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

Direct and Absolute Quantification of over 1800 Yeast Proteins via Selected Reaction Monitoring

(2016) Craig Lawless et al.   MOLECULAR & CELLULAR PROTEOMICS

Quantitative Performance of Internal Standard Platforms for Absolute Protein Quantification Using Multiple Reaction Monitoring-Mass Spectrometry

(2015) Kerry Bauer Scott et al.   ANALYTICAL CHEMISTRY

Application of an LC–MS/MS method for the simultaneous quantification of human intestinal transporter proteins absolute abundance using a QconCAT technique

(2015) M.D. Harwood et al.   JOURNAL OF PHARMACEUTICAL AND BIOMEDICAL ANALYSIS

Plasma QconCATs reveal a gender-specific proteomic signature in apheresis platelet plasma supernatants

(2015) Monika Dzieciatkowska et al.   Journal of Proteomics

Proteomic analysis of protein methylation in the yeast Saccharomyces cerevisiae

(2015) Keyun Wang et al.   Journal of Proteomics

Yeast Interspecies Comparative Proteomics Reveals Divergence in Expression Profiles and Provides Insights into Proteome Resource Allocation and Evolutionary Roles of Gene Duplication

(2015) Keiji Kito et al.   MOLECULAR & CELLULAR PROTEOMICS

Quantitative proteomic analysis reveals a simple strategy of global resource allocation in bacteria

(2015) S. Hui et al.   Molecular Systems Biology

Overflow metabolism in Escherichia coli results from efficient proteome allocation

(2015) Markus Basan et al.   NATURE

Studying macromolecular complex stoichiometries by peptide-based mass spectrometry

(2015) Ingo Wohlgemuth et al.   PROTEOMICS

Version 4.0 of PaxDb: Protein abundance data, integrated across model organisms, tissues, and cell-lines

(2015) Mingcong Wang et al.   PROTEOMICS

Natural Flanking Sequences for Peptides Included in a Quantification Concatamer Internal Standard

(2014) Crystal S. F. Cheung et al.   ANALYTICAL CHEMISTRY

Quantifying Absolute Protein Synthesis Rates Reveals Principles Underlying Allocation of Cellular Resources

(2014) Gene-Wei Li et al.   CELL

Quantification of the Proteins of the Bacterial Ribosome Using QconCAT Technology

(2014) Zubida M. Al-Majdoub et al.   JOURNAL OF PROTEOME RESEARCH

Protein Quantification Using a Cleavable Reporter Peptide

(2014) Elodie Duriez et al.   JOURNAL OF PROTEOME RESEARCH

Development of a Method for Absolute Quantification of Equine Acute Phase Proteins Using Concatenated Peptide Standards and Selected Reaction Monitoring

(2014) Louise Bundgaard et al.   JOURNAL OF PROTEOME RESEARCH

Emergence of robust growth laws from optimal regulation of ribosome synthesis

(2014) M. Scott et al.   Molecular Systems Biology

ProteomeXchange provides globally coordinated proteomics data submission and dissemination

(2014) Juan A Vizcaíno et al.   NATURE BIOTECHNOLOGY

Rsp5/Nedd4 is the main ubiquitin ligase that targets cytosolic misfolded proteins following heat stress

(2014) Nancy N. Fang et al.   NATURE CELL BIOLOGY

Global Proteome Turnover Analyses of the Yeasts S. cerevisiae and S. pombe

(2014) Romain Christiano et al.   Cell Reports

The Cotranslational Function of Ribosome-Associated Hsp70 in Eukaryotic Protein Homeostasis

(2013) Felix Willmund et al.   CELL

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

(2013) Kieran Smallbone et al.   FEBS LETTERS

Alternative Fusion Protein Strategies to Express Recalcitrant QconCAT Proteins for Quantitative Proteomics of Human Drug Metabolizing Enzymes and Transporters

(2013) Matthew R. Russell et al.   JOURNAL OF PROTEOME RESEARCH

Cleaved and Missed Sites for Trypsin, Lys-C, and Lys-N Can Be Predicted with High Confidence on the Basis of Sequence Context

(2013) Paul D. Gershon   JOURNAL OF PROTEOME RESEARCH

Accurate Label-Free Protein Quantitation with High- and Low-Resolution Mass Spectrometers

(2013) Jocelyn F. Krey et al.   JOURNAL OF PROTEOME RESEARCH

Isotope dilution mass spectrometry for absolute quantification in proteomics: Concepts and strategies

(2013) Joan Villanueva et al.   Journal of Proteomics

Perturbations to the Ubiquitin Conjugate Proteome in Yeast ΔubxMutants Identify Ubx2 as a Regulator of Membrane Lipid Composition

(2013) Natalie Kolawa et al.   MOLECULAR & CELLULAR PROTEOMICS

The Ribosome as a Hub for Protein Quality Control

(2013) Sebastian Pechmann et al.   MOLECULAR CELL

Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation

(2013) Danielle L Swaney et al.   NATURE METHODS

Glycolytic strategy as a tradeoff between energy yield and protein cost

(2013) A. Flamholz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Quantitative analysis of chaperone network throughput in budding yeast

(2013) Philip Brownridge et al.   PROTEOMICS

Critical assessment of proteome-wide label-free absolute abundance estimation strategies

(2013) Erik Ahrné et al.   PROTEOMICS

Lysine Succinylation Is a Frequently Occurring Modification in Prokaryotes and Eukaryotes and Extensively Overlaps with Acetylation

(2013) Brian T. Weinert et al.   Cell Reports

Quantitative Analysis of Fission Yeast Transcriptomes and Proteomes in Proliferating and Quiescent Cells

(2012) Samuel Marguerat et al.   CELL

Quantotypic Properties of QconCAT Peptides Targeting Bovine Host Response to Streptococcus uberis

(2012) Stine L. Bislev et al.   JOURNAL OF PROTEOME RESEARCH

Proteome-wide Analysis of Lysine Acetylation Suggests its Broad Regulatory Scope inSaccharomyces cerevisiae

(2012) Peter Henriksen et al.   MOLECULAR & CELLULAR PROTEOMICS

Peptide Production and Decay Rates Affect the Quantitative Accuracy of Protein Cleavage Isotope Dilution Mass Spectrometry (PC-IDMS)

(2012) Christopher M. Shuford 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

Mass spectrometry quantification of clusterin in the human brain

(2012) Junjun Chen et al.   Molecular Neurodegeneration

Digestion and depletion of abundant proteins improves proteomic coverage

(2012) Bryan R Fonslow et al.   NATURE METHODS

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

(2012) Paola Picotti et al.   NATURE METHODS

Protease bias in absolute protein quantitation

(2012) Mao Peng et al.   NATURE METHODS

Prediction of Missed Proteolytic Cleavages for the Selection of Surrogate Peptides for Quantitative Proteomics

(2012) Craig Lawless et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

The importance of the digest: Proteolysis and absolute quantification in proteomics

(2011) Philip Brownridge et al.   METHODS

Absolute Quantification of the Glycolytic Pathway in Yeast:

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

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

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

A Protein Epitope Signature Tag (PrEST) Library Allows SILAC-based Absolute Quantification and Multiplexed Determination of Protein Copy Numbers in Cell Lines

(2011) Marlis Zeiler et al.   MOLECULAR & CELLULAR PROTEOMICS

Global quantification of mammalian gene expression control

(2011) Björn Schwanhäusser et al.   NATURE

Subunit Stoichiometry, Evolution, and Functional Implications of an Asymmetric Plant Plastid ClpP/R Protease Complex inArabidopsis

(2011) Paul Dominic B. Olinares et al.   PLANT CELL

Global absolute quantification of a proteome: Challenges in the deployment of a QconCAT strategy

(2011) Philip Brownridge et al.   PROTEOMICS

Recombinant Isotope Labeled and Selenium Quantified Proteins for Absolute Protein Quantification

(2010) Nico Zinn et al.   ANALYTICAL CHEMISTRY

The ribosome-bound Hsp70 homolog Ssb of Saccharomyces cerevisiae

(2010) Kristin Peisker et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH

Perturbation of the yeast N-acetyltransferase NatB induces elevation of protein phosphorylation levels

(2010) Andreas O Helbig et al.   BMC GENOMICS

Interdependence of Cell Growth and Gene Expression: Origins and Consequences

(2010) M. Scott et al.   SCIENCE

Effect of Dynamic Exclusion Duration on Spectral Count Based Quantitative Proteomics

(2009) Ying Zhang et al.   ANALYTICAL CHEMISTRY

Stoichiometry Determination of the MP1−p14 Complex Using a Novel and Cost-Efficient Method To Produce an Equimolar Mixture of Standard Peptides

(2009) Johann Holzmann et al.   ANALYTICAL CHEMISTRY

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

(2009) Paola Picotti et al.   CELL

FLEXIQuant: A Novel Tool for the Absolute Quantification of Proteins, and the Simultaneous Identification and Quantification of Potentially Modified Peptides

(2009) Sasha Singh et al.   JOURNAL OF PROTEOME RESEARCH

Isotope dilution strategies for absolute quantitative proteomics

(2009) Virginie Brun et al.   Journal of Proteomics

Multiple Reaction Monitoring-based, Multiplexed, Absolute Quantitation of 45 Proteins in Human Plasma

(2009) Michael A. Kuzyk et al.   MOLECULAR & CELLULAR PROTEOMICS

Global analysis of the yeast osmotic stress response by quantitative proteomics

(2009) Boumediene Soufi et al.   Molecular BioSystems

Quantitative proteomics in biological research

(2009) Matthias Wilm   PROTEOMICS

High-accuracy identification and bioinformatic analysis ofin vivoprotein phosphorylation sites in yeast

(2009) Florian Gnad et al.   PROTEOMICS

Global Analysis of Cdk1 Substrate Phosphorylation Sites Provides Insights into Evolution

(2009) L. J. Holt et al.   SCIENCE

Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling

(2009) N. T. Ingolia et al.   SCIENCE

Protein Quantification by Isotope Dilution Mass Spectrometry of Proteolytic Fragments: Cleavage Rate and Accuracy

(2008) Cristian G. Arsene et al.   ANALYTICAL CHEMISTRY

Absolute quantification of the budding yeast transcriptome by means of competitive PCR between genomic and complementary DNAs

(2008) Fumihito Miura et al.   BMC GENOMICS

A quantitative estimation of the global translational activity in logarithmically growing yeast cells

(2008) Tobias von der Haar   BMC Systems Biology

Mass Spectrometry-Based Approaches Toward Absolute Quantitative Proteomics

(2008) Keiji Kito et al.   CURRENT GENOMICS

Absolute SILAC for Accurate Quantitation of Proteins in Complex Mixtures Down to the Attomole Level

(2008) Stefan Hanke et al.   JOURNAL OF PROTEOME RESEARCH

Proteomic approaches to the analysis of multiprotein signaling complexes

(2008) Wei Yang et al.   PROTEOMICS

The origin and control ofex vivo oxidative peptide modifications prior to mass spectrometry analysis

(2008) Jennifer M. Froelich et al.   PROTEOMICS

Protein Standard Absolute Quantification (PSAQ) for improved investigation of staphylococcal food poisoning outbreaks

(2008) Alain Dupuis et al.   PROTEOMICS