Boosting Detection of Low-Abundance Proteins in Thermal Proteome Profiling Experiments by Addition of an Isobaric Trigger Channel to TMT Multiplexes

Protein Phosphatases in G1 Regulation

(2020) Ruth Martín et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

An improved Boosting to Amplify Signal with Isobaric Labeling (iBASIL) strategy for precise quantitative single-cell proteomics

(2020) Chia-Feng Tsai et al.   MOLECULAR & CELLULAR PROTEOMICS

Tandem Mass Tag approach utilizing pervanadate BOOST channels delivers deeper quantitative characterization of the tyrosine phosphoproteome

(2020) Xien Yu Chua et al.   MOLECULAR & CELLULAR PROTEOMICS

Thermal proteome profiling for interrogating protein interactions

(2020) André Mateus et al.   Molecular Systems Biology

RNA Polymerase II CTD phosphatase Rtr1 fine-tunes transcription termination

(2020) Jose F. Victorino et al.   PLoS Genetics

Mutant thermal proteome profiling for characterization of missense protein variants and their associated phenotypes within the proteome

(2020) Sarah A. Peck Justice et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Defining the carrier proteome limit for single-cell proteomics

(2020) Tommy K. Cheung et al.   NATURE METHODS

The Gene Ontology resource: enriching a GOld mine

(2020) et al.   NUCLEIC ACIDS RESEARCH

Single-cell protein analysis by mass spectrometry

(2020) Nikolai Slavov   CURRENT OPINION IN CHEMICAL BIOLOGY

Boosting to Amplify Signal with Isobaric Labeling (BASIL) Strategy for Comprehensive Quantitative Phosphoproteomic Characterization of Small Populations of Cells

(2019) Lian Yi et al.   ANALYTICAL CHEMISTRY

High-Throughput Single Cell Proteomics Enabled by Multiplex Isobaric Labeling in a Nanodroplet Sample Preparation Platform

(2019) Maowei Dou et al.   ANALYTICAL CHEMISTRY

RNA polymerase II plays an active role in the formation of gene loops through the Rpb4 subunit

(2019) Paula Allepuz-Fuster et al.   NUCLEIC ACIDS RESEARCH

TMTpro: Design, Synthesis, and Initial Evaluation of a Proline-Based Isobaric 16-Plex Tandem Mass Tag Reagent Set

(2019) Andrew Thompson et al.   ANALYTICAL CHEMISTRY

Extensive disruption of protein interactions by genetic variants across the allele frequency spectrum in human populations

(2019) Robert Fragoza et al.   Nature Communications

Single-cell proteomics reveals changes in expression during hair-cell development

(2019) Ying Zhu et al.   eLife

Functional Translatome Proteomics Reveal Converging and Dose-Dependent Regulation by mTORC1 and eIF2α

(2019) Kevin Klann et al.   MOLECULAR CELL

Xrn2 accelerates termination by RNA polymerase II, which is underpinned by CPSF73 activity

(2018) Joshua D. Eaton et al.   GENES & DEVELOPMENT

Comparison of In-Solution, FASP, and S-Trap Based Digestion Methods for Bottom-Up Proteomic Studies

(2018) Katelyn R. Ludwig et al.   JOURNAL OF PROTEOME RESEARCH

Defeating Major Contaminants in Fe3+- Immobilized Metal Ion Affinity Chromatography (IMAC) Phosphopeptide Enrichment

(2018) Clement M. Potel et al.   MOLECULAR & CELLULAR PROTEOMICS

BoxCar acquisition method enables single-shot proteomics at a depth of 10,000 proteins in 100 minutes

(2018) Florian Meier et al.   NATURE METHODS

Reproducible workflow for multiplexed deep-scale proteome and phosphoproteome analysis of tumor tissues by liquid chromatography–mass spectrometry

(2018) Philipp Mertins et al.   Nature Protocols

Benchmarking common quantification strategies for large-scale phosphoproteomics

(2018) Alexander Hogrebe et al.   Nature Communications

Unification of Protein Abundance Datasets Yields a Quantitative Saccharomyces cerevisiae Proteome

(2018) Brandon Ho et al.   Cell Systems

Endoplasmic reticulum stress alters ryanodine receptor function in the murine pancreatic β cell

(2018) Wataru R. Yamamoto et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The PRIDE database and related tools and resources in 2019: improving support for quantification data

(2018) Yasset Perez-Riverol et al.   NUCLEIC ACIDS RESEARCH

Architecture of the human interactome defines protein communities and disease networks

(2017) Edward L. Huttlin et al.   NATURE

Architecture of eukaryotic mRNA 3′-end processing machinery

(2017) Ana Casañal et al.   SCIENCE

A Defective mRNA Cleavage and Polyadenylation Complex Facilitates Expansions of Transcribed (GAA) n Repeats Associated with Friedreich’s Ataxia

(2017) Ryan J. McGinty et al.   Cell Reports

Transcription factors GAF and HSF act at distinct regulatory steps to modulate stress-induced gene activation

(2016) Fabiana M. Duarte et al.   GENES & DEVELOPMENT

Quantitative Analysis of Dynamic Protein Interactions during Transcription Reveals a Role for Casein Kinase II in Polymerase-associated Factor (PAF) Complex Phosphorylation and Regulation of Histone H2B Monoubiquitylation

(2016) Lynn Glowczewski Bedard et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Mammalian Heat Shock Response and Mechanisms Underlying Its Genome-wide Transcriptional Regulation

(2016) Dig B. Mahat et al.   MOLECULAR CELL

Defining the consequences of genetic variation on a proteome-wide scale

(2016) Joel M. Chick et al.   NATURE

Mass-spectrometric exploration of proteome structure and function

(2016) Ruedi Aebersold et al.   NATURE

PANTHER version 11: expanded annotation data from Gene Ontology and Reactome pathways, and data analysis tool enhancements

(2016) Huaiyu Mi et al.   NUCLEIC ACIDS RESEARCH

Transcriptional termination in mammals: Stopping the RNA polymerase II juggernaut

(2016) N. J. Proudfoot   SCIENCE

Widespread Macromolecular Interaction Perturbations in Human Genetic Disorders

(2015) Nidhi Sahni et al.   CELL

High-throughput phosphoproteomics reveals in vivo insulin signaling dynamics

(2015) Sean J Humphrey et al.   NATURE BIOTECHNOLOGY

Thermal proteome profiling for unbiased identification of direct and indirect drug targets using multiplexed quantitative mass spectrometry

(2015) Holger Franken et al.   Nature Protocols

A Proteome-Scale Map of the Human Interactome Network

(2014) Thomas Rolland et al.   CELL

Off-Line High-pH Reversed-Phase Fractionation for In-Depth Phosphoproteomics

(2014) Tanveer S. Batth et al.   JOURNAL OF PROTEOME RESEARCH

The interactome of the atypical phosphatase Rtr1 in Saccharomyces cerevisiae

(2014) Whitney R. Smith-Kinnaman et al.   Molecular BioSystems

Tracking cancer drugs in living cells by thermal profiling of the proteome

(2014) M. M. Savitski et al.   SCIENCE

Comprehensive Analysis of Protein Digestion Using Six Trypsins Reveals the Origin of Trypsin As a Significant Source of Variability in Proteomics

(2013) Scott J. Walmsley et al.   JOURNAL OF PROTEOME RESEARCH

Quantitative Proteomics Demonstrates That the RNA Polymerase II Subunits Rpb4 and Rpb7 Dissociate during Transcriptional Elongation

(2013) Amber L. Mosley et al.   MOLECULAR & CELLULAR PROTEOMICS

Mapping differential interactomes by affinity purification coupled with data-independent mass spectrometry acquisition

(2013) Jean-Philippe Lambert et al.   NATURE METHODS

Increasing the Multiplexing Capacity of TMTs Using Reporter Ion Isotopologues with Isobaric Masses

(2012) Graeme C. McAlister et al.   ANALYTICAL CHEMISTRY

Ssu72 Phosphatase-dependent Erasure of Phospho-Ser7 Marks on the RNA Polymerase II C-terminal Domain Is Essential for Viability and Transcription Termination

(2012) David W. Zhang et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Next-generation proteomics: towards an integrative view of proteome dynamics

(2012) A. F. Maarten Altelaar et al.   NATURE REVIEWS GENETICS

A genetic screen for terminator function in yeast identifies a role for a new functional domain in termination factor Nab3

(2012) T. J. Loya et al.   NUCLEIC ACIDS RESEARCH

Gene Loops Enhance Transcriptional Directionality

(2012) S. M. Tan-Wong et al.   SCIENCE

Systematic and quantitative comparison of digest efficiency and specificity reveals the impact of trypsin quality on MS-based proteomics

(2011) Julia Maria Burkhart et al.   Journal of Proteomics

Deep proteome and transcriptome mapping of a human cancer cell line

(2011) N. Nagaraj et al.   Molecular Systems Biology

Reversed-phase chromatography with multiple fraction concatenation strategy for proteome profiling of human MCF10A cells

(2011) Yuexi Wang et al.   PROTEOMICS

Highly Reproducible Label Free Quantitative Proteomic Analysis of RNA Polymerase Complexes

(2010) Amber L. Mosley et al.   MOLECULAR & CELLULAR PROTEOMICS

Small epitope-linker modules for PCR-based C-terminal tagging inSaccharomyces cerevisiae

(2009) Minoru Funakoshi et al.   YEAST