Formalin-Fixed, Paraffin-Embedded Tissues (FFPE) as a Robust Source for the Profiling of Native and Protease-Generated Protein Amino Termini*
暂无分享,去创建一个
Fabrizio Costa | Peter Bronsert | Oliver Schilling | Lars Nilse | L. Nilse | O. Schilling | Z. W. Lai | J. Kizhakkedathu | M. Biniossek | P. Bronsert | Jayachandran N Kizhakkedathu | Martina Tholen | Martina Tholen | Zon Weng Lai | Juliane Weisser | Eva Keller | Martin Biniossek | Fabrizio Costa | J. Weißer | Eva Keller
[1] Fulvio Magni,et al. A MALDI-Mass Spectrometry Imaging method applicable to different formalin-fixed paraffin-embedded human tissues. , 2015, Molecular bioSystems.
[2] Tesshi Yamada,et al. Quantitative proteomics using formalin‐fixed paraffin‐embedded tissues of oral squamous cell carcinoma , 2009, Cancer science.
[3] A. Heck,et al. Unbiased Selective Isolation of Protein N-terminal Peptides from Complex Proteome Samples Using Phospho Tagging (PTAG) and TiO2-based Depletion* , 2012, Molecular & Cellular Proteomics.
[4] A. Tanca,et al. Critical comparison of sample preparation strategies for shotgun proteomic analysis of formalin-fixed, paraffin-embedded samples: insights from liver tissue , 2014, Clinical Proteomics.
[5] L. Coussens,et al. Protective role of cathepsin L in mouse skin carcinogenesis , 2012, Molecular carcinogenesis.
[6] T. Arnesen,et al. Protein alpha‐N‐acetylation studied by N‐terminomics , 2011, The FEBS journal.
[7] Cathy H. Wu,et al. The Universal Protein Resource (UniProt) , 2004, Nucleic Acids Res..
[8] G. Bodvarsson,et al. A Corrected and Generalized Successive Random Additions Algorithm for Simulating Fractional Levy Motions , 2004 .
[9] B. Crossett,et al. Comprehensive tissue processing strategy for quantitative proteomics of formalin-fixed multiple sclerosis lesions. , 2011, Journal of proteome research.
[10] M. Mann,et al. Proteome, phosphoproteome, and N-glycoproteome are quantitatively preserved in formalin-fixed paraffin-embedded tissue and analyzable by high-resolution mass spectrometry. , 2010, Journal of proteome research.
[11] Baris E. Suzek,et al. The Universal Protein Resource (UniProt) in 2010 , 2009, Nucleic Acids Res..
[12] Yongheng Chen,et al. Quantitative Proteomic Analysis of Formalin-fixed and Paraffin-embedded Nasopharyngeal Carcinoma Using iTRAQ Labeling, Two-dimensional Liquid Chromatography, and Tandem Mass Spectrometry , 2010, The journal of histochemistry and cytochemistry : official journal of the Histochemistry Society.
[13] I. Fournier,et al. On-tissue protein identification and imaging by MALDI-Ion mobility mass spectrometry , 2010, Journal of the American Society for Mass Spectrometry.
[14] Shu-Hui Chen,et al. Dimethyl isotope-coded affinity selection for the analysis of free and blocked N-termini of proteins using LC-MS/MS. , 2007, Analytical chemistry.
[15] K. Gevaert,et al. Exploring proteomes and analyzing protein processing by mass spectrometric identification of sorted N-terminal peptides , 2003, Nature Biotechnology.
[16] M. Mann,et al. Stop and go extraction tips for matrix-assisted laser desorption/ionization, nanoelectrospray, and LC/MS sample pretreatment in proteomics. , 2003, Analytical chemistry.
[17] C. Overall,et al. TopFIND, a knowledgebase linking protein termini with function , 2011, Nature Methods.
[18] Andrew R. Jones,et al. ProteomeXchange provides globally co-ordinated proteomics data submission and dissemination , 2014, Nature Biotechnology.
[19] Q. Tang,et al. Lysosomal cysteine peptidase cathepsin L protects against cardiac hypertrophy through blocking AKT/GSK3β signaling , 2009, Journal of Molecular Medicine.
[20] Kejia Wang,et al. Morphological dependence of power spectra from two-dimensional passive random media , 2004 .
[21] T. Veenstra,et al. Liquid Tissue: proteomic profiling of formalin-fixed tissues. , 2005, BioTechniques.
[22] C. Peters,et al. Major Role of Cathepsin L for Producing the Peptide Hormones ACTH, β-Endorphin, and α-MSH, Illustrated by Protease Gene Knockout and Expression* , 2008, Journal of Biological Chemistry.
[23] E. Deutsch. mzML: A single, unifying data format for mass spectrometer output , 2008, Proteomics.
[24] T. Reinheckel,et al. Double deficiency of cathepsins B and L results in massive secretome alterations and suggests a degradative cathepsin-MMP axis , 2013, Cellular and Molecular Life Sciences.
[25] Daniel C. Liebler,et al. Equivalence of Protein Inventories Obtained from Formalin-fixed Paraffin-embedded and Frozen Tissue in Multidimensional Liquid Chromatography-Tandem Mass Spectrometry Shotgun Proteomic Analysis* , 2009, Molecular & Cellular Proteomics.
[26] O. Vasiljeva,et al. Cell Type-specific Functions of the Lysosomal Protease Cathepsin L in the Heart* , 2007, Journal of Biological Chemistry.
[27] P. Pevzner,et al. Spectral probabilities and generating functions of tandem mass spectra: a strike against decoy databases. , 2008, Journal of proteome research.
[28] O. Schilling,et al. Quantitative proteomic analysis of formalin–fixed, paraffin–embedded clear cell renal cell carcinoma tissue using stable isotopic dimethylation of primary amines , 2015, BMC Genomics.
[29] J. Yates,et al. A model for random sampling and estimation of relative protein abundance in shotgun proteomics. , 2004, Analytical chemistry.
[30] Oliver Schilling,et al. Toward improved peptide feature detection in quantitative proteomics using stable isotope labeling , 2015, Proteomics. Clinical applications.
[31] A. Rudensky,et al. Cathepsin L: critical role in Ii degradation and CD4 T cell selection in the thymus. , 1998, Science.
[32] O. Schilling,et al. Enrichment of protein N‐termini by charge reversal of internal peptides , 2015, Proteomics.
[33] P. Roller,et al. Formaldehyde fixation. , 1985, The journal of histochemistry and cytochemistry : official journal of the Histochemistry Society.
[34] J. Langridge,et al. Initial Development and Validation of a Novel Extraction Method for Quantitative Mining of the Formalin-Fixed, Paraffin-Embedded Tissue Proteome for Biomarker Investigations , 2010, Journal of proteome research.
[35] Peter R Baker,et al. MS-Viewer: A Web-based Spectral Viewer for Proteomics Results* , 2014, Molecular & Cellular Proteomics.
[36] M. Aubele,et al. Formalin-fixed paraffin-embedded (FFPE) proteome analysis using gel-free and gel-based proteomics. , 2010, Journal of proteome research.
[37] María Martín,et al. The Universal Protein Resource (UniProt) in 2010 , 2010 .
[38] Robert Burke,et al. ProteoWizard: open source software for rapid proteomics tools development , 2008, Bioinform..
[39] D. Hanahan,et al. Distinct roles for cysteine cathepsin genes in multistage tumorigenesis. , 2006, Genes & development.
[40] A. Borowsky,et al. Grade-dependent Proteomics Characterization of Kidney Cancer*S , 2009, Molecular & Cellular Proteomics.
[41] C. Peters,et al. Deficiency for the cysteine protease cathepsin L promotes tumor progression in mouse epidermis , 2010, Oncogene.
[42] J. Joyce,et al. IL-4 induces cathepsin protease activity in tumor-associated macrophages to promote cancer growth and invasion. , 2010, Genes & development.
[43] Nathan L. Avaritt,et al. A quantitative proteomic analysis of FFPE melanoma , 2011, Journal of cutaneous pathology.
[44] W. Grizzle,et al. Validation of a robust proteomic analysis carried out on formalin‐fixed paraffin‐embedded tissues of the pancreas obtained from mouse and human , 2012, Proteomics.
[45] J. Deussing,et al. Thyroid functions of mouse cathepsins B, K, and L. , 2003, The Journal of clinical investigation.
[46] O. Schilling,et al. Impact of routinely employed procedures for tissue processing on the proteomic analysis of formalin‐fixed paraffin‐embedded tissue , 2014, Proteomics. Clinical applications.
[47] M. Mann,et al. Proteomic workflow for analysis of archival formalin‐fixed and paraffin‐embedded clinical samples to a depth of 10 000 proteins , 2013, Proteomics. Clinical applications.
[48] Knut Reinert,et al. OpenMS – An open-source software framework for mass spectrometry , 2008, BMC Bioinformatics.
[49] Liang Li,et al. Stable-isotope dimethylation labeling combined with LC-ESI MS for quantification of amine-containing metabolites in biological samples. , 2007, Analytical chemistry.
[50] O. Schilling,et al. Proteomic identification of protease cleavage sites: cell-biological and biomedical applications , 2013, Expert review of proteomics.
[51] P. Selby,et al. 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 , 2013, Proteomics. Clinical applications.
[52] K. Gevaert,et al. Improved visualization of protein consensus sequences by iceLogo , 2009, Nature Methods.
[53] R. Zahedi,et al. Novel highly sensitive, specific, and straightforward strategy for comprehensive N-terminal proteomics reveals unknown substrates of the mitochondrial peptidase Icp55. , 2013, Journal of proteome research.
[54] W. Hennink,et al. Identification of formaldehyde-induced modifications in proteins: reactions with insulin. , 2006, Bioconjugate chemistry.
[55] T. Nakajima,et al. Novel protein extraction approach using micro-sized chamber for evaluation of proteins eluted from formalin-fixed paraffin-embedded tissue sections , 2012, Proteome Science.
[56] Christoph Peters,et al. Cathepsin L Regulates CD4+ T Cell Selection Independently of Its Effect on Invariant Chain , 2002, The Journal of experimental medicine.
[57] Tong Liu,et al. Quantitative Proteomic Analysis of Formalin Fixed Paraffin Embedded Oral HPV Lesions from HIV Patients. , 2008, The open proteomics journal.
[58] Brian L Hood,et al. Proteomic Analysis of Formalin-fixed Prostate Cancer Tissue*S , 2005, Molecular & Cellular Proteomics.
[59] T. Reinheckel,et al. Deletion of Cysteine Cathepsins B or L Yields Differential Impacts on Murine Skin Proteome and Degradome* , 2012, Molecular & Cellular Proteomics.
[60] O. Schilling,et al. Protein amino-terminal modifications and proteomic approaches for N-terminal profiling. , 2015, Current opinion in chemical biology.
[61] Juergen Kast,et al. Mass spectrometric identification of formaldehyde-induced peptide modifications under in vivo protein cross-linking conditions. , 2008, Analytica chimica acta.
[62] L. Foster,et al. Isotopic labeling of terminal amines in complex samples identifies protein N-termini and protease cleavage products , 2010, Nature Biotechnology.