Daniel Figeys

Summary

Affiliation: University of Ottawa
Country: Canada

Publications

  1. doi request reprint A charge-suppressing strategy for probing protein methylation
    Zhibin Ning
    Ottawa Institute of Systems Biology, Department of Biochemistry, Immunology and Microbiology, Faculty of Medicine, University of Ottawa, Ontario, Canada
    Chem Commun (Camb) 52:5474-7. 2016
  2. pmc Platelet-activating factors are associated with cognitive deficits in depressed coronary artery disease patients: a hypothesis-generating study
    Graham Mazereeuw
    Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, 2075 Bayview Avenue, Room FG08, Toronto, ON M4N 3M5, Canada
    J Neuroinflammation 11:119. 2014
  3. pmc Large-scale mapping of human protein-protein interactions by mass spectrometry
    Rob M Ewing
    Protana, Toronto, Ontario, Canada
    Mol Syst Biol 3:89. 2007
  4. doi request reprint Mapping the human protein interactome
    Daniel Figeys
    The Ottawa Institute of Systems Biology, The Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
    Cell Res 18:716-24. 2008
  5. pmc Improved recovery and identification of membrane proteins from rat hepatic cells using a centrifugal proteomic reactor
    Hu Zhou
    Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, Canada
    Mol Cell Proteomics 10:O111.008425. 2011
  6. doi request reprint Analysis of the subcellular phosphoproteome using a novel phosphoproteomic reactor
    Houjiang Zhou
    Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ontario, Canada
    J Proteome Res 9:1279-88. 2010
  7. ncbi request reprint Systematic determination of ion score cutoffs based on calculated false positive rates: application for identifying ubiquitinated proteins by tandem mass spectrometry
    Julian Vasilescu
    Ottawa Institute of Systems Biology, University of Ottawa, 451 Smyth Road, Ottawa, ON, K1H 8M5, Canada
    J Mass Spectrom 43:296-304. 2008
  8. pmc Defining the budding yeast chromatin-associated interactome
    Jean Philippe Lambert
    Department of Biochemistry, Microbiology and Immunology, Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada
    Mol Syst Biol 6:448. 2010
  9. pmc Regulation of septin dynamics by the Saccharomyces cerevisiae lysine acetyltransferase NuA4
    Leslie Mitchell
    Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Ontario, Canada
    PLoS ONE 6:e25336. 2011
  10. doi request reprint Proteomic analyses of the SMYD family interactomes identify HSP90 as a novel target for SMYD2
    Mohamed Abu-Farha
    Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, ON
    J Mol Cell Biol 3:301-8. 2011

Collaborators

Detail Information

Publications84

  1. doi request reprint A charge-suppressing strategy for probing protein methylation
    Zhibin Ning
    Ottawa Institute of Systems Biology, Department of Biochemistry, Immunology and Microbiology, Faculty of Medicine, University of Ottawa, Ontario, Canada
    Chem Commun (Camb) 52:5474-7. 2016
    ..Peptides containing methylated RK residues remain positively charged and are then enriched by strong cation exchange chromatography, followed by high-resolution mass spectrometry identification. ..
  2. pmc Platelet-activating factors are associated with cognitive deficits in depressed coronary artery disease patients: a hypothesis-generating study
    Graham Mazereeuw
    Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, 2075 Bayview Avenue, Room FG08, Toronto, ON M4N 3M5, Canada
    J Neuroinflammation 11:119. 2014
    ..Platelet-activating factors (PAFs) are emerging as key lipid mediators that may be central to those processes and highly relevant to cognitive decline in CAD...
  3. pmc Large-scale mapping of human protein-protein interactions by mass spectrometry
    Rob M Ewing
    Protana, Toronto, Ontario, Canada
    Mol Syst Biol 3:89. 2007
    ..In addition, via our preliminary analysis, we report many novel protein interactions and pathway associations...
  4. doi request reprint Mapping the human protein interactome
    Daniel Figeys
    The Ottawa Institute of Systems Biology, The Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
    Cell Res 18:716-24. 2008
    ..Here, we review the developments in protein interaction mapping and we discuss issues and strategies for the mapping of the human protein interactome...
  5. pmc Improved recovery and identification of membrane proteins from rat hepatic cells using a centrifugal proteomic reactor
    Hu Zhou
    Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, Canada
    Mol Cell Proteomics 10:O111.008425. 2011
    ..Thus, the centrifugal proteomic reactor offers a new analytical tool for structure and function studies of membrane proteins involved in lipid and lipoprotein metabolism...
  6. doi request reprint Analysis of the subcellular phosphoproteome using a novel phosphoproteomic reactor
    Houjiang Zhou
    Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ontario, Canada
    J Proteome Res 9:1279-88. 2010
    ..Overall, this approach provides a new avenue for studying the phosphoproteome of the subcellular organelles...
  7. ncbi request reprint Systematic determination of ion score cutoffs based on calculated false positive rates: application for identifying ubiquitinated proteins by tandem mass spectrometry
    Julian Vasilescu
    Ottawa Institute of Systems Biology, University of Ottawa, 451 Smyth Road, Ottawa, ON, K1H 8M5, Canada
    J Mass Spectrom 43:296-304. 2008
    ..Finally, we found that FPR for ubiquitinated proteins are affected by the size of the protein database that is searched. These observations may be applicable for the study of other post-translational modifications...
  8. pmc Defining the budding yeast chromatin-associated interactome
    Jean Philippe Lambert
    Department of Biochemistry, Microbiology and Immunology, Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada
    Mol Syst Biol 6:448. 2010
    ....
  9. pmc Regulation of septin dynamics by the Saccharomyces cerevisiae lysine acetyltransferase NuA4
    Leslie Mitchell
    Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Ontario, Canada
    PLoS ONE 6:e25336. 2011
    ..These findings provide the first evidence that yeast septin proteins are acetylated and that NuA4 impacts septin dynamics...
  10. doi request reprint Proteomic analyses of the SMYD family interactomes identify HSP90 as a novel target for SMYD2
    Mohamed Abu-Farha
    Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, ON
    J Mol Cell Biol 3:301-8. 2011
    ..Altogether, this study highlights the ability of SMYD proteins to form unique protein complexes that may underlie their various biological functions and the SMYD2-mediated methylation of the key molecular chaperone HSP90...
  11. doi request reprint Quantitative proteomic analysis of PCSK9 gain of function in human hepatic HuH7 cells
    Nicholas Denis
    Ottawa Institute of Systems Biology, University of Ottawa, Ontario, Canada
    J Proteome Res 10:2011-26. 2011
    ..Moreover, we documented the novel down-regulation of the EH domain binding protein-1 (EHBP1) in a transgenic PCSK9 mouse model and its up-regulation in a PCSK9 knockout mouse model...
  12. ncbi request reprint The proteomic reactor facilitates the analysis of affinity-purified proteins by mass spectrometry: application for identifying ubiquitinated proteins in human cells
    Julian Vasilescu
    Ottawa Institute of Systems Biology, 451 Smyth Road, Ottawa, Ontario, K1H 8M5, Canada
    J Proteome Res 6:298-305. 2007
    ..The Proteomic Reactor is a novel technology that facilitates the analysis of affinity-purified proteins and has the potential to aid future biological studies...
  13. doi request reprint The precursor to the germ cell-specific PCSK4 proteinase is inefficiently activated in transfected somatic cells: evidence of interaction with the BiP chaperone
    Charles Gyamera-Acheampong
    Chronic Disease Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
    Mol Cell Biochem 348:43-52. 2011
    ..These cells may lack the intracellular environment and the interacting molecules specific to testicular germ cells where this enzyme is normally expressed...
  14. doi request reprint Microsome-associated lumenal lipid droplets in the regulation of lipoprotein secretion
    Zemin Yao
    Department of Biochemistry, Microbiology and Immunology, Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada
    Curr Opin Lipidol 24:160-70. 2013
    ..Recent experimental evidence has suggested that the lumenal triglyceride associated with endoplasmic reticulum (ER)/Golgi may represent an entity serving as precursors for large VLDL1...
  15. pmc Amyloid-beta42 signals tau hyperphosphorylation and compromises neuronal viability by disrupting alkylacylglycerophosphocholine metabolism
    Scott D Ryan
    Neural Regeneration Laboratory and Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Ontario, Canada, K1H 8M5
    Proc Natl Acad Sci U S A 106:20936-41. 2009
    ..Together, these data provide mechanistic insight into how disruptions in lipid metabolism can determine neuronal response to accumulating oligomeric amyloid-beta(42)...
  16. pmc Srf1 is a novel regulator of phospholipase D activity and is essential to buffer the toxic effects of C16:0 platelet activating factor
    Michael A Kennedy
    Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Canada
    PLoS Genet 7:e1001299. 2011
    ..Together, these findings implicate PLD as a potential neuroprotective target capable of ameliorating disruptions in lipid metabolism in response to accumulating oligomeric amyloid-β₄₂...
  17. ncbi request reprint Tryptic digestion of ubiquitin standards reveals an improved strategy for identifying ubiquitinated proteins by mass spectrometry
    Nicholas J Denis
    Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON, Canada
    Proteomics 7:868-74. 2007
    ..4-fold increase in the number of ubiquitination sites that could be identified over standard methods. Our improved MS-based strategy will aid future studies which aim to identify and/or characterize ubiquitinated proteins in human cells...
  18. ncbi request reprint Proteomic analysis of ubiquitinated proteins from human MCF-7 breast cancer cells by immunoaffinity purification and mass spectrometry
    Julian Vasilescu
    Ottawa Institute of Systems Biology, Ontario, Canada
    J Proteome Res 4:2192-200. 2005
    ..This method will aid the study of protein ubiquitination and may be used as a tool for the discovery of novel biomarkers that are associated with disease progression...
  19. doi request reprint Lipidomics era: accomplishments and challenges
    Maroun Bou Khalil
    Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON, Canada K1H 8M5
    Mass Spectrom Rev 29:877-929. 2010
    ..The latest technological developments in mass spectrometry, the role of bioinformatics, and the applications of lipidomics in lipid metabolism and cellular physiology and pathology are also discussed...
  20. ncbi request reprint Multiplexed proteomic reactor for the processing of proteomic samples
    Weimin Hou
    The Ottawa Institute of Systems Biology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, K1H 8M5 Canada
    Anal Chem 79:39-44. 2007
    ..More relaxed searching conditions associated with a 1% false positive rate led to the identification of 2683 unique proteins, meaning that one protein was identified per 3-10 ng of total protein lysate loaded on the reactor plate...
  21. doi request reprint Proteomic analysis of ascending colon biopsies from a paediatric inflammatory bowel disease inception cohort identifies protein biomarkers that differentiate Crohn's disease from UC
    Amanda E Starr
    Department of Biochemistry, Microbiology and Immunology, Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada
    Gut . 2016
    ..Accurate differentiation between Crohn's disease (CD) and UC is important to ensure early and appropriate therapeutic intervention. We sought to identify proteins that enable differentiation between CD and UC in children with new onset IBD...
  22. pmc A novel proteomics approach for the discovery of chromatin-associated protein networks
    Jean Philippe Lambert
    Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
    Mol Cell Proteomics 8:870-82. 2009
    ....
  23. pmc Functional dissection of the NuA4 histone acetyltransferase reveals its role as a genetic hub and that Eaf1 is essential for complex integrity
    Leslie Mitchell
    Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Roger Guidon Hall, 451 Smyth Rd, Ottawa, ONT K1H 8M5, Canada
    Mol Cell Biol 28:2244-56. 2008
    ..Our integrative study demonstrates that genetic interaction maps are valuable in dissecting complex structure and provides insight into why the human NuA4 complex, Tip60, has been associated with a diverse range of pathologies...
  24. pmc The liver connexin32 interactome is a novel plasma membrane-mitochondrial signaling nexus
    Stephanie L Fowler
    Neural Regeneration Laboratory, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
    J Proteome Res 12:2597-610. 2013
    ..Complex formation increases the pool of sideroflexin-1 that is present at the plasma membrane. Together, these data identify a novel plasma membrane/mitochondrial signaling nexus in the connexin32 interactome...
  25. doi request reprint Lyso-form fragment ions facilitate the determination of stereospecificity of diacyl glycerophospholipids
    Weimin Hou
    Ottawa Institute of Systems Biology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, Canada
    Rapid Commun Mass Spectrom 25:205-17. 2011
    ....
  26. pmc Rare cell proteomic reactor applied to stable isotope labeling by amino acids in cell culture (SILAC)-based quantitative proteomics study of human embryonic stem cell differentiation
    Ruijun Tian
    Ottawa Institute of Systems Biology, Ottawa, Ontario, Canada
    Mol Cell Proteomics 10:M110.000679. 2011
    ..This work provides a new platform for the study of rare cells and in particular for further elucidating proteins that govern the mesoderm lineage specification of human pluripotent stem cells...
  27. doi request reprint Analysis of low-abundance proteins using the proteomic reactor with pH fractionation
    Hu Zhou
    Ottawa Institute of Systems Biology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, Canada
    Talanta 80:1526-31. 2010
    ....
  28. doi request reprint Identification of lysophosphatidylcholine (LPC) and platelet activating factor (PAF) from PC12 cells and mouse cortex using liquid chromatography/multi-stage mass spectrometry (LC/MS3)
    Jeffrey C Smith
    Ottawa Institute of Systems Biology and Neural Regeneration Laboratory, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada, K1H 8M5
    Rapid Commun Mass Spectrom 22:3579-87. 2008
    ..We demonstrate the application of this technique to unambiguously identify these species within complex cellular lysates and tissue extracts...
  29. doi request reprint Proteomic reactors and their applications in biology
    Hu Zhou
    Ottawa Institute of Systems Biology OISB, University of Ottawa, Ottawa, ON, Canada
    FEBS J 278:3796-806. 2011
    ..This review summarizes the technical developments and biological applications of the proteomic reactor over the last decade...
  30. doi request reprint In Vitro Metabolic Labeling of Intestinal Microbiota for Quantitative Metaproteomics
    Xu Zhang
    Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada, K1H 8M5
    Anal Chem 88:6120-5. 2016
    ..Our methodology improves the accuracy of quantitative intestinal metaproteomics, which would promote the application of proteomics for functional studies of intestinal microbiota. ..
  31. ncbi request reprint A differential phosphoproteomic analysis of retinoic acid-treated P19 cells
    Jeffrey C Smith
    Ottawa Institute of Systems Biology and Biochemistry, Microbiology and Immunology Department, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
    J Proteome Res 6:3174-86. 2007
    ..This study represents the first global gel-free analysis that elucidates protein phosphorylation dynamics during cellular differentiation...
  32. ncbi request reprint The proteomic reactor: a microfluidic device for processing minute amounts of protein prior to mass spectrometry analysis
    Martin Ethier
    Ottawa Institute of Systems Biology, Ottawa, Canada
    J Proteome Res 5:2754-9. 2006
    ..Furthermore, as little as 300 cells can be directly introduced on the proteomic reactor and analyzed by mass spectrometry...
  33. pmc Restriction of histone gene transcription to S phase by phosphorylation of a chromatin boundary protein
    Christoph F Kurat
    The Donnelly Center, University of Toronto, Toronto, Ontario M5S 3E1, Canada
    Genes Dev 25:2489-501. 2011
    ..Our study identified the chromatin boundary protein Yta7 as a key regulator that links S-phase kinases with RNAPII function at cell cycle-regulated histone gene promoters...
  34. pmc Functional analysis of the missense APOC3 mutation Ala23Thr associated with human hypotriglyceridemia
    Meenakshi Sundaram
    Department of Biochemistry, Ottawa Institute of Systems Biology, University of Ottawa, Canada
    J Lipid Res 51:1524-34. 2010
    ..Thus, the current study reveals an important structural element residing within the N-terminal region of apoC-III that governs the second step VLDL(1) maturation...
  35. ncbi request reprint Strategy to design improved proteomic experiments based on statistical analyses of the chemical properties of identified peptides
    Martin Ethier
    Ottawa Institute of Systems Biology, Ottawa, Canada
    J Proteome Res 4:2201-6. 2005
    ..The algorithm can thus be used as an exploratory tool to suggest a minimal number of complementary experiments in order to maximize experimental efficiency...
  36. pmc MetaPro-IQ: a universal metaproteomic approach to studying human and mouse gut microbiota
    Xu Zhang
    Department of Biochemistry, Ottawa Institute of Systems Biology, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
    Microbiome 4:31. 2016
    ..However, the application of gut metaproteomics has largely been limited due to the low efficiency of protein identification. Thus, a high-performance and easy-to-implement gut metaproteomic approach is required...
  37. pmc Differential regulation of wild-type and mutant alpha-synuclein binding to synaptic membranes by cytosolic factors
    Sabine Wislet-Gendebien
    Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, Ontario, M5S 3H2 Canada
    BMC Neurosci 9:92. 2008
    ..However, the regulation of alpha-syn's cellular localization in neurons and the effects of the PD-linked mutations are poorly understood...
  38. doi request reprint Technological developments in lipidomics
    Weimin Hou
    Chemistry Department, University of Ottawa, Ottawa, Ontario, Canada K1H 8M5
    Brief Funct Genomic Proteomic 7:395-409. 2008
    ..In this review, we will discuss the technical developments in the field of lipidomics and the current limitations of this nascent field...
  39. ncbi request reprint Definition and characterization of a "trypsinosome" from specific peptide characteristics by nano-HPLC-MS/MS and in silico analysis of complex protein mixtures
    Thierry Le Bihan
    Protana Inc, 251 Attwell Drive, Toronto, Ontario, Canada M9W 7H4
    J Proteome Res 3:1138-48. 2004
    ..This approach is based on experimentally derived data to calibrate the method and therefore may theoretically be applied to any HPLC-MS/MS system on which data are being generated...
  40. ncbi request reprint Proteomics in 2005/2006: developments, applications and challenges
    Jeffrey C Smith
    Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ontario, Canada K1H 8M5
    Anal Chem 79:4325-43. 2007
  41. doi request reprint An enhanced chemically defined SILAC culture system for quantitative proteomics study of human embryonic stem cells
    Shuai Wang
    Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
    Proteomics 11:4040-6. 2011
    ..As such, it provides a new platform that can be readily adapted by general laboratory for further comprehensive SILAC-based proteomics analysis of hESCs and induced pluripotent stem cells...
  42. doi request reprint Of proteins and DNA--proteomic role in the field of chromatin research
    Jean Philippe Lambert
    Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada
    Mol Biosyst 6:30-7. 2010
    ..This review will focus on the past contributions as well as on emerging mass spectrometry-based methodologies attempting to better define the complex relationship between proteins, protein complexes and DNA...
  43. doi request reprint New ammunition for the proteomic reactor: strong anion exchange beads and multiple enzymes enhance protein identification and sequence coverage
    Hu Zhou
    Ottawa Institute of Systems Biology, University of Ottawa, Health Sciences Campus, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
    Anal Bioanal Chem 397:3421-30. 2010
    ..Furthermore, we show that the number of protein identified can be increased further by up to 40% using different proteolytic enzymes on the proteomic reactor...
  44. ncbi request reprint The tale of two domains: proteomics and genomics analysis of SMYD2, a new histone methyltransferase
    Mohamed Abu-Farha
    Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario K1H 8M5, Canada
    Mol Cell Proteomics 7:560-72. 2008
    ..Furthermore the combination of the SMYD2 interactome with the gene expression data suggests that some of the genes regulated by SMYD2 are closely associated with SMYD2-interacting proteins...
  45. doi request reprint GRK2 Fine-Tunes Circadian Clock Speed and Entrainment via Transcriptional and Post-translational Control of PERIOD Proteins
    Neel Mehta
    Department of Biology, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, ON L5L 1C6, Canada Department of Cell and Systems Biology, University of Toronto, 25 Harbord Street, Toronto, ON M5S 3G5, Canada
    Cell Rep 12:1272-88. 2015
    ..Together, our findings identify GRK2 as an important modulator of circadian clock speed, amplitude, and entrainment by controlling PERIOD at the transcriptional and post-translational levels. ..
  46. doi request reprint Discovery of substrates for a SET domain lysine methyltransferase predicted by multistate computational protein design
    Sylvain Lanouette
    Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
    Structure 23:206-15. 2015
    ..Our methodology paves the way to systematically predict and validate posttranslational modification sites while simultaneously pairing them with their associated enzymes. ..
  47. doi request reprint Glycoproteomic reactor for human plasma
    Hu Zhou
    Department of Biochemistry, University of Ottawa, Ottawa, Ontario, Canada K1H 8M5
    J Proteome Res 8:556-66. 2009
    ....
  48. ncbi request reprint Proteomics: from gel based to gel free
    Jean Philippe Lambert
    Ottawa Institute of Systems Biology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, Canada K1H 8M5
    Anal Chem 77:3771-87. 2005
  49. ncbi request reprint Identification and quantitation of changes in the platelet activating factor family of glycerophospholipids over the course of neuronal differentiation by high-performance liquid chromatography electrospray ionization tandem mass spectrometry
    Shawn N Whitehead
    Neural Regeneration Laboratory and Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada K1H 8M5
    Anal Chem 79:8539-48. 2007
    ..Furthermore, application to the PC12 model identified a quantifiable difference between PAF molecular species produced over the course of neuronal differentiation...
  50. doi request reprint Mass spectrometric analysis reveals remnants of host-pathogen molecular interactions at the starch granule surface in wheat endosperm
    Michael L Wall
    Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Canada
    Phytopathology 100:848-54. 2010
    ..During development and maturation, wheat seed appeared to have resisted infection and lysed the pathogens where, upon desiccation, the molecular evidence remained fixed at the starch granule surface...
  51. pmc Activation of the Cdc42p GTPase by cyclin-dependent protein kinases in budding yeast
    Richelle Sopko
    Department of Medical Genetics and Microbiology, University of Toronto, Toronto, Ontario, Canada
    EMBO J 26:4487-500. 2007
    ..Inhibition of GAPs by CDK phosphorylation may be a general mechanism to promote proper G1-phase progression...
  52. ncbi request reprint Novel approaches to map protein interactions
    Daniel Figeys
    MDS Proteomics, 251 Atwell Drive, Ontario, Toronto, Canada
    Curr Opin Biotechnol 14:119-25. 2003
    ..The challenge of mapping protein interactions is vast and many novel approaches have recently been developed for this task using molecular biology, mass spectrometry and chemiproteomic techniques...
  53. ncbi request reprint Proteomics technology in systems biology
    Jeffrey C Smith
    Ottawa Institute of Systems Biology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
    Mol Biosyst 2:364-70. 2006
    ..This short review summarizes a selection of technological innovations in proteomics that contribute to systems biology studies...
  54. doi request reprint PCSK4-null sperm display enhanced protein tyrosine phosphorylation and ADAM2 proteolytic processing during in vitro capacitation
    Charles Gyamera-Acheampong
    Chronic Disease Program, Ottawa Health Research Institute, Ottawa, Ontario, Canada
    Fertil Steril 93:1112-23. 2010
    ..To study the molecular basis for the accelerated capacitation rate in PCSK4-null sperm...
  55. doi request reprint Targeted lipidomics - advances in profiling lysophosphocholine and platelet-activating factor second messengers
    Hongbin Xu
    Ottawa Institute of Systems Biology, University of Ottawa, Ontario, Canada Neural Regeneration Laboratory, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ontario, Canada
    FEBS J 280:5652-67. 2013
    ....
  56. pmc Visualization and Phospholipid Identification (VaLID): online integrated search engine capable of identifying and visualizing glycerophospholipids with given mass
    Alexandre P Blanchard
    Ottawa Institute of Systems Biology, CIHR Training Program in Neurodegenerative Lipidomics, Biochemistry, Microbiology, and Immunology, University of Ottawa, Ontario K1H 8M5, Canada
    Bioinformatics 29:284-5. 2013
    ..Curated lipids detected by the Canadian Institutes of Health Research Training Program in Neurodegenerative Lipidomics are provided as high-resolution structures...
  57. doi request reprint Recent developments in mass spectrometry-based quantitative phosphoproteomics
    Jeffrey C Smith
    Ottawa Institute of Systems Biology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
    Biochem Cell Biol 86:137-48. 2008
    ..The majority of the focus is placed on detailing strategies that are currently used to conduct MS-based quantitative phosphoproteomics...
  58. pmc MFG-E8 Is Critical for Embryonic Stem Cell-Mediated T Cell Immunomodulation
    Yuan Tan
    Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
    Stem Cell Reports 5:741-52. 2015
    ..Our findings offer an approach to facilitate transplantation acceptance. ..
  59. pmc A Regulatory Network Involving β-Catenin, e-Cadherin, PI3k/Akt, and Slug Balances Self-Renewal and Differentiation of Human Pluripotent Stem Cells In Response to Wnt Signaling
    Tyng Shyan Huang
    Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
    Stem Cells 33:1419-33. 2015
    ..The formation of such a framework reinforces hESCs to switch from a state of temporal self-renewal associated with short-term Wnt/β-catenin activation to definitive differentiation. Stem Cells 2015;33:1419-1433. ..
  60. pmc The proteomic landscape of the suprachiasmatic nucleus clock reveals large-scale coordination of key biological processes
    Cheng Kang Chiang
    Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
    PLoS Genet 10:e1004695. 2014
    ..These insights into the proteomic landscape of the SCN will facilitate a more integrative understanding of cellular control within the SCN clock. ..
  61. doi request reprint Detecting protein-protein interactions/complex components using mass spectrometry coupled techniques
    Zhibin Ning
    Department of Biochemistry, Microbiology and Immunology, Ottawa Institute of Systems Biology, University of Ottawa, Roger Guindon Hall, 451 Smyth Road, Ottawa, ON, Canada, K1H 8M5
    Methods Mol Biol 1164:1-13. 2014
    ..This protocol provides an overview of the technique as well as practical tips. ..
  62. pmc Skeletal myosin light chain kinase regulates skeletal myogenesis by phosphorylation of MEF2C
    Ashraf Said Al Madhoun
    Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Ontario, Canada
    EMBO J 30:2477-89. 2011
    ..This work identifies the first kinase that regulates MyoD and Myf5 expression in ES or satellite cells...
  63. ncbi request reprint Mapping protein-protein interactions by mass spectrometry
    Julian Vasilescu
    The Ottawa Institute of Systems Biology, Ottawa, ON, Canada
    Curr Opin Biotechnol 17:394-9. 2006
    ..In the future, information gained from human protein interaction studies could lead to the discovery of novel pathway associations and therapeutic targets...
  64. pmc Predicting glycerophosphoinositol identities in lipidomic datasets using VaLID (Visualization and Phospholipid Identification)--an online bioinformatic search engine
    Graeme S V McDowell
    Neural Regeneration Laboratory, Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, ON, Canada K1H 8M5 Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, ON, Canada K1H 8M5 CIHR Training Program in Neurodegenerative Lipidomics, Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, ON, Canada K1H 8M5
    Biomed Res Int 2014:818670. 2014
    ..VaLID is freely available and responds to all users through the CTPNL resources web site. ..
  65. doi request reprint From cells to peptides: "one-stop" integrated proteomic processing using amphipols
    Zhibin Ning
    Ottawa Institute of Systems Biology, Department of Biochemistry, Immunology and Microbiology, University of Ottawa, Ontario, Canada
    J Proteome Res 12:1512-9. 2013
    ..This protocol is much faster, can be performed in a single tube, and can readily replace the conventional detergent/chaotrope approaches for total and membrane proteome analysis...
  66. doi request reprint Identification of protein-protein interactions by mass spectrometry coupled techniques
    Mohamed Abu-Farha
    Ottawa Institute of Systems Biology OISB, University of Ottawa, 451 Smyth Road Ottawa, K1H 8M5, Ontario, Canada
    Adv Biochem Eng Biotechnol 110:67-80. 2008
    ..These different affinity purification methods are used to purify proteins that are further identified by either ESI-MS or MALDI-MS...
  67. doi request reprint Lipin - The bridge between hepatic glycerolipid biosynthesis and lipoprotein metabolism
    Maroun Bou Khalil
    Ottawa Institute of System Biology, Ontario, Canada
    Biochim Biophys Acta 1801:1249-59. 2010
    ....
  68. pmc APols-aided protein precipitation: a rapid method for concentrating proteins for proteomic analysis
    Zhibin Ning
    Department of Biochemistry, Immunology and Microbiology, Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON, Canada
    J Membr Biol 247:941-7. 2014
    ..Also, we have been able to demonstrate that APols-aided protein precipitation works well on diluted samples, such as secretome sample, and provides a rapid method for protein concentration. ..
  69. pmc β-Estradiol results in a proprotein convertase subtilisin/kexin type 9-dependent increase in low-density lipoprotein receptor levels in human hepatic HuH7 cells
    Amanda E Starr
    Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ontario, Canada
    FEBS J 282:2682-96. 2015
    ....
  70. pmc Time-of-day- and light-dependent expression of ubiquitin protein ligase E3 component N-recognin 4 (UBR4) in the suprachiasmatic nucleus circadian clock
    Harrod H Ling
    Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada
    PLoS ONE 9:e103103. 2014
    ..This study is the first to identify a novel E3 ubiquitin ligase component, UBR4, in the murine SCN and to implicate the N-end rule degradation pathway as a potential player in regulating core clock mechanisms and photic entrainment. ..
  71. ncbi request reprint Combining different 'omics' technologies to map and validate protein-protein interactions in humans
    Daniel Figeys
    MDS Proteomics, 251 Attwell Drive, Toronto, Ontario M9W 7H4, Canada
    Brief Funct Genomic Proteomic 2:357-65. 2004
    ..In this paper, an approach for combining different 'omics' technologies to achieve efficient mapping and validation of protein interactions in human cell lines is presented...
  72. pmc Phospholipase C activity affinity purifies with the Torpedo nicotinic acetylcholine receptor
    Jonathan M Labriola
    Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Ontario K1H 8M5, Canada
    J Biol Chem 285:10337-43. 2010
    ..The acetylcholine receptor may directly or indirectly influence lipid metabolism in a manner that enhances its own function...
  73. ncbi request reprint Adapting arrays and lab-on-a-chip technology for proteomics
    Daniel Figeys
    MDS Proteomics, Toronto, Ontario, Canada
    Proteomics 2:373-82. 2002
    ..Here, we review the changes in the field of proteomics and their impact on the development in protein arrays and lab-on-a-chip...
  74. pmc Nonsynonymous mutations within APOB in human familial hypobetalipoproteinemia: evidence for feedback inhibition of lipogenesis and postendoplasmic reticulum degradation of apolipoprotein B
    Shumei Zhong
    Department of Biochemistry, Microbiology and Immunology, Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario K1H 8M5, Canada
    J Biol Chem 285:6453-64. 2010
    ..These results suggest that feedback inhibition of hepatic lipogenesis in conjunction with post-ER degradation of misfolded apoB proteins can contribute to reduce fat accumulation in the FHBL liver...
  75. pmc Myosin phosphatase modulates the cardiac cell fate by regulating the subcellular localization of Nkx2.5 in a Wnt/Rho-associated protein kinase-dependent pathway
    Tammy Ryan
    Department of Biochemistry, Microbiology, and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
    Circ Res 112:257-66. 2013
    ..5 has been implicated in the regulation of many cellular processes that ultimately contribute to cardiomyogenesis and morphogenesis of the mature heart, relatively little is known about how it is regulated at a functional level...
  76. pmc A novel whole-cell lysate kinase assay identifies substrates of the p38 MAPK in differentiating myoblasts
    James Dr Knight
    Regenerative Medicine Program, Ottawa Hospital Research Institute, 501 Smyth Road, Ottawa, ON, K1H 8L6, Canada
    Skelet Muscle 2:5. 2012
    ..However, whether p38α is involved in processes other than gene regulation during myogenesis is currently unknown, and why other p38 isoforms cannot compensate for its loss is unclear...
  77. pmc Uncovering the proteome response of the master circadian clock to light using an AutoProteome system
    Ruijun Tian
    Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada K1H 8M5
    Mol Cell Proteomics 10:M110.007252. 2011
    ..The AutoProteome system opens a new avenue to systematically explore the proteome-wide events that occur in the SCN, either in response to light or other stimuli, or as a consequence of its intrinsic pacemaker capacity...
  78. ncbi request reprint Functional proteomics: mapping protein-protein interactions and pathways
    Daniel Figeys
    MDS Proteomics, Toronto, Ontario, Canada
    Curr Opin Mol Ther 4:210-5. 2002
    ..In this article we review recent developments in functional proteomics...
  79. doi request reprint Human Proteinpedia enables sharing of human protein data
    Suresh Mathivanan
    Nat Biotechnol 26:164-7. 2008
  80. ncbi request reprint Biomarker assay translation from discovery to clinical studies in cancer drug development: quantification of emerging protein biomarkers
    Jean W Lee
    Amgen Inc, Thousand Oaks, California 91320, USA
    Adv Cancer Res 96:269-98. 2007
    ..Specific references to protein biomarkers for cancer drug development are also discussed...
  81. ncbi request reprint On-line strong cation exchange micro-HPLC-ESI-MS/MS for protein identification and process optimization
    Thierry Le Bihan
    MDS Proteomics, Toronto, Ontario, Canada
    J Am Soc Mass Spectrom 14:719-27. 2003
    ..Both methods used in tandem complement each other and can lead to a greater number of peptide identifications from a given sample...
  82. ncbi request reprint N-glycosylation analysis using the StrOligo algorithm
    Martin Ethier
    Department of Chemistry, University of Manitoba, Winnipeg, Canada
    Methods Mol Biol 328:187-97. 2006
    ..As well, the MS/MS spectrum is displayed with relevant peaks labeled for the proposed structure with the highest discrimination score, using a modified nomenclature...
  83. ncbi request reprint Proteomics in 2002: a year of technical development and wide-ranging applications
    Daniel Figeys
    MDS Proteomics, 251 Attwell Drive, Toronto, Ontario, Canada M9W 7H4
    Anal Chem 75:2891-905. 2003
  84. 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
    ....