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

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

Protein amino-terminal modifications and proteomic approaches for N-terminal profiling

(2015) Zon W Lai et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

A MALDI-Mass Spectrometry Imaging method applicable to different formalin-fixed paraffin-embedded human tissues

(2015) Gabriele De Sio et al.   Molecular BioSystems

Enrichment of protein N-termini by charge reversal of internal peptides

(2015) Zon W. Lai et al.   PROTEOMICS

Toward improved peptide feature detection in quantitative proteomics using stable isotope labeling

(2015) Lars Nilse et al.   Proteomics Clinical Applications

MS-Viewer: A Web-based Spectral Viewer for Proteomics Results

(2014) Peter R. Baker et al.   MOLECULAR & CELLULAR PROTEOMICS

ProteomeXchange provides globally coordinated proteomics data submission and dissemination

(2014) Juan A Vizcaíno et al.   NATURE BIOTECHNOLOGY

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

Double deficiency of cathepsins B and L results in massive secretome alterations and suggests a degradative cathepsin-MMP axis

(2013) Stefan Tholen et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Proteomic identification of protease cleavage sites: cell-biological and biomedical applications

(2013) Hasmik Shahinian et al.   Expert Review of Proteomics

Novel Highly Sensitive, Specific, and Straightforward Strategy for Comprehensive N-Terminal Proteomics Reveals Unknown Substrates of the Mitochondrial Peptidase Icp55

(2013) A. Saskia Venne et al.   JOURNAL OF PROTEOME RESEARCH

Deletion of Cysteine Cathepsins B or L Yields Differential Impacts on Murine Skin Proteome and Degradome

(2012) Stefan Tholen et al.   MOLECULAR & CELLULAR PROTEOMICS

Unbiased Selective Isolation of Protein N-terminal Peptides from Complex Proteome Samples Using Phospho Tagging (PTAG) and TiO2-based Depletion

(2012) Geert P. M. Mommen et al.   MOLECULAR & CELLULAR PROTEOMICS

Novel protein extraction approach using micro-sized chamber for evaluation of proteins eluted from formalin-fixed paraffin-embedded tissue sections

(2012) Keiichi Hatakeyama et al.   Proteome Science

Validation of a robust proteomic analysis carried out on formalin-fixed paraffin-embedded tissues of the pancreas obtained from mouse and human

(2012) Kyoko Kojima et al.   PROTEOMICS

Proteomic analysis of formalin-fixed paraffin-embedded renal tissue samples by label-free MS: Assessment of overall technical variability and the impact of block age

(2012) Rachel A. Craven 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

Protein alpha-N-acetylation studied by N-terminomics

(2011) Petra Van Damme et al.   FEBS Journal

A quantitative proteomic analysis of FFPE melanoma

(2011) Stephanie Byrum et al.   JOURNAL OF CUTANEOUS PATHOLOGY

Comprehensive Tissue Processing Strategy for Quantitative Proteomics of Formalin-fixed Multiple Sclerosis Lesions

(2011) Linda Ly et al.   JOURNAL OF PROTEOME RESEARCH

Protective role of cathepsin L in mouse skin carcinogenesis

(2011) Fernando Benavides et al.   MOLECULAR CARCINOGENESIS

TopFIND, a knowledgebase linking protein termini with function

(2011) Philipp F Lange et al.   NATURE METHODS

IL-4 induces cathepsin protease activity in tumor-associated macrophages to promote cancer growth and invasion

(2010) V. Gocheva et al.   GENES & DEVELOPMENT

Quantitative Proteomic Analysis of Formalin-fixed and Paraffin-embedded Nasopharyngeal Carcinoma Using iTRAQ Labeling, Two-dimensional Liquid Chromatography, and Tandem Mass Spectrometry

(2010) Zhefeng Xiao et al.   JOURNAL OF HISTOCHEMISTRY & CYTOCHEMISTRY

Formalin-Fixed Paraffin-Embedded (FFPE) Proteome Analysis Using Gel-Free and Gel-Based Proteomics

(2010) Omid Azimzadeh et al.   JOURNAL OF PROTEOME RESEARCH

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

Isotopic labeling of terminal amines in complex samples identifies protein N-termini and protease cleavage products

(2010) Oded Kleifeld et al.   NATURE BIOTECHNOLOGY

Quantitative proteomics using formalin-fixed paraffin-embedded tissues of oral squamous cell carcinoma

(2009) Ayako Negishi et al.   CANCER SCIENCE

On-tissue protein identification and imaging by MALDI-Ion mobility mass spectrometry

(2009) Jonathan Stauber et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

Grade-dependent Proteomics Characterization of Kidney Cancer

(2009) Bertrand Perroud et al.   MOLECULAR & CELLULAR PROTEOMICS

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

Improved visualization of protein consensus sequences by iceLogo

(2009) Niklaas Colaert et al.   NATURE METHODS

The Universal Protein Resource (UniProt) in 2010

(2009)   NUCLEIC ACIDS RESEARCH

Deficiency for the cysteine protease cathepsin L promotes tumor progression in mouse epidermis

(2009) J Dennemärker et al.   ONCOGENE

Mass spectrometric identification of formaldehyde-induced peptide modifications under in vivo protein cross-linking conditions

(2008) Judy Toews et al.   ANALYTICA CHIMICA ACTA

ProteoWizard: open source software for rapid proteomics tools development

(2008) Darren Kessner et al.   BIOINFORMATICS

OpenMS – An open-source software framework for mass spectrometry

(2008) Marc Sturm et al.   BMC BIOINFORMATICS

Major Role of Cathepsin L for Producing the Peptide Hormones ACTH, β-Endorphin, and α-MSH, Illustrated by Protease Gene Knockout and Expression

(2008) Lydiane Funkelstein et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Lysosomal cysteine peptidase cathepsin L protects against cardiac hypertrophy through blocking AKT/GSK3β signaling

(2008) Qizhu Tang et al.   JOURNAL OF MOLECULAR MEDICINE-JMM

Spectral Probabilities and Generating Functions of Tandem Mass Spectra: A Strike against Decoy Databases

(2008) Sangtae Kim et al.   JOURNAL OF PROTEOME RESEARCH

mzML: A single, unifying data format for mass spectrometer output

(2008) Eric Deutsch   PROTEOMICS