics of signaling through the GRB2 adaptor

(2011) Nicolas Bisson et al.   NATURE BIOTECHNOLOGY

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

(2010) Brendan MacLean et al.   BIOINFORMATICS

Fission yeast TORC1 regulates phosphorylation of ribosomal S6 proteins in response to nutrients and its activity is inhibited by rapamycin

(2010) A. Nakashima et al.   JOURNAL OF CELL SCIENCE

The Rapamycin-sensitive Phosphoproteome Reveals That TOR Controls Protein Kinase A Toward Some But Not All Substrates

(2010) Alexandre Soulard et al.   MOLECULAR BIOLOGY OF THE CELL

Phosphoproteomic Analysis Reveals Interconnected System-Wide Responses to Perturbations of Kinases and Phosphatases in Yeast

(2010) B. Bodenmiller et al.   Science Signaling

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

(2009) Paola Picotti et al.   CELL

Compounds from an unbiased chemical screen reverse both ER-to-Golgi trafficking defects and mitochondrial dysfunction in Parkinson's disease models

(2009) L. J. Su et al.   Disease Models & Mechanisms

Global analysis of the yeast osmotic stress response by quantitative proteomics

(2009) Boumediene Soufi et al.   Molecular BioSystems

High-throughput generation of selected reaction-monitoring assays for proteins and proteomes

(2009) Paola Picotti et al.   NATURE METHODS

Global Analysis of Cdk1 Substrate Phosphorylation Sites Provides Insights into Evolution

(2009) L. J. Holt et al.   SCIENCE

Building consensus spectral libraries for peptide identification in proteomics

(2008) Henry Lam et al.   NATURE METHODS

Secreted 3-Isopropylmalate Methyl Ester Signals Invasive Growth during Amino Acid Starvation inSaccharomyces cerevisiae†

(2007) Darren S. Dumlao et al.   BIOCHEMISTRY