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

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

(2015) Kerry Bauer Scott et al.   ANALYTICAL CHEMISTRY

Accounting for Experimental Noise Reveals That mRNA Levels, Amplified by Post-Transcriptional Processes, Largely Determine Steady-State Protein Levels in Yeast

(2015) Gábor Csárdi et al.   PLoS Genetics

Global mRNA selection mechanisms for translation initiation

(2015) Joseph Costello et al.   GENOME BIOLOGY

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

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

Global Analysis of mRNA Isoform Half-Lives Reveals Stabilizing and Destabilizing Elements in Yeast

(2014) Joseph V. Geisberg et al.   CELL

Predicting the Dynamics of Protein Abundance

(2014) Ahmed M. Mehdi et al.   MOLECULAR & CELLULAR PROTEOMICS

A “Proteomic Ruler” for Protein Copy Number and Concentration Estimation without Spike-in Standards

(2014) Jacek R. Wiśniewski et al.   MOLECULAR & CELLULAR PROTEOMICS

Poly(A)-tail profiling reveals an embryonic switch in translational control

(2014) Alexander O. Subtelny et al.   NATURE

Multi-platform assessment of transcriptome profiling using RNA-seq in the ABRF next-generation sequencing study

(2014) Sheng Li et al.   NATURE BIOTECHNOLOGY

Detecting and correcting systematic variation in large-scale RNA sequencing data

(2014) Sheng Li et al.   NATURE BIOTECHNOLOGY

Minimal, encapsulated proteomic-sample processing applied to copy-number estimation in eukaryotic cells

(2014) Nils A Kulak et al.   NATURE METHODS

Trends in QconCATs for targeted proteomics

(2014) Junjun Chen et al.   TRAC-TRENDS IN ANALYTICAL CHEMISTRY

System wide analyses have underestimated protein abundances and the importance of transcription in mammals

(2014) Jingyi Jessica Li et al.   PeerJ

Accurate Determination of Peptide Phosphorylation Stoichiometry Via Automated Diagonal Capillary Electrophoresis Coupled with Mass Spectrometry: Proof of Principle

(2013) Si Mou et al.   ANALYTICAL CHEMISTRY

Quantitative Bottom-Up Proteomics Depends on Digestion Conditions

(2013) Mark S. Lowenthal et al.   ANALYTICAL CHEMISTRY

What is the total number of protein molecules per cell volume? A call to rethink some published values

(2013) Ron Milo   BIOESSAYS

Computational tools for copy number variation (CNV) detection using next-generation sequencing data: features and perspectives

(2013) Min Zhao et al.   BMC BIOINFORMATICS

The One Hour Yeast Proteome

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

Statistical Approach to Protein Quantification

(2013) Sarah Gerster et al.   MOLECULAR & CELLULAR PROTEOMICS

The Coming Age of Complete, Accurate, and Ubiquitous Proteomes

(2013) Matthias Mann et al.   MOLECULAR CELL

A complete mass-spectrometric map of the yeast proteome applied to quantitative trait analysis

(2013) Paola Picotti et al.   NATURE

Systematic measurement of transcription factor-DNA interactions by targeted mass spectrometry identifies candidate gene regulatory proteins

(2013) Hamid Mirzaei 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

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

(2012) Samuel Marguerat et al.   CELL

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

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

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

(2012) Paola Picotti et al.   NATURE METHODS

Insights into the regulation of protein abundance from proteomic and transcriptomic analyses

(2012) Christine Vogel et al.   NATURE REVIEWS GENETICS

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

Genome-wide ribosome profiling reveals complex translational regulation in response to oxidative stress

(2012) M. V. Gerashchenko et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The use of selected reaction monitoring in quantitative proteomics

(2012) Stephen W Holman et al.   Bioanalysis

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

Absolute Quantification of the Glycolytic Pathway in Yeast:

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

Estimation of Absolute Protein Quantities of Unlabeled Samples by Selected Reaction Monitoring Mass Spectrometry

(2011) Christina Ludwig 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 dynamic model of proteome changes reveals new roles for transcript alteration in yeast

(2011) M. V. Lee et al.   Molecular Systems Biology

Structural basis for the subunit assembly of the anaphase-promoting complex

(2011) Anne Schreiber et al.   NATURE

mProphet: automated data processing and statistical validation for large-scale SRM experiments

(2011) Lukas Reiter et al.   NATURE METHODS

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

(2011) Philip Brownridge et al.   PROTEOMICS

The Effect of Dilution Rate upon Protein Content and Cellular Amino Acid Profiles in Chemostat Cultures of Saccharomyces Cerevisiae CABI 039916

(2010) Beverley Finn et al.   International Journal of Food Engineering

Sequence signatures and mRNA concentration can explain two-thirds of protein abundance variation in a human cell line

(2010) Christine Vogel et al.   Molecular Systems Biology

Genome-wide measurement of RNA secondary structure in yeast

(2010) Michael Kertesz et al.   NATURE

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Protein abundances are more conserved than mRNA abundances across diverse taxa

(2010) Jon M. Laurent et al.   PROTEOMICS

Shotgun proteomics data from multiple organisms reveals remarkable quantitative conservation of the eukaryotic core proteome

(2010) Manuel Weiss et al.   PROTEOMICS

Integrated multilaboratory systems biology reveals differences in protein metabolism between two reference yeast strains

(2010) André B. Canelas et al.   Nature Communications

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

(2009) Paola Picotti et al.   CELL

Rigorous determination of the stoichiometry of protein phosphorylation using mass spectrometry

(2009) Hannah Johnson et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

Interlaboratory Study Characterizing a Yeast Performance Standard for Benchmarking LC-MS Platform Performance

(2009) Amanda G. Paulovich et al.   MOLECULAR & CELLULAR PROTEOMICS

Proteome-wide cellular protein concentrations of the human pathogen Leptospira interrogans

(2009) Johan Malmström et al.   NATURE

The stoichiometry of protein phosphorylation in adipocyte lipid droplets: Analysis by N-terminal isotope tagging and enzymatic dephosphorylation

(2009) Evgeny Kanshin et al.   PROTEOMICS

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

(2009) N. T. Ingolia et al.   SCIENCE

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast

(2008) Lyris M. F. de Godoy et al.   NATURE

Single-RNA counting reveals alternative modes of gene expression in yeast

(2008) Daniel Zenklusen et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY