Reproducible proteomics sample preparation for single FFPE tissue slices using acid-labile surfactant and direct trypsinization

A laser microdissection-based workflow for FFPE tissue microproteomics: Important considerations for small sample processing

(2016) Rémi Longuespée et al.   METHODS

Formalin-Fixed, Paraffin-Embedded Tissues (FFPE) as a Robust Source for the Profiling of Native and Protease-Generated Protein Amino Termini

(2016) Zon Weng Lai et al.   MOLECULAR & CELLULAR PROTEOMICS

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

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update

(2016) Enis Afgan et al.   NUCLEIC ACIDS RESEARCH

Quantitative proteomic analysis of formalin–fixed, paraffin–embedded clear cell renal cell carcinoma tissue using stable isotopic dimethylation of primary amines

(2015) J. Weißer et al.   BMC GENOMICS

Mass-spectrometry-based quantitation of Her2 in gastroesophageal tumor tissue: comparison to IHC and FISH

(2015) Daniel V. T. Catenacci et al.   Gastric Cancer

Absolute Proteome Analysis of Colorectal Mucosa, Adenoma, and Cancer Reveals Drastic Changes in Fatty Acid Metabolism and Plasma Membrane Transporters

(2015) Jacek R. Wiśniewski et al.   JOURNAL OF PROTEOME RESEARCH

2016 update of the PRIDE database and its related tools

(2015) Juan Antonio Vizcaíno et al.   NUCLEIC ACIDS RESEARCH

Proteomic analysis of neurons microdissected from formalin-fixed, paraffin-embedded Alzheimer’s disease brain tissue

(2015) Eleanor S Drummond et al.   Scientific Reports

Accurate Proteome-wide Label-free Quantification by Delayed Normalization and Maximal Peptide Ratio Extraction, Termed MaxLFQ

(2014) Jürgen Cox et al.   MOLECULAR & CELLULAR PROTEOMICS

Ultrasensitive proteome analysis using paramagnetic bead technology

(2014) C. S. Hughes et al.   Molecular Systems Biology

Impact of routinely employed procedures for tissue processing on the proteomic analysis of formalin-fixed paraffin-embedded tissue

(2014) Peter Bronsert et al.   Proteomics Clinical Applications

Large-scale gene function analysis with the PANTHER classification system

(2013) Huaiyu Mi et al.   Nature Protocols

Galaxy tools and workflows for sequence analysis with applications in molecular plant pathology

(2013) Peter J.A. Cock et al.   PeerJ

Impact of pre-analytical factors on the proteomic analysis of formalin-fixed paraffin-embedded tissue

(2012) Seonaid M. Thompson et al.   Proteomics Clinical Applications

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

(2012) Jacek R. Wiśniewski et al.   Proteomics Clinical Applications

Standardization of a Sample Preparation and Analytical Workflow for Proteomics of Archival Endometrial Cancer Tissue

(2011) Addie Alkhas et al.   JOURNAL OF PROTEOME RESEARCH

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

Comparison of ultrafiltration units for proteomic and N-glycoproteomic analysis by the filter-aided sample preparation method

(2010) Jacek R. Wiśniewski et al.   ANALYTICAL BIOCHEMISTRY

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

Cell-based proteome analysis: The first stage in the pipeline for biomarker discovery

(2009) Gereon Poschmann et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

N-Linked Glycoproteomic Analysis of Formalin-Fixed and Paraffin-Embedded Tissues

(2009) Yuan Tian et al.   JOURNAL OF PROTEOME RESEARCH

Equivalence of Protein Inventories Obtained from Formalin-fixed Paraffin-embedded and Frozen Tissue in Multidimensional Liquid Chromatography-Tandem Mass Spectrometry Shotgun Proteomic Analysis

(2009) Robert W. Sprung et al.   MOLECULAR & CELLULAR PROTEOMICS

Reply to “Spin filter–based sample preparation for shotgun proteomics”

(2009) Jacek R Wiśniewski et al.   NATURE METHODS

Spin filter–based sample preparation for shotgun proteomics

(2009) Daniel C Liebler et al.   NATURE METHODS

Universal sample preparation method for proteome analysis

(2009) Jacek R Wiśniewski et al.   NATURE METHODS

Generation of high-quality protein extracts from formalin-fixed, paraffin-embedded tissues

(2009) Maria Filippa Addis et al.   PROTEOMICS

BioVenn – a web application for the comparison and visualization of biological lists using area-proportional Venn diagrams

(2008) Tim Hulsen et al.   BMC GENOMICS

Antigen Retrieval for Proteomic Characterization of Formalin-Fixed and Paraffin-Embedded Tissues

(2008) Haifeng Xu et al.   JOURNAL OF PROTEOME RESEARCH

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

Protein profiling of formalin fixed paraffin embedded tissue: Identification of potential biomarkers for pediatric brainstem glioma

(2008) Javad Nazarian et al.   Proteomics Clinical Applications

Guided protein extraction from formalin-fixed tissues for quantitative multiplex analysis avoids detrimental effects of histological stains

(2008) Karl-Friedrich Becker et al.   Proteomics Clinical Applications