PUB - Publikationen an der Universität Bielefeld

Proteomic profiling of mechanistically distinct enzyme classes using a common chemotype.
Adam GC, Sorensen EJ, Cravatt BF., Nat. Biotechnol. 20(8), 2002
PMID: 12091914

Chemical strategies for functional proteomics.
Adam GC, Sorensen EJ, Cravatt BF., Mol. Cell Proteomics 1(10), 2002
PMID: 12438561

Profiling the specific reactivity of the proteome with non-directed activity-based probes.
Adam GC, Cravatt BF, Sorensen EJ., Chem. Biol. 8(1), 2001
PMID: 11182321

Mapping enzyme active sites in complex proteomes.
Adam GC, Burbaum J, Kozarich JW, Patricelli MP, Cravatt BF., J. Am. Chem. Soc. 126(5), 2004
PMID: 14759193

A new chemical probe for proteomics of carbohydrate-binding proteins.
Ballell L, Alink KJ, Slijper M, Versluis C, Liskamp RM, Pieters RJ., Chembiochem 6(2), 2005
PMID: 15578642

Discovering disease-associated enzymes by proteome reactivity profiling.
Barglow KT, Cravatt BF., Chem. Biol. 11(11), 2004
PMID: 15556003

Selective targeting of lysosomal cysteine proteases with radiolabeled electrophilic substrate analogs.
Bogyo M, Verhelst S, Bellingard-Dubouchaud V, Toba S, Greenbaum D., Chem. Biol. 7(1), 2000
PMID: 10662686

Substrate binding and sequence preference of the proteasome revealed by active-site-directed affinity probes.
Bogyo M, Shin S, McMaster JS, Ploegh HL., Chem. Biol. 5(6), 1998
PMID: 9653549

Design and synthesis of visible isotope-coded affinity tags for the absolute quantification of specific proteins in complex mixtures.
Bottari P, Aebersold R, Turecek F, Gelb MH., Bioconjug. Chem. 15(2), 2004
PMID: 15025535

Proteome-wide identification of cellular targets affected by bisindolylmaleimide-type protein kinase C inhibitors.
Brehmer D, Godl K, Zech B, Wissing J, Daub H., Mol. Cell Proteomics 3(5), 2004
PMID: 14769951

Cellular targets of gefitinib.
Brehmer D, Greff Z, Godl K, Blencke S, Kurtenbach A, Weber M, Muller S, Klebl B, Cotten M, Keri G, Wissing J, Daub H., Cancer Res. 65(2), 2005
PMID: 15695376

Enrichment and analysis of peptide subsets using fluorous affinity tags and mass spectrometry.
Brittain SM, Ficarro SB, Brock A, Peters EC., Nat. Biotechnol. 23(4), 2005
PMID: 15768030

Developing photoactive affinity probes for proteomic profiling: hydroxamate-based probes for metalloproteases.
Chan EW, Chattopadhaya S, Panicker RC, Huang X, Yao SQ., J. Am. Chem. Soc. 126(44), 2004
PMID: 15521763

An affinity based probe for the proteomic profiling of aspartic proteases
Chattopadhaya, Tetrahedron Lett. 46(), 2005

Evaluation of kinase inhibitor selectivity by chemical proteomics.
Daub H, Godl K, Brehmer D, Klebl B, Muller G., Assay Drug Dev Technol 2(2), 2004
PMID: 15165517

DNA microarrays: experimental issues, data analysis, and application to bacterial systems.
Dharmadi Y, Gonzalez R., Biotechnol. Prog. 20(5), 2004
PMID: 15458312

Using photolabile ligands in drug discovery and development.
Dorman G, Prestwich GD., Trends Biotechnol. 18(2), 2000
PMID: 10652511

An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database.
Eng JK, McCormack AL, Yates JR., J. Am. Soc. Mass Spectrom. 5(11), 1994
PMID: c6781

Multiple species of CPP32 and Mch2 are the major active caspases present in apoptotic cells.
Faleiro L, Kobayashi R, Fearnhead H, Lazebnik Y., EMBO J. 16(9), 1997
PMID: 9171342

Chemical reagents in photoaffinity labeling
Fleming, Tetrahedron 51(), 1995

Activity-based enrichment of matrix metalloproteinases using reversible inhibitors as affinity ligands.
Freije JR, Bischoff R., J Chromatogr A 1009(1-2), 2003
PMID: 13677656

Enzyme family-specific and activity-based screening of chemical libraries using enzyme microarrays.
Funeriu DP, Eppinger J, Denizot L, Miyake M, Miyake J., Nat. Biotechnol. 23(5), 2005
PMID: 15821728

Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS.
Gerber SA, Rush J, Stemman O, Kirschner MW, Gygi SP., Proc. Natl. Acad. Sci. U.S.A. 100(12), 2003
PMID: 12771378

Evaluation of two-dimensional differential gel electrophoresis for proteomic expression analysis of a model breast cancer cell system.
Gharbi S, Gaffney P, Yang A, Zvelebil MJ, Cramer R, Waterfield MD, Timms JF., Mol. Cell Proteomics 1(2), 2002
PMID: 12096126

Current two-dimensional electrophoresis technology for proteomics.
Gorg A, Weiss W, Dunn MJ., Proteomics 4(12), 2004
PMID: 15543535

The current state of two-dimensional electrophoresis with immobilized pH gradients.
Gorg A, Postel W, Gunther S., Electrophoresis 9(9), 1988
PMID: 3072185

Epoxide electrophiles as activity-dependent cysteine protease profiling and discovery tools.
Greenbaum D, Medzihradszky KF, Burlingame A, Bogyo M., Chem. Biol. 7(8), 2000
PMID: 11048948

Chemical approaches for functionally probing the proteome.
Greenbaum D, Baruch A, Hayrapetian L, Darula Z, Burlingame A, Medzihradszky KF, Bogyo M., Mol. Cell Proteomics 1(1), 2002
PMID: 12096141

Evaluation of two-dimensional gel electrophoresis-based proteome analysis technology.
Gygi SP, Corthals GL, Zhang Y, Rochon Y, Aebersold R., Proc. Natl. Acad. Sci. U.S.A. 97(17), 2000
PMID: 10920198

Proteome analysis of low-abundance proteins using multidimensional chromatography and isotope-coded affinity tags.
Gygi SP, Rist B, Griffin TJ, Eng J, Aebersold R., J. Proteome Res. 1(1), 2002
PMID: 12643526

Quantitative analysis of complex protein mixtures using isotope-coded affinity tags.
Gygi SP, Rist B, Gerber SA, Turecek F, Gelb MH, Aebersold R., Nat. Biotechnol. 17(10), 1999
PMID: 10504701

Affinity-based tagging of protein families with reversible inhibitors: a concept for functional proteomics.
Hagenstein MC, Mussgnug JH, Lotte K, Plessow R, Brockhinke A, Kruse O, Sewald N., Angew. Chem. Int. Ed. Engl. 42(45), 2003
PMID: 14639736

Mass spectrometric analysis of protein mixtures at low levels using cleavable 13C-isotope-coded affinity tag and multidimensional chromatography.
Hansen KC, Schmitt-Ulms G, Chalkley RJ, Hirsch J, Baldwin MA, Burlingame AL., Mol. Cell Proteomics 2(5), 2003
PMID: 12766231

Photoaffinity labeling in drug discovery and developments: chemical gateway for entering proteomic frontier.
Hatanaka Y, Sadakane Y., Curr Top Med Chem 2(3), 2002
PMID: 11944820

Chemical proteomics and its application to drug discovery.
Jeffery DA, Bogyo M., Curr. Opin. Biotechnol. 14(1), 2003
PMID: 12566007

Synthesis of marimastat and a marimastat conjugate for affinity chromatography and surface plasmon resonance studies.
Jenssen K, Sewald K, Sewald N., Bioconjug. Chem. 15(3), 2004
PMID: 15149188

AUTHOR UNKNOWN, 0

Enzyme activity profiles of the secreted and membrane proteome that depict cancer cell invasiveness.
Jessani N, Liu Y, Humphrey M, Cravatt BF., Proc. Natl. Acad. Sci. U.S.A. 99(16), 2002
PMID: 12149457

Activity-based probes that target diverse cysteine protease families.
Kato D, Boatright KM, Berger AB, Nazif T, Blum G, Ryan C, Chehade KA, Salvesen GS, Bogyo M., Nat. Chem. Biol. 1(1), 2005
PMID: 16407991

Profiling serine hydrolase activities in complex proteomes.
Kidd D, Liu Y, Cravatt BF., Biochemistry 40(13), 2001
PMID: 11300781

Active site-directed protein regulation.
Kobe B, Kemp BE., Nature 402(6760), 1999
PMID: 10586874

Click Chemistry: Diverse Chemical Function from a Few Good Reactions.
Kolb HC, Finn MG, Sharpless KB., Angew. Chem. Int. Ed. Engl. 40(11), 2001
PMID: 11433435

Activity-based probes for protein tyrosine phosphatases.
Kumar S, Zhou B, Liang F, Wang WQ, Huang Z, Zhang ZY., Proc. Natl. Acad. Sci. U.S.A. 101(21), 2004
PMID: 15148367

Protein microarrays as tools for functional proteomics.
LaBaer J, Ramachandran N., Curr Opin Chem Biol 9(1), 2005
PMID: 15701447

Initial sequencing and analysis of the human genome.
Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, Kann L, Lehoczky J, LeVine R, McEwan P, McKernan K, Meldrim J, Mesirov JP, Miranda C, Morris W, Naylor J, Raymond C, Rosetti M, Santos R, Sheridan A, Sougnez C, Stange-Thomann Y, Stojanovic N, Subramanian A, Wyman D, Rogers J, Sulston J, Ainscough R, Beck S, Bentley D, Burton J, Clee C, Carter N, Coulson A, Deadman R, Deloukas P, Dunham A, Dunham I, Durbin R, French L, Grafham D, Gregory S, Hubbard T, Humphray S, Hunt A, Jones M, Lloyd C, McMurray A, Matthews L, Mercer S, Milne S, Mullikin JC, Mungall A, Plumb R, Ross M, Shownkeen R, Sims S, Waterston RH, Wilson RK, Hillier LW, McPherson JD, Marra MA, Mardis ER, Fulton LA, Chinwalla AT, Pepin KH, Gish WR, Chissoe SL, Wendl MC, Delehaunty KD, Miner TL, Delehaunty A, Kramer JB, Cook LL, Fulton RS, Johnson DL, Minx PJ, Clifton SW, Hawkins T, Branscomb E, Predki P, Richardson P, Wenning S, Slezak T, Doggett N, Cheng JF, Olsen A, Lucas S, Elkin C, Uberbacher E, Frazier M, Gibbs RA, Muzny DM, Scherer SE, Bouck JB, Sodergren EJ, Worley KC, Rives CM, Gorrell JH, Metzker ML, Naylor SL, Kucherlapati RS, Nelson DL, Weinstock GM, Sakaki Y, Fujiyama A, Hattori M, Yada T, Toyoda A, Itoh T, Kawagoe C, Watanabe H, Totoki Y, Taylor T, Weissenbach J, Heilig R, Saurin W, Artiguenave F, Brottier P, Bruls T, Pelletier E, Robert C, Wincker P, Smith DR, Doucette-Stamm L, Rubenfield M, Weinstock K, Lee HM, Dubois J, Rosenthal A, Platzer M, Nyakatura G, Taudien S, Rump A, Yang H, Yu J, Wang J, Huang G, Gu J, Hood L, Rowen L, Madan A, Qin S, Davis RW, Federspiel NA, Abola AP, Proctor MJ, Myers RM, Schmutz J, Dickson M, Grimwood J, Cox DR, Olson MV, Kaul R, Raymond C, Shimizu N, Kawasaki K, Minoshima S, Evans GA, Athanasiou M, Schultz R, Roe BA, Chen F, Pan H, Ramser J, Lehrach H, Reinhardt R, McCombie WR, de la Bastide M, Dedhia N, Blocker H, Hornischer K, Nordsiek G, Agarwala R, Aravind L, Bailey JA, Bateman A, Batzoglou S, Birney E, Bork P, Brown DG, Burge CB, Cerutti L, Chen HC, Church D, Clamp M, Copley RR, Doerks T, Eddy SR, Eichler EE, Furey TS, Galagan J, Gilbert JG, Harmon C, Hayashizaki Y, Haussler D, Hermjakob H, Hokamp K, Jang W, Johnson LS, Jones TA, Kasif S, Kaspryzk A, Kennedy S, Kent WJ, Kitts P, Koonin EV, Korf I, Kulp D, Lancet D, Lowe TM, McLysaght A, Mikkelsen T, Moran JV, Mulder N, Pollara VJ, Ponting CP, Schuler G, Schultz J, Slater G, Smit AF, Stupka E, Szustakowki J, Thierry-Mieg D, Thierry-Mieg J, Wagner L, Wallis J, Wheeler R, Williams A, Wolf YI, Wolfe KH, Yang SP, Yeh RF, Collins F, Guyer MS, Peterson J, Felsenfeld A, Wetterstrand KA, Patrinos A, Morgan MJ, de Jong P, Catanese JJ, Osoegawa K, Shizuya H, Choi S, Chen YJ, Szustakowki J; International Human Genome Sequencing Consortium., Nature 409(6822), 2001
PMID: 11237011

Click chemistry in situ: acetylcholinesterase as a reaction vessel for the selective assembly of a femtomolar inhibitor from an array of building blocks.
Lewis WG, Green LG, Grynszpan F, Radic Z, Carlier PR, Taylor P, Finn MG, Sharpless KB., Angew. Chem. Int. Ed. Engl. 41(6), 2002
PMID: 12491310

Protein profiling with cleavable isotope-coded affinity tag (cICAT) reagents: the yeast salinity stress response.
Li J, Steen H, Gygi SP., Mol. Cell Proteomics 2(11), 2003
PMID: 14506205

Photoactivated gamma-secretase inhibitors directed to the active site covalently label presenilin 1.
Li YM, Xu M, Lai MT, Huang Q, Castro JL, DiMuzio-Mower J, Harrison T, Lellis C, Nadin A, Neduvelil JG, Register RB, Sardana MK, Shearman MS, Smith AL, Shi XP, Yin KC, Shafer JA, Gardell SJ., Nature 405(6787), 2000
PMID: 10864326

Design and synthesis of an affinity probe that targets caspases in proteomic experiments
Liau, Tetrahedron Lett. 44(), 2003

Direct analysis of protein complexes using mass spectrometry.
Link AJ, Eng J, Schieltz DM, Carmack E, Mize GJ, Morris DR, Garvik BM, Yates JR 3rd., Nat. Biotechnol. 17(7), 1999
PMID: 10404161

Activity-based protein profiling: the serine hydrolases.
Liu Y, Patricelli MP, Cravatt BF., Proc. Natl. Acad. Sci. U.S.A. 96(26), 1999
PMID: 10611275

Design and synthesis of class-selective activity probes for protein tyrosine phosphatases.
Lo LC, Pang TL, Kuo CH, Chiang YL, Wang HY, Lin JJ., J. Proteome Res. 1(1), 2002
PMID: 12643524

Inhibitor affinity chromatography: profiling the specific reactivity of the proteome with immobilized molecules.
Lolli G, Thaler F, Valsasina B, Roletto F, Knapp S, Uggeri M, Bachi A, Matafora V, Storici P, Stewart A, Kalisz HM, Isacchi A., Proteomics 3(7), 2003
PMID: 12872229

Proteome Analysis: A Pathway to the Functional Analysis of Proteins.
Lottspeich F., Angew. Chem. Int. Ed. Engl. 38(17), 1999
PMID: 10508327

Absolute quantification of specific proteins in complex mixtures using visible isotope-coded affinity tags.
Lu Y, Bottari P, Turecek F, Aebersold R, Gelb MH., Anal. Chem. 76(14), 2004
PMID: 15253649

Activation of multiple interleukin-1beta converting enzyme homologues in cytosol and nuclei of HL-60 cells during etoposide-induced apoptosis.
Martins LM, Kottke T, Mesner PW, Basi GS, Sinha S, Frigon N Jr, Tatar E, Tung JS, Bryant K, Takahashi A, Svingen PA, Madden BJ, McCormick DJ, Earnshaw WC, Kaufmann SH., J. Biol. Chem. 272(11), 1997
PMID: 9054443

Comparison of three directly coupled HPLC MS/MS strategies for identification of proteins from complex mixtures: single-dimension LC–MS/MS, 2-phase MudPIT, and 3-phase MudPIT
McDonald, Int. J. Mass Spectrom. 219(), 2002

Global analysis of proteasomal substrate specificity using positional-scanning libraries of covalent inhibitors.
Nazif T, Bogyo M., Proc. Natl. Acad. Sci. U.S.A. 98(6), 2001
PMID: 11248015

High resolution two-dimensional electrophoresis of proteins.
O'Farrell PH., J. Biol. Chem. 250(10), 1975
PMID: 236308

High-resolution functional proteomics by active-site peptide profiling.
Okerberg ES, Wu J, Zhang B, Samii B, Blackford K, Winn DT, Shreder KR, Burbaum JJ, Patricelli MP., Proc. Natl. Acad. Sci. U.S.A. 102(14), 2005
PMID: 15795380

AUTHOR UNKNOWN, 0

Solid phase synthesis of peptide vinyl sulfone and peptide epoxyketone proteasome inhibitors
Overkleeft, Tetrahedron Lett. 41(), 2000

Direct visualization of serine hydrolase activities in complex proteomes using fluorescent active site-directed probes.
Patricelli MP, Giang DK, Stamp LM, Burbaum JJ., Proteomics 1(9), 2001
PMID: 11990500

Chemistry in living systems.
Prescher JA, Bertozzi CR., Nat. Chem. Biol. 1(1), 2005
PMID: 16407987

Large-scale proteomic analysis of the human spliceosome.
Rappsilber J, Ryder U, Lamond AI, Mann M., Genome Res. 12(8), 2002
PMID: 12176931

Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents.
Ross PL, Huang YN, Marchese JN, Williamson B, Parker K, Hattan S, Khainovski N, Pillai S, Dey S, Daniels S, Purkayastha S, Juhasz P, Martin S, Bartlet-Jones M, He F, Jacobson A, Pappin DJ., Mol. Cell Proteomics 3(12), 2004
PMID: 15385600

A stepwise huisgen cycloaddition process: copper(I)-catalyzed regioselective "ligation" of azides and terminal alkynes.
Rostovtsev VV, Green LG, Fokin VV, Sharpless KB., Angew. Chem. Int. Ed. Engl. 41(14), 2002
PMID: 12203546

Activity-based probes for the proteomic profiling of metalloproteases.
Saghatelian A, Jessani N, Joseph A, Humphrey M, Cravatt BF., Proc. Natl. Acad. Sci. U.S.A. 101(27), 2004
PMID: 15220480

Membrane proteins and proteomics: un amour impossible?
Santoni V, Molloy M, Rabilloud T., Electrophoresis 21(6), 2000
PMID: 10786880

Substrate/propeptide-derived endo-epoxysuccinyl peptides as highly potent and selective cathepsin B inhibitors.
Schaschke N, Assfalg-Machleidt I, Machleidt W, Moroder L., FEBS Lett. 421(1), 1998
PMID: 9462845

Epoxysuccinyl peptide-derived affinity labels for cathepsin B.
Schaschke N, Assfalg-Machleidt I, Lassleben T, Sommerhoff CP, Moroder L, Machleidt W., FEBS Lett. 482(1-2), 2000
PMID: 11018529

A novel strategy for quantitative proteomics using isotope-coded protein labels.
Schmidt A, Kellermann J, Lottspeich F., Proteomics 5(1), 2005
PMID: 15602776

Microarray platform for profiling enzyme activities in complex proteomes.
Sieber SA, Mondala TS, Head SR, Cravatt BF., J. Am. Chem. Soc. 126(48), 2004
PMID: 15571375

Quantitative protein profiling using two-dimensional gel electrophoresis, isotope-coded affinity tag labeling, and mass spectrometry.
Smolka M, Zhou H, Aebersold R., Mol. Cell Proteomics 1(1), 2002
PMID: 12096137

Chemical strategies for activity-based proteomics.
Speers AE, Cravatt BF., Chembiochem 5(1), 2004
PMID: 14695510

Activity-based protein profiling in vivo using a copper(i)-catalyzed azide-alkyne [3 + 2] cycloaddition.
Speers AE, Adam GC, Cravatt BF., J. Am. Chem. Soc. 125(16), 2003
PMID: 12696868

Profiling enzyme activities in vivo using click chemistry methods.
Speers AE, Cravatt BF., Chem. Biol. 11(4), 2004
PMID: 15123248

Crystal structure of NS-134 in complex with bovine cathepsin B: a two-headed epoxysuccinyl inhibitor extends along the entire active-site cleft.
Stern I, Schaschke N, Moroder L, Turk D., Biochem. J. 381(Pt 2), 2004
PMID: 15084146

Inactivation of interleukin-1 beta converting enzyme by peptide (acyloxy)methyl ketones.
Thornberry NA, Peterson EP, Zhao JJ, Howard AD, Griffin PR, Chapman KT., Biochemistry 33(13), 1994
PMID: 8142397

Design and synthesis of activity probes for glycosidases.
Tsai CS, Li YK, Lo LC., Org. Lett. 4(21), 2002
PMID: 12375899

Difference gel electrophoresis: a single gel method for detecting changes in protein extracts.
Unlu M, Morgan ME, Minden JS., Electrophoresis 18(11), 1997
PMID: 9420172

Dissecting protein function using chemical proteomic methods
Verhelst, QSAR Comb. Sci. 24(), 2005

Bioconjugation by copper(I)-catalyzed azide-alkyne [3 + 2] cycloaddition.
Wang Q, Chan TR, Hilgraf R, Fokin VV, Sharpless KB, Finn MG., J. Am. Chem. Soc. 125(11), 2003
PMID: 12630856

Solid-phase synthesis of peptide vinyl sulfones as potential inhibitors and activity-based probes of cysteine proteases.
Wang G, Mahesh U, Chen GY, Yao SQ., Org. Lett. 5(5), 2003
PMID: 12605503

Large-scale analysis of the yeast proteome by multidimensional protein identification technology.
Washburn MP, Wolters D, Yates JR 3rd., Nat. Biotechnol. 19(3), 2001
PMID: 11231557

Progress with gene-product mapping of the Mollicutes: Mycoplasma genitalium.
Wasinger VC, Cordwell SJ, Cerpa-Poljak A, Yan JX, Gooley AA, Wilkins MR, Duncan MW, Harris R, Williams KL, Humphery-Smith I., Electrophoresis 16(7), 1995
PMID: 7498152

Profiling protein function with small molecule microarrays.
Winssinger N, Ficarro S, Schultz PG, Harris JL., Proc. Natl. Acad. Sci. U.S.A. 99(17), 2002
PMID: 12167675

Chemical proteomic analysis reveals alternative modes of action for pyrido[2,3-d]pyrimidine kinase inhibitors.
Wissing J, Godl K, Brehmer D, Blencke S, Weber M, Habenberger P, Stein-Gerlach M, Missio A, Cotten M, Muller S, Daub H., Mol. Cell Proteomics 3(12), 2004
PMID: 15475568

Quantitative proteome analysis by solid-phase isotope tagging and mass spectrometry.
Zhou H, Ranish JA, Watts JD, Aebersold R., Nat. Biotechnol. 20(5), 2002
PMID: 11981568

Activity-based fluorescent probes that target phosphatases
Zhu, Tetrahedron Lett. 44(), 2003

Developing novel activity-based fluorescent probes that target different classes of proteases.
Zhu Q, Girish A, Chattopadhaya S, Yao SQ., Chem. Commun. (Camb.) (13), 2004
PMID: 15216356