Proteomic workflow for analysis of archival formalin-fixed and paraffin-embedded clinical samples to a depth of 10 000 proteins

Consecutive Proteolytic Digestion in an Enzyme Reactor Increases Depth of Proteomic and Phosphoproteomic Analysis

(2012) Jacek R. Wiśniewski et al.   ANALYTICAL CHEMISTRY

Proteomic Portrait of Human Breast Cancer Progression Identifies Novel Prognostic Markers

(2012) T. Geiger et al.   CANCER RESEARCH

Toward deciphering proteomes of formalin-fixed paraffin-embedded (FFPE) tissues

(2012) Sameh Magdeldin et al.   PROTEOMICS

Molecular Genetics of Colorectal Cancer

(2011) Eric R. Fearon   Annual Review of Pathology-Mechanisms of Disease

Cell surface proteomics identifies glucose transporter type 1 and prion protein as candidate biomarkers for colorectal adenoma-to-carcinoma progression

(2011) Meike de Wit et al.   GUT

Microproteomic analysis of 10,000 laser captured microdissected breast tumor cells using short-range sodium dodecyl sulfate-polyacrylamide gel electrophoresis and porous layer open tubular liquid chromatography tandem mass spectrometry

(2011) Dipak Thakur et al.   JOURNAL OF CHROMATOGRAPHY A

High Recovery FASP Applied to the Proteomic Analysis of Microdissected Formalin Fixed Paraffin Embedded Cancer Tissues Retrieves Known Colon Cancer Markers

(2011) Jacek R. Wiśniewski et al.   JOURNAL OF PROTEOME RESEARCH

Deep and Highly Sensitive Proteome Coverage by LC-MS/MS Without Prefractionation

(2011) Suman S. Thakur et al.   MOLECULAR & CELLULAR PROTEOMICS

Mass Spectrometry-based Proteomics Using Q Exactive, a High-performance Benchtop Quadrupole Orbitrap Mass Spectrometer

(2011) Annette Michalski et al.   MOLECULAR & CELLULAR PROTEOMICS

Deep proteome and transcriptome mapping of a human cancer cell line

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

The quantitative proteome of a human cell line

(2011) M. Beck et al.   Molecular Systems Biology

Global quantification of mammalian gene expression control

(2011) Björn Schwanhäusser et al.   NATURE

Successful Protein Extraction from Over-Fixed and Long-Term Stored Formalin-Fixed Tissues

(2011) Claudia Wolff et al.   PLoS One

Tools for phospho- and glycoproteomics of plasma membranes

(2010) Jacek R. Wiśniewski   AMINO ACIDS

Quantitative Proteomics Reveals Subset-Specific Viral Recognition in Dendritic Cells

(2010) Christian A. Luber et al.   IMMUNITY

Proteome, Phosphoproteome, and N-Glycoproteome Are Quantitatively Preserved in Formalin-Fixed Paraffin-Embedded Tissue and Analyzable by High-Resolution Mass Spectrometry

(2010) Paweł Ostasiewicz et al.   JOURNAL OF PROTEOME RESEARCH

Initial Development and Validation of a Novel Extraction Method for Quantitative Mining of the Formalin-Fixed, Paraffin-Embedded Tissue Proteome for Biomarker Investigations

(2010) Niroshini J. Nirmalan et al.   JOURNAL OF PROTEOME RESEARCH

Differential Proteomic Analysis of Late-Stage and Recurrent Breast Cancer from Formalin-Fixed Paraffin-Embedded Tissues

(2010) Nicholas W. Bateman et al.   JOURNAL OF PROTEOME RESEARCH

Proteomics of colorectal cancer: Overview of discovery studies and identification of commonly identified cancer-associated proteins and candidate CRC serum markers

(2010) Connie R. Jimenez et al.   Journal of Proteomics

Advancing RNA-Seq analysis

(2010) Brian J Haas et al.   NATURE BIOTECHNOLOGY

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

(2010) Cole Trapnell 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

Proteomic Changes Resulting from Gene Copy Number Variations in Cancer Cells

(2010) Tamar Geiger et al.   PLoS Genetics

Comparative Proteomic Profiling of Membrane Proteins in Rat Cerebellum, Spinal Cord, and Sciatic Nerve

(2009) Aiping Lu et al.   JOURNAL OF PROTEOME RESEARCH

Combination of FASP and StageTip-Based Fractionation Allows In-Depth Analysis of the Hippocampal Membrane Proteome

(2009) Jacek R. Wiśniewski et al.   JOURNAL OF PROTEOME RESEARCH

Universal sample preparation method for proteome analysis

(2009) Jacek R Wiśniewski et al.   NATURE METHODS

A census of human transcription factors: function, expression and evolution

(2009) Juan M. Vaquerizas et al.   NATURE REVIEWS GENETICS

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

(2008) Jürgen Cox et al.   NATURE BIOTECHNOLOGY

Peptide separation with immobilized pI strips is an attractive alternative to in-gel protein digestion for proteome analysis

(2008) Nina C. Hubner et al.   PROTEOMICS