Jacek R Wisniewski

Summary

Country: Germany

Publications

  1. ncbi request reprint Mass spectrometric mapping of linker histone H1 variants reveals multiple acetylations, methylations, and phosphorylation as well as differences between cell culture and tissue
    Jacek R Wisniewski
    Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, D 82152 Martinsried, Germany
    Mol Cell Proteomics 6:72-87. 2007
  2. ncbi request reprint Design and analysis of quantitative differential proteomics investigations using LC-MS technology
    Yury V Bukhman
    Protana Inc, Toronto, Ontario, Canada
    J Bioinform Comput Biol 6:107-23. 2008
  3. pmc Extensive quantitative remodeling of the proteome between normal colon tissue and adenocarcinoma
    Jacek R Wisniewski
    Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
    Mol Syst Biol 8:611. 2012
  4. doi request reprint Consecutive proteolytic digestion in an enzyme reactor increases depth of proteomic and phosphoproteomic analysis
    Jacek R Wisniewski
    Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
    Anal Chem 84:2631-7. 2012
  5. doi request reprint Universal sample preparation method for proteome analysis
    Jacek R Wisniewski
    Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Martinsried, Germany
    Nat Methods 6:359-62. 2009
  6. doi request reprint Combination of FASP and StageTip-based fractionation allows in-depth analysis of the hippocampal membrane proteome
    Jacek R Wisniewski
    Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, D 82152 Martinsried, Germany
    J Proteome Res 8:5674-8. 2009
  7. doi request reprint Mass spectrometry-based proteomics: principles, perspectives, and challenges
    Jacek R Wisniewski
    Department of Proteomics and Signal Transduction, The Max Planck Institute for Biochemistry, Martinsried, Germany
    Arch Pathol Lab Med 132:1566-9. 2008
  8. doi request reprint Constitutive and dynamic phosphorylation and acetylation sites on NUCKS, a hypermodified nuclear protein, studied by quantitative proteomics
    Jacek R Wisniewski
    Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Martinsried, Germany
    Proteins 73:710-8. 2008
  9. doi request reprint Brain phosphoproteome obtained by a FASP-based method reveals plasma membrane protein topology
    Jacek R Wisniewski
    Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, Martinsried near Munich, Germany
    J Proteome Res 9:3280-9. 2010
  10. pmc Nepsilon-formylation of lysine is a widespread post-translational modification of nuclear proteins occurring at residues involved in regulation of chromatin function
    Jacek R Wisniewski
    Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, D 82152 Martinsried, Germany
    Nucleic Acids Res 36:570-7. 2008

Collaborators

Detail Information

Publications34

  1. ncbi request reprint Mass spectrometric mapping of linker histone H1 variants reveals multiple acetylations, methylations, and phosphorylation as well as differences between cell culture and tissue
    Jacek R Wisniewski
    Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, D 82152 Martinsried, Germany
    Mol Cell Proteomics 6:72-87. 2007
    ..For example, whereas methylation sites are frequent in tissues, this type of modification was much less abundant in cultured cells and escaped detection. Our study significantly extends the known spectrum of linker histone variability...
  2. ncbi request reprint Design and analysis of quantitative differential proteomics investigations using LC-MS technology
    Yury V Bukhman
    Protana Inc, Toronto, Ontario, Canada
    J Bioinform Comput Biol 6:107-23. 2008
    ..Supplementary material is available at http://iec01.mie.utoronto.ca/~thodoros/Bukhman/...
  3. pmc Extensive quantitative remodeling of the proteome between normal colon tissue and adenocarcinoma
    Jacek R Wisniewski
    Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
    Mol Syst Biol 8:611. 2012
    ..Our proteomic data set furthermore allows mapping quantitative changes of functional protein classes, enabling novel insights into the biology of colon cancer...
  4. doi request reprint Consecutive proteolytic digestion in an enzyme reactor increases depth of proteomic and phosphoproteomic analysis
    Jacek R Wisniewski
    Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
    Anal Chem 84:2631-7. 2012
    ..MED-FASP offers efficient exploration of previously unused sample material, increasing depth of proteomic analyses and sequence coverage...
  5. doi request reprint Universal sample preparation method for proteome analysis
    Jacek R Wisniewski
    Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Martinsried, Germany
    Nat Methods 6:359-62. 2009
    ..Peptides eluted after digestion on the filter were pure, allowing single-run analyses of organelles and an unprecedented depth of proteome coverage...
  6. doi request reprint Combination of FASP and StageTip-based fractionation allows in-depth analysis of the hippocampal membrane proteome
    Jacek R Wisniewski
    Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, D 82152 Martinsried, Germany
    J Proteome Res 8:5674-8. 2009
    ..We also provide a generic protocol for combining FASP with StageTip-based ion exchange fractionation, which is generally applicable to proteome analysis...
  7. doi request reprint Mass spectrometry-based proteomics: principles, perspectives, and challenges
    Jacek R Wisniewski
    Department of Proteomics and Signal Transduction, The Max Planck Institute for Biochemistry, Martinsried, Germany
    Arch Pathol Lab Med 132:1566-9. 2008
    ..It enables characterization of entire proteomes with unprecedented sensitivity and precision, providing platforms for identification of biomarkers and drug targets...
  8. doi request reprint Constitutive and dynamic phosphorylation and acetylation sites on NUCKS, a hypermodified nuclear protein, studied by quantitative proteomics
    Jacek R Wisniewski
    Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Martinsried, Germany
    Proteins 73:710-8. 2008
    ..Of the 243 amino acids, at least 36 can be modified with a total of 57 posttranslational modifications. Thus, NUCKS appears to have the highest ratio of modified to unmodified residues of any protein so far described...
  9. doi request reprint Brain phosphoproteome obtained by a FASP-based method reveals plasma membrane protein topology
    Jacek R Wisniewski
    Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, Martinsried near Munich, Germany
    J Proteome Res 9:3280-9. 2010
    ..Together with the glycosylation sites from a recent large-scale study, they can confirm or correct predicted membrane topologies of these proteins, as we show for the examples calcium channels and glutamate receptors...
  10. pmc Nepsilon-formylation of lysine is a widespread post-translational modification of nuclear proteins occurring at residues involved in regulation of chromatin function
    Jacek R Wisniewski
    Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, D 82152 Martinsried, Germany
    Nucleic Acids Res 36:570-7. 2008
    ..N(epsilon)-lysine formylation in chromosomal proteins is relatively abundant, suggesting that it may interfere with epigenetic mechanisms governing chromatin function, which could lead to deregulation of the cell and disease...
  11. doi request reprint Tools for phospho- and glycoproteomics of plasma membranes
    Jacek R Wisniewski
    Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
    Amino Acids 41:223-33. 2011
    ..In the focus are approaches allowing large scale mapping rather than analytical methods suitable for studying individual proteins or non-complex mixtures...
  12. doi request reprint Comparison of ultrafiltration units for proteomic and N-glycoproteomic analysis by the filter-aided sample preparation method
    Jacek R Wisniewski
    Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, D 82152 Martinsried, Germany
    Anal Biochem 410:307-9. 2011
    ..The use of filters with these relatively large cutoffs facilitates depletion of detergents...
  13. doi request reprint High recovery FASP applied to the proteomic analysis of microdissected formalin fixed paraffin embedded cancer tissues retrieves known colon cancer markers
    Jacek R Wisniewski
    Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, D 82152 Martinsried, Germany
    J Proteome Res 10:3040-9. 2011
    ..These results show that FASP is suitable for the low level analysis of microdissected tissue and that it has the potential for exploration of clinical samples for biomarker and drug target discovery...
  14. doi request reprint Proteome, phosphoproteome, and N-glycoproteome are quantitatively preserved in formalin-fixed paraffin-embedded tissue and analyzable by high-resolution mass spectrometry
    Paweł Ostasiewicz
    Department for Proteomics and Signal Transduction at Max Planck Institute for Biochemistry, 82152 Martinsried, Germany
    J Proteome Res 9:3688-700. 2010
    ..Thus, FFPE biobank material can be analyzed by quantitative proteomics at the level of proteins and post-translational modifications...
  15. doi request reprint Mapping of lysine monomethylation of linker histones in human breast and its cancer
    Aiping Lu
    Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Munich, Germany
    J Proteome Res 8:4207-15. 2009
    ..4. In H1.0 five less abundant (<1% of H1.0) sites were identified. Analysis of patient matched pairs of cancer and adjacent normal breast demonstrated high variation in H1 methylation between individuals...
  16. pmc Quantification of the N-glycosylated secretome by super-SILAC during breast cancer progression and in human blood samples
    Paul J Boersema
    Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, D 82152 Martinsried, Germany
    Mol Cell Proteomics 12:158-71. 2013
    ..The combination of quantifying the secretome of cancer cell lines and of human plasma with a super-SILAC approach appears to be a promising new approach for finding markers of disease...
  17. doi request reprint Mapping N-glycosylation sites across seven evolutionarily distant species reveals a divergent substrate proteome despite a common core machinery
    Dorota F Zielinska
    Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
    Mol Cell 46:542-8. 2012
    ..Many N-glycosylated proteins coevolved with the rise of extracellular processes that are specific within corresponding phylogenetic groups and essential for organismal development, body growth, and organ formation...
  18. doi request reprint Deep proteome and transcriptome mapping of a human cancer cell line
    Nagarjuna Nagaraj
    Department for Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
    Mol Syst Biol 7:548. 2011
    ..Comparisons of the proteome and the transcriptome, and analysis of protein complex databases and GO categories, suggest that we achieved deep coverage of the functional transcriptome and the proteome of a single cell type...
  19. doi request reprint Caenorhabditis elegans has a phosphoproteome atypical for metazoans that is enriched in developmental and sex determination proteins
    Dorota F Zielinska
    Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Martinsried, Germany
    J Proteome Res 8:4039-49. 2009
    ..Availability of the C. elegans phosphoproteome should add a novel dimension to functional data obtained by genetic screens in this organism...
  20. doi request reprint Super-SILAC mix for quantitative proteomics of human tumor tissue
    Tamar Geiger
    Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Martinsried, Germany
    Nat Methods 7:383-5. 2010
    ..By decoupling the labeling from the measurement, this super-SILAC method broadens the scope of SILAC-based proteomics...
  21. doi request reprint Detergent-based but gel-free method allows identification of several hundred membrane proteins in single LC-MS runs
    Nagarjuna Nagaraj
    Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Martinsried, Germany
    J Proteome Res 7:5028-32. 2008
    ..Our results demonstrate that membrane proteins can be analyzed as efficiently as soluble proteins...
  22. doi request reprint Precision mapping of an in vivo N-glycoproteome reveals rigid topological and sequence constraints
    Dorota F Zielinska
    Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried D 82152, Germany
    Cell 141:897-907. 2010
    ..The N-glycoproteome contains a plethora of modification sites on factors important in development, organ-specific functions, and disease...
  23. doi request reprint Comparative proteomic profiling of membrane proteins in rat cerebellum, spinal cord, and sciatic nerve
    Aiping Lu
    Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
    J Proteome Res 8:2418-25. 2009
    ..The methods applied here can be directly applied to studying nerve systems and their disorders...
  24. doi request reprint Evidence for insertional RNA editing in humans
    Alexandre Zougman
    Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, D 82152 Martinsried, Germany
    Curr Biol 18:1760-5. 2008
    ..To our knowledge, this is the first report of RNA-insertion editing in humans and may be an example of the type of discoveries possible with modern proteomics methods...
  25. doi request reprint Use of stable isotope labeling by amino acids in cell culture as a spike-in standard in quantitative proteomics
    Tamar Geiger
    Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
    Nat Protoc 6:147-57. 2011
    ..It includes the selection and preparation of the spike-in SILAC standard, the sample preparation procedure, and analysis and evaluation of the results...
  26. ncbi request reprint Analysis of the mouse liver proteome using advanced mass spectrometry
    Rong Shi
    Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
    J Proteome Res 6:2963-72. 2007
    ..3%, transmembrane domains were predicted. For potential application in toxicology or clinical studies, we demonstrate that it is possible to consistently identify more than 1000 proteins in a single run...
  27. pmc Identification and characterization of a novel ubiquitous nucleolar protein 'NARR' encoded by a gene overlapping the rab34 oncogene
    Alexandre Zougman
    Max Planck Institute for Biochemistry, Department of Proteomics and Signal Trasduction, Am Klopferspitz 18, Martinsried D 82152, Germany
    Nucleic Acids Res 39:7103-13. 2011
    ..NARR only partially colocalizes with fibrillarin, the pre-ribosomal RNA-processing protein, positioning NARR in a separate niche within the rDNA cluster...
  28. pmc MAPU: Max-Planck Unified database of organellar, cellular, tissue and body fluid proteomes
    Yanling Zhang
    Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
    Nucleic Acids Res 35:D771-9. 2007
    ..More than 4500 mouse and 2500 human proteins have already been identified in at least one proteome. Basic annotation information and links to other public databases are provided in MAPU and we plan to add further analysis tools...
  29. doi request reprint Protocol to enrich and analyze plasma membrane proteins from frozen tissues
    Jacek R Wisniewski
    Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
    Methods Mol Biol 432:175-83. 2008
    ..The entire procedure allows processing and preparation of samples of minute amounts as 10-20 mg tissue and therefore can be extremely helpful for proteomic profiling of small pieces of tissue and clinical material...
  30. doi request reprint Proteomic workflow for analysis of archival formalin-fixed and paraffin-embedded clinical samples to a depth of 10 000 proteins
    Jacek R Wisniewski
    Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
    Proteomics Clin Appl 7:225-33. 2013
    ..Here, we describe an analytical workflow for analysis of laser-capture microdissected formalin-fixed and paraffin-embedded samples that allows studying proteomes to a depth of 10 000 proteins per sample...
  31. ncbi request reprint Proteomic mapping of brain plasma membrane proteins
    Peter Aa Nielsen
    MDS Inc Denmark, 5230 Odense M, Denmark
    Mol Cell Proteomics 4:402-8. 2005
    ..Our work now allows in-depth study of brain membrane proteomes, such as of mouse models of neurological disease...
  32. ncbi request reprint Experimental Peptide Identification Repository (EPIR): an integrated peptide-centric platform for validation and mining of tandem mass spectrometry data
    Dan Bach Kristensen
    MDS Inc, Denmark, Staermosegaardsvej 6, DK 5230 Odense M, Denmark
    Mol Cell Proteomics 3:1023-38. 2004
    ....
  33. ncbi request reprint Integrated analysis of protein composition, tissue diversity, and gene regulation in mouse mitochondria
    Vamsi K Mootha
    MDS Proteomics, Odense 5230, Denmark
    Cell 115:629-40. 2003
    ....
  34. ncbi request reprint HysTag--a novel proteomic quantification tool applied to differential display analysis of membrane proteins from distinct areas of mouse brain
    Jesper V Olsen
    MDS Proteomics A S, Staermosegårdsvej 6, DK 5230 Odense M, Denmark
    Mol Cell Proteomics 3:82-92. 2004
    ....