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  1. Article ; Online: Current progress in protein profiling of complex samples.

    Resing, Katheryn A

    Expert review of proteomics

    2004  Volume 1, Issue 2, Page(s) 137–140

    MeSH term(s) Animals ; Bacterial Proteins/genetics ; Gene Expression Profiling/trends ; Mammals ; Proteins/genetics ; Proteome
    Chemical Substances Bacterial Proteins ; Proteins ; Proteome
    Language English
    Publishing date 2004-08
    Publishing country England
    Document type Editorial
    ZDB-ID 2299100-1
    ISSN 1744-8387 ; 1478-9450
    ISSN (online) 1744-8387
    ISSN 1478-9450
    DOI 10.1586/14789450.1.2.137
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  2. Article: Proteomics for cell protein expression profiling.

    Resing, Katheryn A

    The Journal of investigative dermatology

    2003  Volume 121, Issue 1, Page(s) XI–XII

    MeSH term(s) Animals ; Epidermis/chemistry ; Epidermis/cytology ; Gene Expression ; Keratinocytes/chemistry ; Proteins/analysis ; Proteins/genetics ; Proteomics
    Chemical Substances Proteins
    Language English
    Publishing date 2003-06-28
    Publishing country United States
    Document type Editorial ; Review ; Comment
    ZDB-ID 80136-7
    ISSN 1523-1747 ; 0022-202X
    ISSN (online) 1523-1747
    ISSN 0022-202X
    DOI 10.1046/j.1523-1747.2003.12338.x
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  3. Article: Proteomics strategies for protein identification.

    Resing, Katheryn A / Ahn, Natalie G

    FEBS letters

    2005  Volume 579, Issue 4, Page(s) 885–889

    Abstract: The information from genome sequencing provides new approaches for systems-wide understanding of protein networks and cellular function. DNA microarray technologies have advanced to the point where nearly complete monitoring of gene expression is ... ...

    Abstract The information from genome sequencing provides new approaches for systems-wide understanding of protein networks and cellular function. DNA microarray technologies have advanced to the point where nearly complete monitoring of gene expression is feasible in several organisms. An equally important goal is to comprehensive survey cellular proteomes and profile protein changes under different cellular states. This presents a complex analytical problem, due to the chemical variability between proteins and peptides. Here, we discuss strategies to improve accuracy and sensitivity of peptide identification, distinguish represented protein isoforms, and quantify relative changes in protein abundance.
    MeSH term(s) Computational Biology/methods ; Databases, Protein ; Peptide Mapping/methods ; Protein Array Analysis ; Protein Interaction Mapping/methods ; Proteins/analysis ; Proteomics/methods
    Chemical Substances Proteins
    Language English
    Publishing date 2005-02-07
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 212746-5
    ISSN 1873-3468 ; 0014-5793
    ISSN (online) 1873-3468
    ISSN 0014-5793
    DOI 10.1016/j.febslet.2004.12.001
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  4. Article ; Online: Cell biology. Lessons in rational drug design for protein kinases.

    Ahn, Natalie G / Resing, Katheryn A

    Science (New York, N.Y.)

    2005  Volume 308, Issue 5726, Page(s) 1266–1267

    MeSH term(s) Adenosine Triphosphate/metabolism ; Alkylation ; Binding Sites ; Computational Biology ; Cysteine/chemistry ; Cysteine/metabolism ; Drug Design ; Drug Resistance/genetics ; Enzyme Inhibitors/chemistry ; Enzyme Inhibitors/metabolism ; Enzyme Inhibitors/pharmacology ; Hydrophobic and Hydrophilic Interactions ; Models, Chemical ; Mutation ; Ribosomal Protein S6 Kinases, 90-kDa/antagonists & inhibitors ; Ribosomal Protein S6 Kinases, 90-kDa/chemistry ; Ribosomal Protein S6 Kinases, 90-kDa/metabolism ; Structure-Activity Relationship
    Chemical Substances Enzyme Inhibitors ; Adenosine Triphosphate (8L70Q75FXE) ; Ribosomal Protein S6 Kinases, 90-kDa (EC 2.7.11.1) ; Cysteine (K848JZ4886)
    Language English
    Publishing date 2005-05-27
    Publishing country United States
    Document type Comment ; Journal Article
    ZDB-ID 128410-1
    ISSN 1095-9203 ; 0036-8075
    ISSN (online) 1095-9203
    ISSN 0036-8075
    DOI 10.1126/science.1113707
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  5. Article: Networks for the allosteric control of protein kinases.

    Shi, Zhengshuang / Resing, Katheryn A / Ahn, Natalie G

    Current opinion in structural biology

    2006  Volume 16, Issue 6, Page(s) 686–692

    Abstract: The allosteric regulation of protein kinases serves as an efficient strategy for molecular communication, event coupling and interconversion between catalytic states. Recent co-crystal structures have revealed novel ways in which kinases control activity ...

    Abstract The allosteric regulation of protein kinases serves as an efficient strategy for molecular communication, event coupling and interconversion between catalytic states. Recent co-crystal structures have revealed novel ways in which kinases control activity and substrate specificity following phosphorylation, dimerization, or binding to regulatory proteins, substrates and scaffolds. In addition, hydrogen exchange coupled with mass spectrometry is emerging as a complementary strategy to probe the solution behavior of kinases; recent results have shown that allosteric regulation may involve transitions in protein motions as well as structural rearrangements.
    MeSH term(s) Allosteric Regulation ; Allosteric Site ; Deuterium ; Dimerization ; Extracellular Signal-Regulated MAP Kinases/chemistry ; Extracellular Signal-Regulated MAP Kinases/metabolism ; Hydrogen ; Mass Spectrometry ; Models, Biological ; Models, Molecular ; Protein Kinases/chemistry ; Protein Kinases/metabolism ; Protein Structure, Quaternary ; Signal Transduction
    Chemical Substances Hydrogen (7YNJ3PO35Z) ; Deuterium (AR09D82C7G) ; Protein Kinases (EC 2.7.-) ; Extracellular Signal-Regulated MAP Kinases (EC 2.7.11.24)
    Language English
    Publishing date 2006-12
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 1068353-7
    ISSN 0959-440X
    ISSN 0959-440X
    DOI 10.1016/j.sbi.2006.10.011
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  6. Article: Practical methods for deuterium exchange/mass spectrometry.

    Hoofnagle, Andrew N / Resing, Katheryn A / Ahn, Natalie G

    Methods in molecular biology (Clifton, N.J.)

    2004  Volume 250, Page(s) 283–298

    MeSH term(s) Chromatography, High Pressure Liquid/methods ; Data Interpretation, Statistical ; Deuterium ; Hydrogen/chemistry ; MAP Kinase Signaling System ; Mass Spectrometry/methods ; Mitogen-Activated Protein Kinase 1/chemistry ; Models, Chemical ; Proteins/chemistry ; Software
    Chemical Substances Proteins ; Hydrogen (7YNJ3PO35Z) ; Deuterium (AR09D82C7G) ; Mitogen-Activated Protein Kinase 1 (EC 2.7.11.24)
    Language English
    Publishing date 2004
    Publishing country United States
    Document type Journal Article
    ISSN 1064-3745
    ISSN 1064-3745
    DOI 10.1385/1-59259-671-1:283
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  7. Article: Applying proteomics to signaling networks.

    Kabuyama, Yukihito / Resing, Katheryn A / Ahn, Natalie G

    Current opinion in genetics & development

    2004  Volume 14, Issue 5, Page(s) 492–498

    Abstract: The information from genome sequencing provides a new framework for a systems-wide understanding of protein networks and cellular function. Whereas microarray technologies provide information about global gene expression within cells, complementary ... ...

    Abstract The information from genome sequencing provides a new framework for a systems-wide understanding of protein networks and cellular function. Whereas microarray technologies provide information about global gene expression within cells, complementary proteomic strategies monitor expression of proteins and their posttranslational modifications. Improved technologies that have emerged for comprehensive and high-throughput protein analysis yield novel insights into cell regulation.
    MeSH term(s) Animals ; Humans ; Protein Array Analysis ; Protein Binding ; Protein Processing, Post-Translational ; Proteomics/methods ; Signal Transduction
    Language English
    Publishing date 2004-10
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 1077312-5
    ISSN 1879-0380 ; 0959-437X
    ISSN (online) 1879-0380
    ISSN 0959-437X
    DOI 10.1016/j.gde.2004.07.001
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  8. Article ; Online: Achieving in-depth proteomics profiling by mass spectrometry.

    Ahn, Natalie G / Shabb, John B / Old, William M / Resing, Katheryn A

    ACS chemical biology

    2007  Volume 2, Issue 1, Page(s) 39–52

    Abstract: Proteomics addresses the important goal of determining the chemistry and composition of proteins in biological samples. Mass-spectrometry-based strategies have been highly successful in identifying and profiling proteins in complex mixtures; however, ... ...

    Abstract Proteomics addresses the important goal of determining the chemistry and composition of proteins in biological samples. Mass-spectrometry-based strategies have been highly successful in identifying and profiling proteins in complex mixtures; however, although depth of sampling continues to improve, a general recognition exists that no study has yet achieved complete protein coverage in any tissue, cell type, subcellular component, or fluid. The development of new approaches for comprehensively surveying highly complex protein mixtures, distinguishing protein isoforms, quantifying changes in protein abundance between different samples, and mapping post-translational modifications are areas of active research. These will be needed to achieve the "systems-wide" protein profiling goals of defining molecular responses to cell perturbations and obtaining biomarker information for disease detection, prognosis, and responses to therapy. We review recent progress in approaching these problems and present examples of successful applications and the outlook for the future.
    MeSH term(s) Animals ; Humans ; Mass Spectrometry/methods ; Protein Array Analysis/methods ; Proteome/analysis ; Proteomics/methods ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods
    Chemical Substances Proteome
    Language English
    Publishing date 2007-01-23
    Publishing country United States
    Document type Journal Article ; Review
    ISSN 1554-8937
    ISSN (online) 1554-8937
    DOI 10.1021/cb600357d
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  9. Article: Mapping protein post-translational modifications with mass spectrometry.

    Witze, Eric S / Old, William M / Resing, Katheryn A / Ahn, Natalie G

    Nature methods

    2007  Volume 4, Issue 10, Page(s) 798–806

    Abstract: Post-translational modifications of proteins control many biological processes, and examining their diversity is critical for understanding mechanisms of cell regulation. Mass spectrometry is a fundamental tool for detecting and mapping covalent ... ...

    Abstract Post-translational modifications of proteins control many biological processes, and examining their diversity is critical for understanding mechanisms of cell regulation. Mass spectrometry is a fundamental tool for detecting and mapping covalent modifications and quantifying their changes. Modern approaches have made large-scale experiments possible, screening complex mixtures of proteins for alterations in chemical modifications. By profiling protein chemistries, biologists can gain deeper insight into biological control. The aim of this review is introduce biologists to current strategies in mass spectrometry-based proteomics that are used to characterize protein post-translational modifications, noting strengths and shortcomings of various approaches.
    MeSH term(s) Acetylation ; Cysteine/chemistry ; Databases, Protein ; Isotope Labeling ; Mass Spectrometry/methods ; Oxidation-Reduction ; Phosphopeptides/isolation & purification ; Phosphorylation ; Protein Interaction Mapping ; Protein Processing, Post-Translational ; Tandem Mass Spectrometry/methods ; Ubiquitin/metabolism
    Chemical Substances Phosphopeptides ; Ubiquitin ; Cysteine (K848JZ4886)
    Language English
    Publishing date 2007-10
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Review
    ZDB-ID 2169522-2
    ISSN 1548-7105 ; 1548-7091
    ISSN (online) 1548-7105
    ISSN 1548-7091
    DOI 10.1038/nmeth1100
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  10. Article: Proteomic informatics.

    Russell, Steven A / Old, William / Resing, Katheryn A / Hunter, Lawrence

    International review of neurobiology

    2004  Volume 61, Page(s) 127–157

    MeSH term(s) Animals ; Computational Biology ; Humans ; Mass Spectrometry/instrumentation ; Mass Spectrometry/methods ; Protein Isoforms ; Proteins/chemistry ; Proteins/metabolism ; Proteomics
    Chemical Substances Protein Isoforms ; Proteins
    Language English
    Publishing date 2004
    Publishing country United States
    Document type Journal Article ; Review
    ZDB-ID 209876-3
    ISSN 0074-7742
    ISSN 0074-7742
    DOI 10.1016/S0074-7742(04)61006-3
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