Research Topics
Genomes and Genes
| Hanno SteenSummaryAffiliation: Harvard University Country: USA Publications
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Detail Information
Publications
NITPICK: peak identification for mass spectrometry dataBernhard Y Renard
Interdisciplinary Center for Scientific Computing, University of Heidelberg, Heidelberg, Germany
BMC Bioinformatics 9:355. 2008..The reliable extraction of features from mass spectra is a fundamental step in the automated analysis of proteomic mass spectrometry (MS) experiments...
Phosphorylation analysis by mass spectrometry: myths, facts, and the consequences for qualitative and quantitative measurementsHanno Steen
Department of Pathology, Harvard Medical School and Children s Hospital, Boston, Massachusetts 02115, USA
Mol Cell Proteomics 5:172-81. 2006....- Integration analysis of quantitative proteomics and transcriptomics data identifies potential targets of frizzled-8 protein-related antiproliferative factor in vivoWei Yang
The Urological Diseases Research Center, Children s Hospital Boston, Boston, USA
BJU Int 110:E1138-46. 2012..Our analysis suggests that this pathway might also be relevant in the design of diagnostic tools and medications targeting IC... - A Src family kinase-Shp2 axis controls RUNX1 activity in megakaryocyte and T-lymphocyte differentiationHui Huang
Department of Pediatric Hematology Oncology, Children s Hospital Boston, Dana Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
Genes Dev 26:1587-601. 2012..These findings link SFK and Shp2 signaling pathways to the regulation of RUNX1 activity in hematopoiesis via control of RUNX1 multiprotein complex assembly... - Identification of pancreas-specific proteins in endoscopically (endoscopic pancreatic function test) collected pancreatic fluid with liquid chromatography--tandem mass spectrometryJoao A Paulo
Center for Pancreatic Disease, Division of Gastroenterology, Hepatology, and Endoscopy, Brigham and Women s Hospital, 75 Francis St, Boston, MA 02115, USA
Pancreas 39:889-96. 2010.... - Proteomic analysis (GeLC-MS/MS) of ePFT-collected pancreatic fluid in chronic pancreatitisJoao A Paulo
Department of Pathology, Children s Hospital Boston, Boston, Massachusettes, United States
J Proteome Res 11:1897-912. 2012..Our workflow provided a mass spectrometry-based approach for the further study of the pancreatic fluid proteome, which may lead to the discovery potential biomarkers of chronic pancreatitis... - Proteomic analysis of formalin-fixed paraffin-embedded pancreatic tissue using liquid chromatography tandem mass spectrometryJoao A Paulo
Department of Pathology, Harvard Medical School, Boston, MA, USA
Pancreas 41:175-85. 2012..We aim to establish liquid chromatography coupled with tandem mass spectrometry analysis of FFPE pancreatic tissue as a suitable strategy for the study of the pancreas proteome... - FLEXIQuant: a novel tool for the absolute quantification of proteins, and the simultaneous identification and quantification of potentially modified peptidesSasha Singh
Department of Pathology, Harvard Medical School and Children s Hospital Boston, Boston, Massachusetts 02115, USA
J Proteome Res 8:2201-10. 2009..We find evidence of differential regulation at different sites, a phenomenon we believe will be very widespread. FLEXIQuant proved itself to be capable of serving as a general quantitative tool... - Optimized sample preparation of endoscopic collected pancreatic fluid for SDS-PAGE analysisJoao A Paulo
Department of Pathology, Children s Hospital Boston and Harvard Medical School, Boston, MA 02115, USA
Electrophoresis 31:2377-87. 2010..We have also determined the addition of protease inhibitors to be assay-dependent. Our optimized sample preparation strategy can be applied to future proteomic analyses of pancreatic fluid... - Cytokine profiling of pancreatic fluid using the ePFT collection method in tandem with a multiplexed microarray assayJoao A Paulo
Department of Pathology, Children s Hospital Boston, Boston, MA, United States
J Immunol Methods 369:98-107. 2011..Further targeted investigation of cytokines in ePFT-collected fluid will broaden our knowledge of pancreatic immune response and pathogenesis in chronic pancreatitis... - Difference gel electrophoresis identifies differentially expressed proteins in endoscopically collected pancreatic fluidJoao A Paulo
Department of Pathology, Children s Hospital Boston and Harvard Medical School, Boston, MA 02115, USA
Electrophoresis 32:1939-51. 2011..Endoscopic collection (ePFT) in tandem with DIGE-LC-MS/MS is a suitable approach for pancreatic fluid proteome analysis; however, further optimization of our protocol, as outlined herein, may improve proteome coverage in future analyses... - Mass spectrometry-based proteomics of endoscopically collected pancreatic fluid in chronic pancreatitis researchJoao A Paulo
Center for Pancreatic Disease, Division of Gastroenterology, Hepatology and Endoscopy, Brigham and Women s Hospital, Harvard Medical School, Boston, MA, USA
Proteomics Clin Appl 5:109-20. 2011..We conclude that pancreatic fluid represents a rich reservoir of potential biomarkers and that the study of the molecular mechanisms of chronic pancreatitis may benefit substantially from MS-based proteomics... 
A practical guide to the FLEXIQuant methodSasha Singh
Department of Pathology, Children s Hospital Boston and Harvard Medical School, Boston, MA, USA
Methods Mol Biol 893:295-319. 2012..FLEXIQuantification allows for the unbiased identification of peptides undergoing PTM as a function of a particular biological state. The extent of PTM is also quantified, providing further insight into the regulation of the protein...- Stable isotope-free relative and absolute quantitation of protein phosphorylation stoichiometry by MSHanno Steen
Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
Proc Natl Acad Sci U S A 102:3948-53. 2005..These approaches were validated and subsequently applied to the phosphorylation of the yeast transcription factor Pho4... - Proteome scale characterization of human S-acylated proteins in lipid raft-enriched and non-raft membranesWei Yang
Urological Diseases Research Center, Department of Urology, Children s Hospital Boston, Boston, Massachusetts 02115, USA
Mol Cell Proteomics 9:54-70. 2010..The PalmPISC approach and the large scale human S-acylated protein data set are expected to provide powerful tools to facilitate our understanding of the functions and mechanisms of protein S-acylation... - PhosphoproteomicsNurhan Ozlu
Proteomics Center at Children s Hospital Boston, Boston, MA, USA
Wiley Interdiscip Rev Syst Biol Med 2:255-76. 2010..We highlight the tremendous steps the field has made in the last 5 years which allow quantitative global analyses while pointing out caveats in experimentation... - Different phosphorylation states of the anaphase promoting complex in response to antimitotic drugs: a quantitative proteomic analysisJudith A J Steen
Departments of Neurobiology and Pathology, Harvard Medical School and Children s Hospital Boston, Boston, MA 02115, USA
Proc Natl Acad Sci U S A 105:6069-74. 2008..We discuss these findings in terms of the variable efficacy of antimitotic drugs in cancer chemotherapy... - Quantitative proteomics analysis reveals molecular networks regulated by epidermal growth factor receptor level in head and neck cancerWei Yang
Urological Diseases Research Center, Department of Urology, Children s Hospital Boston, Boston, Massachusetts 02115, USA
J Proteome Res 9:3073-82. 2010..Further investigation of these molecular networks may not only enhance our understanding of the antitumor mechanisms of EGFR targeting but also improve patient selection and provide novel targets for better therapeutics... - Analysis of endoscopic pancreatic function test (ePFT)-collected pancreatic fluid proteins precipitated via ultracentrifugationJoao A Paulo
Department of Pathology, Children s Hospital Boston and Harvard Medical School, Boston, MA 02115, USA
JOP 14:176-86. 2013..We have shown previously that trichloroacetic acid precipitation is an effective method of protein extraction from pancreatic fluid for downstream biomarker discovery, compared to other common extraction methods tested... - Post-translational modification: nature's escape from genetic imprisonment and the basis for dynamic information encodingSudhakaran Prabakaran
Department of Systems Biology, Harvard Medical School, Boston, MA, USA
Wiley Interdiscip Rev Syst Biol Med 4:565-83. 2012..We focus particularly on examples other than the well-known 'histone code', to emphasize the pervasive use of information encoding in molecular biology. Finally, we touch briefly on new methods for measuring mod-form distributions... - Detection and diagnostic value of urine leucine-rich α-2-glycoprotein in children with suspected acute appendicitisAlex Kentsis
Department of Pediatric Oncology, Dana Farber Cancer Institute, and Division of Hematology Oncology, Department of Medicine, Children s Hospital Boston, Harvard Medical School, Boston, MA, USA
Ann Emerg Med 60:78-83.e1. 2012..Here, we sought to evaluate the diagnostic utility of enzyme-linked immunosorbent assay (ELISA) of urine LRG in a blinded, prospective, cohort study of children being evaluated for acute abdominal pain... - Mass spectrometry-based proteomics for translational research: a technical overviewJoao A Paulo
Center for Pancreatic Disease, Division of Gastroenterology, Hepatology and Endoscopy, Brigham and Women s Hospital and Department of Medicine, Harvard Medical School, Boston, MA, USA
Yale J Biol Med 85:59-73. 2012..Mass spectrometry-based proteome elucidation can reveal potential biomarkers and aid in the development of hypotheses for downstream investigation of the molecular mechanisms of disease... - Binding partner switching on microtubules and aurora-B in the mitosis to cytokinesis transitionNurhan Ozlu
Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
Mol Cell Proteomics 9:336-50. 2010..Concretely, we report a central role for Aurora-B in regulating the C phase cytoskeleton... - Computational protein profile similarity screening for quantitative mass spectrometry experimentsMarc Kirchner
Department of Pathology, Proteomics Center, Children s Hospital Boston, Boston, MA, USA
Bioinformatics 26:77-83. 2010..This optimizes power and delivers more intuitive and efficient results than existing methods that do not take these circumstances into account... - One-step sample concentration, purification, and albumin depletion method for urinary proteomicsAli R Vaezzadeh
Department of Urology, Harvard Medical School, Boston, Massachusetts 02115, USA
J Proteome Res 9:6082-9. 2010.... - Proteomic analysis of a rat pancreatic stellate cell line using liquid chromatography tandem mass spectrometry (LC-MS/MS)Joao A Paulo
Department of Pathology, Children s Hospital Boston, Boston, MA 02115, USA
J Proteomics 75:708-17. 2011.... - Design and validation of a high-throughput matrix-assisted laser desorption ionization time-of-flight mass spectrometry method for quantification of hepcidin in human plasmaDamon S Anderson
Departments of Pathology, Children s Hospital Boston, Boston, Massachusetts 02115, United States
Anal Chem 83:8357-62. 2011..0096). We discuss these preliminary reference ranges and correlations with additional parameters in light of the utility and limitations of hepcidin measurements as a stand-alone diagnostic and as a tool for therapeutic intervention... - Optimizing sample handling for urinary proteomicsRichard S Lee
Department of Urology, Urological Diseases Research Center, Harvard Medical School and Children s Hospital Boston, Boston, Massachusetts 02115, USA
J Proteome Res 7:4022-30. 2008.... - Extensive phosphorylation with overlapping specificity by Mycobacterium tuberculosis serine/threonine protein kinasesSladjana Prisic
Division of Infectious Diseases, Children s Hospital Boston, Harvard Medical School, Boston, MA 02115, USA
Proc Natl Acad Sci U S A 107:7521-6. 2010..tuberculosis and create a resource for understanding how specific phosphorylation events modulate protein activity. The results further provide the potential to predict likely cognate STPKs for newly identified phosphoproteins... - MGFp: an open Mascot Generic Format parser library implementationMarc Kirchner
Proteomics Center, Children s Hospital Boston, Boston, Massachusettes 02115, USA
J Proteome Res 9:2762-3. 2010..We provide a formal grammar and a portable, efficient C++ implementation for a Mascot Generic Format (MGF) parser. Software and technical documentation are available from http://software.steenlab.org/mgfp/... - Subcellular fractionation enhances proteome coverage of pancreatic duct cellsJoao A Paulo
Department of Pathology, Children s Hospital Boston, Boston, MA, USA
Biochim Biophys Acta 1834:791-7. 2013.... - Mass Spectrometry-Based (GeLC-MS/MS) Comparative Proteomic Analysis of Endoscopically (ePFT) Collected Pancreatic and Gastroduodenal FluidsJoao A Paulo
1 Department of Pathology, Children s Hospital Boston and Harvard Medical School, Boston, Massachusetts, USA 2 Proteomics Center at Children s Hospital Boston, Boston, Massachusetts, USA 3 Center for Pancreatic Disease, Division of Gastroenterology, Hepatology and Endoscopy, Brigham and Women s Hospital and Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
Clin Transl Gastroenterol 3:e14. 2012..We test the hypothesis that these endoscopically collected fluids have different proteomes. As such, we aim to show that the ePFT method can be used to collect fluid enriched in pancreatic proteins to test for pancreatic function... - Optimization of cell lysis and protein digestion protocols for the analysis of HeLa S3 cells by LC-MS/MSDominic Winter
Department of Pathology, Children s Hospital Boston and Harvard Medical School, Boston, MA 02115, USA
Proteomics 11:4726-30. 2011..The result is a proposal for an optimized protocol to prepare the whole cell lysate samples from HeLa S3 cells... - mz5: space- and time-efficient storage of mass spectrometry data setsMathias Wilhelm
Proteomics Center, Children s Hospital Boston, Boston, Massachusetts, USA
Mol Cell Proteomics 11:O111.011379. 2012..The format is implemented as part of the ProteoWizard project and is available under a permissive Apache license. Additional information and download links are available from http://software.steenlab.org/mz5... - Rapid preparation of nuclei-depleted detergent-resistant membrane fractions suitable for proteomics analysisRosalyn M Adam
Urological Diseases Research Center, Children s Hospital Boston and Department of Surgery, Harvard Medical School, Boston, MA 02115, USA
BMC Cell Biol 9:30. 2008..To address these issues, we have modified a published differential detergent extraction method to enable rapid DRM isolation that minimizes nuclear contamination and yields fractions compatible with mass spectrometry... - libfbi: a C++ implementation for fast box intersection and application to sparse mass spectrometry dataMarc Kirchner
Proteomics Center, Department of Pathology, Children s Hospital Boston, Harvard Medical School, Boston, MA 02115, USA
Bioinformatics 27:1166-7. 2011.... - Proteomic analysis of palmitoylated platelet proteinsLouisa Dowal
Division of Hemostasis and Thrombosis, Beth Israel Deaconess Medical Center, Boston, MA, USA
Blood 118:e62-73. 2011..The discovery of new platelet palmitoyl protein candidates will provide a resource for subsequent investigations to validate the palmitoylation of these proteins and to determine the role palmitoylation plays in their function... - Non-linear classification for on-the-fly fractional mass filtering and targeted precursor fragmentation in mass spectrometry experimentsMarc Kirchner
Proteomics Center, Children s Hospital Boston, Boston, MA, USA
Bioinformatics 26:791-7. 2010..DDA/IDA methods do not exploit valuable information that is contained in the fractional mass of high-accuracy precursor mass measurements delivered by current instrumentation... - Proteomic approaches to the analysis of multiprotein signaling complexesWei Yang
The Urological Diseases Research Center, Department of Urology, Children s Hospital Boston, Boston, MA 02115, USA
Proteomics 8:832-51. 2008..Challenges associated with proteomic analysis of signaling complexes are also discussed... - Proteomics and opportunities for clinical translation in urological diseaseAli R Vaezzadeh
Department of Urology, Children s Hospital Boston, Harvard Medical School, Boston, Massachusetts, USA
J Urol 182:835-43. 2009..We present an overview of current proteomics technologies, a review of proteomics applications in urology and a perspective on the future of proteomics in clinical medicine... - The mechanism and pattern of yolk consumption provide insight into embryonic nutrition in XenopusPaul Jorgensen
Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
Development 136:1539-48. 2009..But yolk consumption does not appear to be triggered by embryonic cells declining to a critically small size. Frog embryos offer a promising platform for the in vivo analysis of metabolism... - Analysis of tyrosine phosphorylation sites in signaling molecules by a phosphotyrosine-specific immonium ion scanning methodHanno Steen
Harvard Medical School, Department of Cell Biology, 240 Longwood Avenue, Boston, MA 02115, USA
Sci STKE 2002:pl16. 2002..Because of its simplicity and specificity, PSI scanning is likely to become an important tool in proteomic studies of pathways involving tyrosine phosphorylation... - Urine proteomics for discovery of improved diagnostic markers of Kawasaki diseaseAlex Kentsis
Division of Hematology Oncology, Department of Pediatric Oncology, Dana Farber Cancer Institute, Boston Children s Hospital, Harvard Medical School, Boston, MA, USA
EMBO Mol Med 5:210-20. 2013.... - Tiki1 is required for head formation via Wnt cleavage-oxidation and inactivationXinjun Zhang
The F M Kirby Neurobiology Center, Boston Children s Hospital, Department of Neurology, Harvard Medical School, Boston, MA 02115, USA
Cell 149:1565-77. 2012..TIKI proteins may represent potential therapeutic targets... - FLEXIQinase, a mass spectrometry-based assay, to unveil multikinase mechanismsSasha A Singh
Department of Pathology, Children s Hospital Boston and Harvard Medical School, Boston, Massachusetts, USA
Nat Methods 9:504-8. 2012.... - Effect of High-Accuracy Precursor Masses on Phosphopeptide Identification from MS(3) SpectraWiebke Timm
Proteomics Center at Children s Hospital Boston, Boston, Massachusetts 02115, Department of Pathology, Harvard Medical School and Children s Hospital Boston, Boston, Massachusetts 02115, Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, F M Kirby Neurobiology Center, Children s Hospital Boston, Boston, Massachusetts 02115, and Department of Neurobiology, Harvard Medical School, Boston, Massachusetts 02115
Anal Chem 82:3977-80. 2010.... - Differentiation-dependent interactions between RUNX-1 and FLI-1 during megakaryocyte developmentHui Huang
Children s Hospital Boston, 300 Longwood Ave, Boston, MA 02115, USA
Mol Cell Biol 29:4103-15. 2009..We propose that dephosphorylation of FLI-1 is a key event in the transcriptional regulation of megakaryocyte maturation. These findings have implications for other cell types where interactions between runx and ets family proteins occur... - Quantitative proteomics identifies a beta-catenin network as an element of the signaling response to Frizzled-8 protein-related antiproliferative factorWei Yang
Urological Diseases Research Center, Children s Hospital Boston, Department of Surgery, Harvard Medical School, Boston, MA 02115, USA
Mol Cell Proteomics 10:M110.007492. 2011.... - Temporal variations of the postnatal rat urinary proteome as a reflection of systemic maturationRichard S Lee
Department of Urology, Harvard Medical School, Urological Diseases Research Center, Children s Hospital Boston, Boston, MA 02115, USA
Proteomics 8:1097-112. 2008..Further characterization of the normal urinary proteome may provide the basis for identification of urinary biomarkers of diseases of the urinary tract... - Discovery and validation of urine markers of acute pediatric appendicitis using high-accuracy mass spectrometryAlex Kentsis
Division of Emergency Medicine, Department of Medicine, Children s Hospital Boston, Harvard Medical School, Boston, MA, USA
Ann Emerg Med 55:62-70.e4. 2010..Here, we sought to profile the urine of patients with appendicitis, with the goal of identifying new diagnostic markers... - A polymorphism in the leptin gene promoter is associated with anemia in patients with HIV diseaseGary J Vanasse
Department of Medicine, Brigham and Women s Hospital, Harvard Medical School, 75 Francis Street, Boston, MA 02115, USA
Blood 118:5401-8. 2011..This association was replicated in an independent cohort of HIV(+) women. Our study provides novel insight into the association between genetic variability in the leptin gene and anemia in HIV(+) individuals... - Etiology of limb girdle muscular dystrophy 1D/1E determined by laser capture microdissection proteomicsSteven A Greenberg
Department of Neurology, Division of Neuromuscular Disease, Brigham and Women s Hospital, Harvard Medical School, Boston, MA 02115, USA
Ann Neurol 71:141-5. 2012..Sequencing in this patient and family members identified the genetic basis of the previously reported 6q23 linked LGMD1D/1E to be due to an intron splice donor site mutation (IVS3+3A>G) of the desmin gene located on chromosome 2q35... - Purification of active TFIID from Saccharomyces cerevisiae. Extensive promoter contacts and co-activator functionRoy Auty
Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
J Biol Chem 279:49973-81. 2004..TFIID supports basal transcription and activated transcription, both of which are enhanced by TFIIA... - Comparative analysis of Erk phosphorylation suggests a mixed strategy for measuring phospho-form distributionsSudhakaran Prabakaran
Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
Mol Syst Biol 7:482. 2011..This combined MS strategy provides an optimal mixture of accuracy and coverage for quantifying distributions, but positional isomers remain a challenging problem... - Brainstem deficiency of the 14-3-3 regulator of serotonin synthesis: a proteomics analysis in the sudden infant death syndromeKevin G Broadbelt
Department of Pathology, Children s Hospital Boston and Harvard Medical School, Boston, Massachusetts 02115, USA
Mol Cell Proteomics 11:M111.009530. 2012..These data suggest a potential molecular defect in SIDS related to TPH2 regulation, as 14-3-3 is critical in this process... - Iron overload in patients with acute leukemia or MDS undergoing myeloablative stem cell transplantationPhilippe Armand
Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA 02115, USA
Biol Blood Marrow Transplant 17:852-60. 2011..These results contribute to our understanding of the prevalence, mechanism, and consequences of iron overload in HSCT... - High-throughput matrix-assisted laser desorption ionization-time-of-flight mass spectrometry method for quantification of hepcidin in human urineDamon S Anderson
Department of Pathology, Children s Hospital Boston, Boston, Massachusetts 02115, USA
Anal Chem 82:1551-5. 2010..The assay is simple, accurate, and efficient, and the high-throughput performance features of the assay make large-scale clinical research studies feasible... - Purification and architecture of the ubiquitous Wave complexAlexis Gautreau
Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
Proc Natl Acad Sci U S A 101:4379-83. 2004..The complex is organized around a core of Nap and Abi. Sra is a peripheral subunit recruited on the Nap side, whereas the Wave and Hspc subunits are recruited on the Abi side of the core... - Proteomic analysis of endoscopically (endoscopic pancreatic function test) collected gastroduodenal fluid using in-gel tryptic digestion followed by LC-MS/MSJoao A Paulo
Department of Pathology, Children s Hospital Boston, Boston, MA, USA
Proteomics Clin Appl 4:715-25. 2010..We use in-gel tryptic digestion followed by LC-MS/MS (GeLC-MS/MS) to profile the proteome of gastroduodenal fluid collected during the endoscopic pancreatic function test (ePFT)... - SALAMI (Spectrum ALignments using high Accuracy Mass and hIgh sensitivity data): how to make the best out of hybrid MS/MS dataFlavio Monigatti
Department of Pathology, Harvard Medical School and Children s Hospital Boston, Boston, MA 02115, USA
J Proteome Res 7:1984-93. 2008..This approach utilizes the parallel spectrum measurement capabilities of the LTQ-Orbitrap. We present our approach to handling this type of hybrid data, explain our alignment program, and discuss the advantages of the chosen methodology... - Protein sulfation analysis--A primerFlavio Monigatti
Department of Pathology/Enders 1130, Harvard Medical School and Children's Hospital Boston, 320 Longwood Ave, Boston, MA 02115, USA
Biochim Biophys Acta 1764:1904-13. 2006..2). We will highlight strengths and limitations of different strategies and approaches (including references), providing a primer for newcomers to protein sulfation analysis... - A quantitative proteomic analysis of growth factor-induced compositional changes in lipid rafts of human smooth muscle cellsDawn L MacLellan
Department of Urology, The Urological Diseases Research Center, Boston, MA, USA
Proteomics 5:4733-42. 2005..In addition, eight Rho family members were localized to rafts by ICAT analysis. Collectively, these observations suggest a role for lipid rafts in regulation of PDGF-stimulated changes in the cytoskeleton... - The ABC's (and XYZ's) of peptide sequencingHanno Steen
Department of Systems Biology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, USA
Nat Rev Mol Cell Biol 5:699-711. 2004..The key - but little understood - technology in mass-spectrometry-based proteomics is peptide sequencing, which we describe and review here in an easily accessible format... - Protein profiling with cleavable isotope-coded affinity tag (cICAT) reagents: the yeast salinity stress responseJiaxu Li
Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115-5730, USA
Mol Cell Proteomics 2:1198-204. 2003..These results indicate that salt stress and amino acid starvation cause overlapping cellular responses and are likely to be physiologically linked... - Proteomics goes quantitative: measuring protein abundanceHanno Steen
Department Cell Biology, Harvard Medical School, Boston, MA 02115, USA
Trends Biotechnol 20:361-4. 2002..Furthermore, methods for the quantitation of relative protein abundance at the protein level are getting more advanced, which should complement gene expression monitoring at the mRNA level... - Tyrosine phosphorylation mapping of the epidermal growth factor receptor signaling pathwayHanno Steen
Protein Interaction Laboratory, Center for Experimental Bioinformatics, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
J Biol Chem 277:1031-9. 2002..Because of its sensitivity and selectivity, this approach will be useful in proteomic approaches to study tyrosine phosphorylation in a number of signal transduction pathways... - Phosphotyrosine mapping in Bcr/Abl oncoprotein using phosphotyrosine-specific immonium ion scanningHanno Steen
Center for Experimental Bioinformatics, Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
Mol Cell Proteomics 2:138-45. 2003..This study shows the power of phosphotyrosine-specific immonium ion scanning for sensitive phosphotyrosine mapping when limited amounts of samples are available... - Analysis of protein-nucleic acid interactions by photochemical cross-linking and mass spectrometryHanno Steen
Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark
Mass Spectrom Rev 21:163-82. 2002.... - Directed proteomic analysis of the human nucleolusJens S Andersen
Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230, Odense M, Denmark
Curr Biol 12:1-11. 2002..The data also show that the protein composition of nucleoli is not static and can alter significantly in response to the metabolic state of the cell... - Analysis of protein phosphorylation using mass spectrometry: deciphering the phosphoproteomeMatthias Mann
Center for Experimental Bioinformatics, University of Southern Denmark, M, DK 5230, Odense, Denmark
Trends Biotechnol 20:261-8. 2002..In this article, we outline several methods for enrichment of phosphorylated proteins and peptides and discuss various options for their identification and quantitation with special emphasis on mass spectrometry-based techniques... - Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomicsShao-En Ong
Protein Interaction Laboratory, University of Southern Denmark, Odense, Denmark
Mol Cell Proteomics 1:376-86. 2002..SILAC is a simple, inexpensive, and accurate procedure that can be used as a quantitative proteomic approach in any cell culture system... - A new derivatization strategy for the analysis of phosphopeptides by precursor ion scanning in positive ion modeHanno Steen
Center for Experimental Bioinformatics, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense
J Am Soc Mass Spectrom 13:996-1003. 2002.... - Robust prediction of the MASCOT score for an improved quality assessment in mass spectrometric proteomicsThomas Koenig
Interdisciplinary Center for Scientific Computing, University of Heidelberg, 69120 Heidelberg, Germany
J Proteome Res 7:3708-17. 2008.... - Autophosphorylation of JAK2 on tyrosines 221 and 570 regulates its activityLawrence S Argetsinger
Department of Molecular and Integrative Physiology, The University of Michigan Medical School, Ann Arbor, MI 48109 0622, USA
Mol Cell Biol 24:4955-67. 2004....
Research Grants
- Defining the true nature of the minimal cell cycle with quantitative proteomicsHanno Steen; Fiscal Year: 2010..Apart from furthering our fundamental understanding of the cell cycle, the development of preventatives, treatments and therapies for/of these diseases and malignancies will benefit greatly from this study. ..