Genome-scale proteome quantification by DEEP SEQ mass spectrometry

Increasing Throughput in Targeted Proteomics Assays: 54-Plex Quantitation in a Single Mass Spectrometry Run

(2013) Robert A. Everley et al.   ANALYTICAL CHEMISTRY

Single-Shot Proteomics Using Capillary Zone Electrophoresis–Electrospray Ionization-Tandem Mass Spectrometry with Production of More than 1 250 Escherichia coli Peptide Identifications in a 50 min Separation

(2013) Guijie Zhu et al.   ANALYTICAL CHEMISTRY

Hydrophilic Strong Anion Exchange (hSAX) Chromatography for Highly Orthogonal Peptide Separation of Complex Proteomes

(2013) Maria Stella Ritorto et al.   JOURNAL OF PROTEOME RESEARCH

An insight into iTRAQ: where do we stand now?

(2012) Caroline Evans et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

Ultra-Low Flow Electrospray Ionization-Mass Spectrometry for Improved Ionization Efficiency in Phosphoproteomics

(2012) Anthonius A. M. Heemskerk et al.   ANALYTICAL CHEMISTRY

Nanoflow Low Pressure High Peak Capacity Single Dimension LC-MS/MS Platform for High-Throughput, In-Depth Analysis of Mammalian Proteomes

(2012) Feng Zhou et al.   ANALYTICAL CHEMISTRY

Improving the Comprehensiveness and Sensitivity of Sheathless Capillary Electrophoresis–Tandem Mass Spectrometry for Proteomic Analysis

(2012) Yueju Wang et al.   ANALYTICAL CHEMISTRY

Key Principles and Clinical Applications of "Next-Generation" DNA Sequencing

(2012) J. M. Rizzo et al.   Cancer Prevention Research

Esrrb Is a Pivotal Target of the Gsk3/Tcf3 Axis Regulating Embryonic Stem Cell Self-Renewal

(2012) Graziano Martello et al.   Cell Stem Cell

Online Nanoscale ERLIC-MS Outperforms RPLC–MS for Shotgun Proteomics in Complex Mixtures

(2012) Ebbing P. de Jong et al.   JOURNAL OF PROTEOME RESEARCH

ENCODE explained

(2012) Joseph R. Ecker et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments

(2012) Nicholas T Ingolia et al.   Nature Protocols

Comparison of the LTQ-Orbitrap Velos and the Q-Exactive for proteomic analysis of 1-1000 ng RAW 264.7 cell lysate digests

(2012) Liangliang Sun et al.   RAPID COMMUNICATIONS IN MASS SPECTROMETRY

Online Nanoflow Reversed Phase-Strong Anion Exchange-Reversed Phase Liquid Chromatography–Tandem Mass Spectrometry Platform for Efficient and In-Depth Proteome Sequence Analysis of Complex Organisms

(2011) Feng Zhou et al.   ANALYTICAL CHEMISTRY

Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity and Dynamics of Mammalian Proteomes

(2011) Nicholas T. Ingolia et al.   CELL

Deep proteome and transcriptome mapping of a human cancer cell line

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

Initial impact of the sequencing of the human genome

(2011) Eric S. Lander   NATURE

Global quantification of mammalian gene expression control

(2011) Björn Schwanhäusser et al.   NATURE

Inhibition of glycogen synthase kinase-3 alleviates Tcf3 repression of the pluripotency network and increases embryonic stem cell resistance to differentiation

(2011) Jason Wray et al.   NATURE CELL BIOLOGY

Gas-phase purification enables accurate, multiplexed proteome quantification with isobaric tagging

(2011) Craig D Wenger et al.   NATURE METHODS

MS3 eliminates ratio distortion in isobaric multiplexed quantitative proteomics

(2011) Lily Ting et al.   NATURE METHODS

Single-Cell Mass Cytometry of Differential Immune and Drug Responses Across a Human Hematopoietic Continuum

(2011) S. C. Bendall et al.   SCIENCE

An Oct4-Centered Protein Interaction Network in Embryonic Stem Cells

(2010) Debbie L.C. van den Berg et al.   Cell Stem Cell

An Expanded Oct4 Interaction Network: Implications for Stem Cell Biology, Development, and Disease

(2010) Mercedes Pardo et al.   Cell Stem Cell

G1 arrest and differentiation can occur independently of Rb family function

(2010) Stacey E. Wirt et al.   JOURNAL OF CELL BIOLOGY

Role of Lef1 in sustaining self-renewal in mouse embryonic stem cells

(2010) Chen Huang et al.   Journal of Genetics and Genomics

PeptideClassifier for protein inference and targeted quantitative proteomics

(2010) Ermir Qeli et al.   NATURE BIOTECHNOLOGY

Ab initio reconstruction of cell type–specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs

(2010) Mitchell Guttman et al.   NATURE BIOTECHNOLOGY

Improved Electrospray Ionization Efficiency Compensates for Diminished Chromatographic Resolution and Enables Proteomics Analysis of Tyrosine Signaling in Embryonic Stem Cells

(2009) Scott B. Ficarro et al.   ANALYTICAL CHEMISTRY

multiplierz: an extensible API based desktop environment for proteomics data analysis

(2009) Jignesh R Parikh et al.   BMC BIOINFORMATICS

Naive and Primed Pluripotent States

(2009) Jennifer Nichols et al.   Cell Stem Cell

Oct4 and LIF/Stat3 Additively Induce Krüppel Factors to Sustain Embryonic Stem Cell Self-Renewal

(2009) John Hall et al.   Cell Stem Cell

A genome-wide RNAi screen identifies a new transcriptional module required for self-renewal

(2009) G. Hu et al.   GENES & DEVELOPMENT

iTRAQ Underestimation in Simple and Complex Mixtures: “The Good, the Bad and the Ugly”

(2009) Saw Yen Ow et al.   JOURNAL OF PROTEOME RESEARCH

A parallel circuit of LIF signalling pathways maintains pluripotency of mouse ES cells

(2009) Hitoshi Niwa et al.   NATURE

mzAPI: a new strategy for efficiently sharing mass spectrometry data

(2009) Manor Askenazi et al.   NATURE METHODS

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

(2009) N. T. Ingolia et al.   SCIENCE

Two-dimensional strong cation exchange/porous layer open tubular/mass spectrometry for ultratrace proteomic analysis using a 10 μm id poly(styrene- divinylbenzene) porous layer open tubular column with an on-line triphasic trapping column

(2008) Quanzhou Luo et al.   ELECTROPHORESIS

The ground state of embryonic stem cell self-renewal

(2008) Qi-Long Ying et al.   NATURE