Items where Subject is "mass spectrometry"

Paper

Amid, C., Frankish, A., Aken, B., Ezkurdia, I., Kokocinsk, F., Gilbert, J., White, S., Carninci, P., Gingeras, T. R., Guigo, R., Searle, S., Tress, M. L., Harrow, J., Hubbard, T. (2010) From identification to validation to gene count. Genome Biology, 11 (Suppl ). ISSN 1474-760X

Antberg, Linn, Cifani, Paolo, Sandin, Marianne, Levander, Fredrik, James, Peter (May 2012) Critical Comparison of Multidimensional Separation Methods for Increasing Protein Expression Coverage. Journal of Proteome Research, 11 (5). pp. 2644-2652. ISSN 1535-3893

Bartlet-Jones, M., Jeffery, W. A., Hansen, H. F., Pappin, D. J. (September 1994) Peptide ladder sequencing by mass spectrometry using a novel, volatile degradation reagent. Rapid Commun Mass Spectrom, 8 (9). pp. 737-42. ISSN 0951-4198 (Print)0951-4198 (Linking)

Bish, Rebecca A., Myers, Michael P. (August 2007) Werner helicase interacting protein 1 (WRNIP1) binds polyubiquitin via its zinc finger domain. J Biol Chem, 282 (32). pp. 23184-23193. ISSN 0021-9258 (Print)

Boersema, P. J., Taouatas, N., Altelaar, A. F. M., Gouw, J. W., Ross, P. L., Pappin, D. J., Heck, A. J. R., Mohammed, S. (April 2009) Straightforward and de Novo Peptide Sequencing by MALDI-MS/MS Using a Lys-N Metalloendopeptidase. Molecular & Cellular Proteomics, 8 (4). pp. 650-660. ISSN 1535-9476

Bonham, ChristopherA, Mandati, Vinay, Singh, RakeshK, Pappin, DarrylJ, Tonks, NicholasK (March 2023) Coupling substrate-trapping with proximity-labeling to identify protein tyrosine phosphatase PTP1B signaling networks. Journal of Biological Chemistry. p. 104582. ISSN 0021-9258

Cai, L., Harris, W. R., Marshak, D. R., Gross, J., Crabb, J. W. (October 1990) Structural analysis of bovine pancreatic thread protein. J Protein Chem, 9 (5). pp. 623-32. ISSN 0277-8033 (Print)0277-8033 (Linking)

Carmel, G., Leichus, B., Cheng, X., Patterson, S. D., Mirza, U., Chait, B. T., Kuret, J. (March 1994) Expression, purification, crystallization, and preliminary x-ray analysis of casein kinase-1 from Schizosaccharomyces pombe. J Biol Chem, 269 (10). pp. 7304-9. ISSN 0021-9258 (Print)

Chavez, J. D., Eng, J. K., Schweppe, D. K., Cilia, M., Rivera, K., Zhong, X., Wu, X., Allen, T., Khurgel, M., Kumar, A., Lampropoulos, A., Larsson, M., Maity, S., Morozov, Y., Pathmasiri, W., Perez-Neut, M., Pineyro-Ruiz, C., Polina, E., Post, S., Rider, M., Tokmina-Roszyk, D., Tyson, K., Vieira Parrine Sant'Ana, D., Bruce, J. E. (December 2016) A General Method for Targeted Quantitative Cross-Linking Mass Spectrometry. PLoS One, 11 (12). e0167547. ISSN 1932-6203

Choe, L., D'Ascenzo, M., Relkin, N. R., Pappin, D., Ross, P., Williamson, B., Guertin, S., Pribil, P., Lee, K. H. (October 2007) 8-plex quantitation of changes in cerebrospinal fluid protein expression in subjects undergoing intravenous immunoglobulin treatment for Alzheimer's disease. Proteomics, 7 (20). pp. 3651-60. ISSN 1615-9853 (Print)1615-9853 (Linking)

Cifani, Paolo, Kentsis, Alex (November 2017) High Sensitivity Quantitative Proteomics Using Automated Multidimensional Nano-flow Chromatography and Accumulated Ion Monitoring on Quadrupole-Orbitrap-Linear Ion Trap Mass Spectrometer. Molecular and Cellular Proteomics, 16 (11). pp. 2006-2016. ISSN 1535-9476

Cifani, Paolo, Kentsis, Alex (October 2022) Quantitative Cell Proteomic Atlas: Pathway-Scale Targeted Mass Spectrometry for High-Resolution Functional Profiling of Cell Signaling. Journal of Proteome Research, 21 (10). pp. 2535-2544. ISSN 1535-3893

Cifani, Paolo, Kentsis, Alex (January 2017) Towards comprehensive and quantitative proteomics for diagnosis and therapy of human disease. Proteomics, 17 (1-2). p. 1600079. ISSN 1615-9853

Cifani, Paolo, Li, Zhi, Luo, Danmeng, Grivainis, Mark, Intlekofer, Andrew M, Fenyö, David, Kentsis, Alex (April 2021) Discovery of Protein Modifications Using Differential Tandem Mass Spectrometry Proteomics. Journal of Proteome Research, 20 (4). pp. 1835-1848. ISSN 1535-3893

Cifani, Paolo, Shakiba, Mojdeh, Chhangawala, Sagar, Kentsis, Alex (December 2017) ProteoModlR for functional proteomic analysis. BMC Bioinformatics, 18 (1). ISSN 1471-2105

Enikolopov, G., Guillermier, C., Wang, M., Trakimas, L., Steinhauser, M. L., Lechene, C. (November 2014) Brain stem cell division and maintenance studied using multi-isotope imaging mass spectrometry (MIMS). Surface and Interface Analysis, 46 (S1). pp. 140-143. ISSN 01422421

Fonseca, F. V., Ravi, K., Wiseman, D., Tummala, M., Harmon, C., Ryzhov, V., Fineman, J. R., Black, S. M. (March 2010) Mass spectroscopy and molecular modeling predict endothelial nitric oxide synthase dimer collapse by hydrogen peroxide through zinc tetrathiolate metal-binding site disruption. DNA and Cell Biology, 29 (3). pp. 149-160.

Gerbasi, V. R., Preall, J. B., Golden, D. E., Powell, D. W., Cummins, T. D., Sontheimer, E. J. (2011) Blanks, a nuclear siRNA/dsRNA-binding complex component, is required for Drosophila spermiogenesis. Proceedings of the National Academy of Sciences of the United States of America, 108 (8). pp. 3204-3209. ISSN 00278424 (ISSN)

Griswold, Andrew R, Cifani, Paolo, Rao, Sahana D, Axelrod, Abram J, Miele, Matthew M, Hendrickson, Ronald C, Kentsis, Alex, Bachovchin, Daniel A (June 2019) A Chemical Strategy for Protease Substrate Profiling. Cell chemical biology, 26 (6). 901-907.e6. ISSN 2451-9456

Gut, I. G., Jeffery, W. A., Pappin, D. J. C., Beck, S. (1997) Analysis of DNA by 'charge tagging' and matrix-assisted laser desorption/ionization mass spectrometry. Rapid Communications in Mass Spectrometry, 11 (1). pp. 43-50. ISSN 09514198 (ISSN)

Hampton, B. S., Marshak, D. R., Burgess, W. H. (January 1992) Structural and functional characterization of full-length heparin-binding growth associated molecule. Mol Biol Cell, 3 (1). pp. 85-93. ISSN 1059-1524 (Print)1059-1524 (Linking)

Hanley, S. Z., Pappin, D. J., Rahman, D., White, A. J., Elborough, K. M., Slabas, A. R. (March 1999) Re-evaluation of the primary structure of Ralstonia eutropha phasin and implications for polyhydroxyalkanoic acid granule binding. FEBS Letters, 447 (1). pp. 99-105. ISSN 0014-5793 (Print)0014-5793 (Linking)

He, C., Bozler, J., Janssen, K. A., Wilusz, J. E., Garcia, B. A., Schorn, A. J., Bonasio, R. (January 2021) TET2 chemically modifies tRNAs and regulates tRNA fragment levels. Nature Structural and Molecular Biology, 28 (1). pp. 62-70. ISSN 1545-9993

Hinton, S. D., Myers, M. P., Roggero, V. R., Allison, L. A., Tonks, N. K. (May 2010) The pseudophosphatase MK-STYX interacts with G3BP and decreases stress granule formation. Biochemical Journal, 427. pp. 349-357. ISSN 0264-6021

Honey, S., Schneider, B. L., Schieltz, D. M., Yates, J. R., Futcher, B. (February 2001) A novel multiple affinity purification tag and its use in identification of proteins associated with a cyclin-CDK complex. Nucleic Acids Res, 29 (4). E24. ISSN 1362-4962 (Electronic)

Hoss, M., Robins, P., Naven, T. J., Pappin, D. J., Sgouros, J., Lindahl, T. (July 1999) A human DNA editing enzyme homologous to the Escherichia coli DnaQ/MutD protein. EMBO Journal, 18 (13). pp. 3868-75. ISSN 0261-4189 (Print)0261-4189 (Linking)

Kalkum, Markus, Lyon, Gholson J., Chait, Brian T. (2003) Detection of secreted peptides by using hypothesis-driven multistage mass spectrometry. Proceedings of the National Academy of Sciences of the United States of America, 100 (5). pp. 2795-2800. ISSN 0027-8424

Kirchner, M., Renard, B. Y., Kothe, U., Pappin, D. J., Hamprecht, F. A., Steen, H., Steen, J. A. J. (January 2010) Computational protein profile similarity screening for quantitative mass spectrometry experiments. Bioinformatics, 26 (1). pp. 77-83. ISSN 1367-4803

Kuhn, E., Whiteaker, J. R., Mani, D. R., Jackson, A. M., Zhao, L., Pope, M. E., Smith, D., Rivera, K. D., Anderson, N. L., Skates, S. J., Pearson, T. W., Paulovich, A. G., Carr, S. A. (June 2012) Interlaboratory Evaluation of Automated, Multiplexed Peptide Immunoaffinity Enrichment Coupled to Multiple Reaction Monitoring Mass Spectrometry for Quantifying Proteins in Plasma. Molecular & Cellular Proteomics, 11 (6). ISSN 1535-9476

Lee, Y. C., Baath, J. A., Bastle, R. M., Bhattacharjee, S., Cantoria, M. J., Dornan, M., Gamero-Estevez, E., Ford, L., Halova, L., Kernan, J., Kurten, C., Li, S., Martinez, J., Sachan, N., Sarr, M., Shan, X., Subramanian, N., Rivera, K., Pappin, D., Lin, S. H. (January 2018) Impact of Detergents on Membrane Protein Complex Isolation. J Proteome Res, 17 (1). pp. 348-358. ISSN 1535-3893

O'Gara, M., Adams, G. M., Gong, W., Kobayashi, R., Blumenthal, R. M., Cheng, X. (August 1997) Expression, purification, mass spectrometry, crystallization and multiwavelength anomalous diffraction of selenomethionyl PvuII DNA methyltransferase (cytosine-N4-specific). European Journal of Biochemistry , 247 (3). pp. 1009-18. ISSN 0014-2956 (Print)

Osterbaan, Larissa J, Hoyle, Victoria, Curtis, Michelle, DeBlasio, Stacy, Rivera, Keith D, Heck, Michelle, Fuchs, Marc (May 2021) Identification of protein interactions of grapevine fanleaf virus RNA-dependent RNA polymerase during infection of by affinity purification and tandem mass spectrometry. The Journal of general virology, 102 (5). ISSN 1465-2099

Pang, C. N. I., Ballouz, S., Weissberger, D., Thibaut, L. M., Hamey, J. J., Gillis, J., Wilkins, M. R., Hart-Smith, G. (August 2020) Analytical guidelines for co-fractionation mass spectrometry obtained through global profiling of gold standard Saccharomyces cerevisiae protein complexes. Mol Cell Proteomics, 19 (11). pp. 1876-1895. ISSN 1535-9476

Pappin, D. J. (2003) Peptide mass fingerprinting using MALDI-TOF mass spectrometry. Methods in Molecular Biology, 211. pp. 211-9. ISSN 1940-6029 (Electronic)1064-3745 (Linking)

Pappin, D. J. (1997) Peptide mass fingerprinting using MALDI-TOF mass spectrometry. Methods in molecular biology (Clifton, N.J.), 64. pp. 165-173. ISSN 10643745 (ISSN)

Pappin, D. J. C., Hojrup, P., Bleasby, A. J. (1993) Rapid identification of proteins by peptide-mass fingerprinting. Current Biology, 3 (6). pp. 327-332. ISSN 09609822 (ISSN)

Perkins, D. N., Pappin, D. J., Creasy, D. M., Cottrell, J. S. (December 1999) Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis, 20 (18). pp. 3551-67. ISSN 0173-0835 (Print)0173-0835 (Linking)

Ragno, S., Romano, M., Howell, S., Pappin, D. J., Jenner, P. J., Colston, M. J. (September 2001) Changes in gene expression in macrophages infected with Mycobacterium tuberculosis: a combined transcriptomic and proteomic approach. Immunology, 104 (1). pp. 99-108. ISSN 0019-2805 (Print)0019-2805 (Linking)

Ramsey, John S., Ammar, El-Desouky, Mahoney, Jaclyn E., Rivera, Keith, Johnson, Richard, Igwe, David O., Thannhauser, Theodore W., MacCoss, Michael J., Hall, David G., Heck, Michelle (January 2022) Host Plant Adaptation Drives Changes in Diaphorina citri Proteome Regulation, Proteoform Expression, and Transmission of ‘Candidatus Liberibacter asiaticus’, the Citrus Greening Pathogen. Phytopathology, 112 (1). pp. 101-115. ISSN 0031-949X

Rasko, T., Der, A., Klement, E., Slaska-Kiss, K., Posfai, E., Medzihradszky, K. F., Marshak, D. R., Roberts, R. J. , Kiss, A. (June 2010) BspRI restriction endonuclease: cloning, expression in Escherichia coli and sequential cleavage mechanism. Nucleic Acids Res, 38 (20). pp. 7155-7166. ISSN 1362-4962 (Electronic) 0305-1048 (Linking)

Ross, P. L., Huang, Y. N., Marchese, J. N., 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, D. J. (December 2004) Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol Cell Proteomics, 3 (12). pp. 1154-69. ISSN 1535-9476 (Print)1535-9476 (Linking)

Ser, Zheng, Cifani, Paolo, Kentsis, Alex (June 2019) Optimized Cross-Linking Mass Spectrometry for in Situ Interaction Proteomics. Journal of Proteome Research, 18 (6). pp. 2545-2558. ISSN 1535-3893

Smirnov, I. P., Zhu, X., Taylor, T., Huang, Y., Ross, P., Papayanopoulos, I. A., Martin, S. A., Pappin, D. J. (May 2004) Suppression of alpha-cyano-4-hydroxycinnamic acid matrix clusters and reduction of chemical noise in MALDI-TOF mass spectrometry. Anal Chem, 76 (10). pp. 2958-65. ISSN 0003-2700 (Print)0003-2700 (Linking)

Spengler, B., Luetzenkirchen, F., Metzger, S., Chaurand, P., Kaufmann, R., Jeffery, W., Bartlet-Jones, M., Pappin, D. J. C. (1997) Peptide sequencing of charged derivatives by postsource decay MALDI mass spectrometry. International Journal of Mass Spectrometry and Ion Processes, 169-17. pp. 127-140. ISSN 01681176 (ISSN)

Stella, Roberto, Cifani, Paolo, Peggion, Caterina, Hansson, Karin, Lazzari, Cristian, Bendz, Maria, Levander, Fredrik, Sorgato, Maria Catia, Bertoli, Alessandro, James, Peter (February 2012) Relative Quantification of Membrane Proteins in Wild-Type and Prion Protein (PrP)-Knockout Cerebellar Granule Neurons. Journal of Proteome Research, 11 (2). pp. 523-536. ISSN 1535-3893

Waldemarson, Sofia, Kurbasic, Emila, Krogh, Morten, Cifani, Paolo, Berggård, Tord, Borg, Åke, James, Peter (December 2016) Proteomic analysis of breast tumors confirms the mRNA intrinsic molecular subtypes using different classifiers: a large-scale analysis of fresh frozen tissue samples. Breast Cancer Research, 18 (1). ISSN 1465-542X

Wilson, J.P., Ipsaro, J. J., Del Giudice, S.N., Turna, N. S., Gauss, C. M., Dusenbury, K.H., Marquart, K., Rivera, K. D., Pappin, D. J. (March 2020) Tryp-N: A Thermostable Protease for the Production of N-terminal Argininyl and Lysinyl Peptides. J Proteome Res, 19 (4). pp. 1459-1469. ISSN 1535-3893 (Public Dataset)

Wu, C., Liu, T., Chen, W., Oka, S., Fu, C. X., Jain, M. R., Parrott, A. M., Baykal, A. T., Sadoshima, J., Li, H. (October 2010) Redox Regulatory Mechanism of Transnitrosylation by Thioredoxin. Molecular & Cellular Proteomics, 9 (10). pp. 2262-2275. ISSN 1535-9476

Wu, Y., Egerton, G., Pappin, D. J., Harrison, R. A., Wilkinson, M. C., Underwood, A., Bianco, A. E. (April 2004) The Secreted Larval Acidic Proteins (SLAPs) of Onchocerca spp. are encoded by orthologues of the alt gene family of Brugia malayi and have host protective potential. Mol Biochem Parasitol, 134 (2). pp. 213-24. ISSN 0166-6851 (Print)0166-6851 (Linking)

Yu, Allen T, Aggarwal, Disha, Pappin, Darryl, Spector, David L (December 2022) Single Oligonucleotide Capture of RNA And Temperature Elution Series ( SOCRATES ) for Identification of RNA-binding Proteins. Bio-protocol, 12 (24). e4572. ISSN 2331-8325

Zhang, Y., Wolf-Yadlin, A., Ross, P. L., Pappin, D. J., Rush, J., Lauffenburger, D. A., White, F. M. (September 2005) Time-resolved mass spectrometry of tyrosine phosphorylation sites in the epidermal growth factor receptor signaling network reveals dynamic modules. Mol Cell Proteomics, 4 (9). pp. 1240-50. ISSN 1535-9476 (Print)1535-9476 (Linking)

van Ham, M., van Lith, M., Lillemeier, B., Tjin, E., Gruneberg, U., Rahman, D., Pastoors, L., van Meijgaarden, K., Roucard, C., Trowsdale, J., Ottenhoff, T., Pappin, D., Neefjes, J. (April 2000) Modulation of the major histocompatibility complex class II-associated peptide repertoire by human histocompatibility leukocyte antigen (HLA)-DO. J Exp Med, 191 (7). pp. 1127-36. ISSN 0022-1007 (Print)0022-1007 (Linking)

Book Section

Marshak, D. R., Fraser, B. A. (1990) Characterization of Synthetic Polypeptides by Mass Spectrometry. In: High performance liquid chromatography in biotechnology. Wiley-Liss, New York, pp. 531-550.

Pappin, D. J. C., Rahman, D., Hansen, H. F., Bartlet-Jones, M., Jeffery, W., Bleasby, A. J. (1996) Chemistry, Mass Spectrometry and Peptide-Mass Databases: Evolution of Methods for the Rapid Identification and Mapping of Cellular Proteins. In: Mass Spectrometry in the Biological Sciences. Humana Press, pp. 135-150. ISBN 978-1-4612-6671-6

Book

Cifani, Paolo (2022) Automated Multidimensional Nanoscale Chromatography for Ultrasensitive Targeted Mass Spectrometry. Methods in Molecular Biology, 1 . Humana Press, New York, New York.

Video

Pappin, D. J. (November 2012) Talk from Darryl Pappin at the Cold Spring Harbor Laboratory In-House Symposium (2012). [Video] (Unpublished)