Journal of Proteome Research, 1535-3893

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  1. Use of ENCODE Resources to Characterize Novel Proteoforms and Missing Proteins in the Human Proteome

    Nilsson, C., Mostovenko, E., Lichti, C., Ruggles, K., Fenyö, D., Rosenbloom, K., Hancock, W., Paik, Y-K., Omenn, G., LaBaer, J., Kroes, R., Uhlén, M., Hober, S., Végvári, Á., Andrén, P., Sulman, E., Lang, F., Fuentes, M., Carlsohn, E., Emmett, M. & 4 others, Moskal, J., Berven, F., Fehniger, T. & György Marko-Varga, 2015, In : Journal of Proteome Research. 14, 2, p. 603-608

    Research output: Contribution to journalArticle

  2. Time-Dependent Proteomic iTRAQ Analysis of Nasal Lavage of Hairdressers Challenged by Persulfate.

    Monica Kåredal, Mörtstedt, H., Jeppsson, M., Diab, K., Jörn Nielsen, Jönsson, B. A. & Christian Lindh, 2010, In : Journal of Proteome Research. okt, p. 5620-5628

    Research output: Contribution to journalArticle

  3. The Proteios Software Environment: an extensible multiuser platform for management and analysis of proteomics data

    Jari Häkkinen, Vincic, G., Månsson, O., Wårell, K. & Fredrik Levander, 2009, In : Journal of Proteome Research. 8, 6, p. 3037-3043

    Research output: Contribution to journalArticle

  4. The protein expression of Streptococcus pyogenes is significantly influenced by human plasma.

    Johansson, B., Fredrik Levander, von Pawel-Rammingen, U., Berggård, T., Lars Björck & Peter James, 2005, In : Journal of Proteome Research. 4, 6, p. 2302-2311

    Research output: Contribution to journalArticle

  5. The Lecticans of Mammalian Brain Perineural Net Are O-Mannosylated

    Pacharra, S., Hanisch, F-G., Muehlenhoff, M., Faissner, A., Uwe Rauch & Breloy, I., 2013, In : Journal of Proteome Research. 12, 4, p. 1764-1771

    Research output: Contribution to journalArticle

  6. The Immune System and the Proteome

    György Marko-Varga & LaBaer, J., 2017 Jan 6, In : Journal of Proteome Research. 16, 1, p. 1 1 p.

    Research output: Contribution to journalDebate/Note/Editorial

  7. Targeted Proteomics Approach for Precision Plant Breeding

    Chawade, A., Alexandersson, E., Bengtsson, T., Andreasson, E. & Fredrik Levander, 2016 Feb 5, In : Journal of Proteome Research. 15, 2, p. 638-642 9 p.

    Research output: Contribution to journalArticle

  8. Targeted Proteomic Analyses of Nasal Lavage Fluid in Persulfate-Challenged Hairdressers with Bleaching Powder-Associated Rhinitis

    Mörtstedt, H., Neserin Ali, Monica Kåredal, Jacobsson, H., Emelie Rietz, Diab, K., Jörn Nielsen, Jönsson, B. A. & Christian Lindh, 2015, In : Journal of Proteome Research. 14, 2, p. 860-873

    Research output: Contribution to journalArticle

  9. Targeted MS Assay Predicting Tamoxifen Resistance in Estrogen-Receptor-Positive Breast Cancer Tissues and Sera

    Tommaso De Marchi, Kuhn, E., Dekker, L. J. M., Stingl, C., Braakman, R. B. H., Opdam, M., Linn, S. C., Sweep, F. C. G. J., Span, P. N., Luider, T. M., Foekens, J. A., Martens, J. W. M., Carr, S. A. & Umar, A., 2016 Apr 1, In : Journal of Proteome Research. 15, 4, p. 1230-42 13 p.

    Research output: Contribution to journalArticle

  10. Systematic Identification of Single Amino Acid Variants in Glioma Stem-Cell-Derived Chromosome 19 Proteins

    Lichti, C., Mostovenko, E., Wadsworth, P., Lynch, G., Pettitt, M., Sulman, E., Wang, Q., Lang, F., Melinda Rezeli, György Marko-Varga, Végvári, Á. & Nilsson, C., 2015, In : Journal of Proteome Research. 14, 2, p. 778-786

    Research output: Contribution to journalArticle

  11. Structural analysis of 2D-gel-separated glycoproteins from human cerebrospinal fluid by tandem high-resolution mass spectrometry

    Håkansson, K., Emmett, M. R., Marshall, A. G., Davidsson, P. & Carol L Nilsson, 2003 Dec 25, In : Journal of Proteome Research. 2, 6, p. 581-8 8 p.

    Research output: Contribution to journalArticle

  12. Standard Guidelines for the Chromosome-Centric Human Proteome Project

    Paik, Y-K., Omenn, G. S., Uhlen, M., Hanash, S., Marko-Varga, G., Aebersold, R., Bairoch, A., Yamamoto, T., Legrain, P., Lee, H-J., Na, K., Jeong, S-K., He, F., Binz, P-A., Nishimura, T., Keown, P., Baker, M. S., Yoo, J. S., Garin, J., Archakov, A. & 3 others, Bergeron, J., Salekdeh, G. H. & Hancock, W. S., 2012, In : Journal of Proteome Research. 11, 4, p. 2005-2013

    Research output: Contribution to journalArticle

  13. Reproducibility of tryptic digestion investigated by quantitative fourier transform ion cyclotron resonance mass spectrometry

    Hagman, C., Ramstrom, M., Bentz, M., Peter James, Hakansson, P. & Bergquist, J., 2005, In : Journal of Proteome Research. 4, 2, p. 394-399

    Research output: Contribution to journalArticle

  14. Relative Quantification of Membrane Proteins in Wild-Type and Prion Protein (PrP)-Knockout Cerebellar Granule Neurons

    Stella, R., Cifani, P., Peggion, C., Hansson, K. M., Lazzari, C., Bendz, M., Fredrik Levander, Sorgato, M. C., Bertoli, A. & Peter James, 2012, In : Journal of Proteome Research. 11, 2, p. 523-536

    Research output: Contribution to journalArticle

  15. Quest for Missing Proteins: Update 2015 on Chromosome-Centric Human Proteome Project

    Horvatovich, P., Lundberg, E., Chen, Y-J., Sung, T-Y., He, F., Nice, E., Goode, R., Yu, S., Ranganathan, S., Baker, M., Domont, R., Valesquez, E., Li, D., Liu, S., Wang, Q., He, Q-Y., Menon, R., Guan, Y., Corrales, F., Segura, V. & 33 others, Casal, I., Pascual-Montano, A., Albar, J. P., Fuentes, M., Gonzalez-Gonzalez, M., Diez, P., Ibarolla, N., Degano, R., Mohammed, Y., Borchers, C., Urbani, A., Soggiu, A., Yamamoto, T., Archakov, A., Ponomarenko, E., Lisitsa, A., Lichti, C., Mostovenko, E., Kroes, R., Melinda Rezeli, Végvári, Á., Fehniger, T., Bischoff, R., Vizcaíno, J. A., Deutsch, E., Lane, L., Nilsson, C., György Marko-Varga, Omenn, G., Jeong, S-K., Cho, J-Y., Paik, Y-K. & Hancock, W., 2015, In : Journal of Proteome Research. 14, 9, p. 3415-3431

    Research output: Contribution to journalArticle

  16. Quantitative Proteomics Profiling of Primary Lung Adenocarcinoma Tumors Reveals Functional Perturbations in Tumor Metabolism

    Pernemalm, M., De Petris, L., Branca, R. M., Forshed, J., Kanter, L., Soria, J-C., Girard, P., Validire, P., Pawitan, Y., van den Oord, J., Lazar, V., Sven Påhlman, Lewensohn, R. & Lehtio, J., 2013, In : Journal of Proteome Research. 12, 9, p. 3934-3943

    Research output: Contribution to journalArticle

  17. Quantitative proteomic analysis of microdissected breast cancer tissues: comparison of label-free and SILAC-based quantification with shotgun, directed, and targeted MS approaches

    Liu, N. Q., Dekker, L. J. M., Stingl, C., Güzel, C., Tommaso De Marchi, Martens, J. W. M., Foekens, J. A., Luider, T. M. & Umar, A., 2013 Oct 4, In : Journal of Proteome Research. 12, 10, p. 4627-41

    Research output: Contribution to journalArticle

  18. Quantitative phosphoproteomic analysis of the STAT3/IL-6/HIF1alpha signaling network: an initial study in GSC11 glioblastoma stem cells

    Carol L Nilsson, Dillon, R., Devakumar, A., Shi, S. D-H., Greig, M. J., Rogers, J. C., Krastins, B., Rosenblatt, M., Kilmer, G., Major, M., Kaboord, B. J., Sarracino, D., Rezai, T., Prakash, A., Lopez, M., Ji, Y., Priebe, W., Lang, F., Colman, H. & Conrad, C. A., 2010 Jan, In : Journal of Proteome Research. 9, 1, p. 430-443 14 p.

    Research output: Contribution to journalArticle

  19. Quantitative Label-Free Phosphoproteomics of Six Different Life Stages of the Late Blight Pathogen Phytophthora infestans Reveals Abundant Phosphorylation of Members of the CRN Effector Family

    Resjo, S., Ali, A., Meijer, H. J. G., Seidl, M. F., Snel, B., Sandin, M., Fredrik Levander, Govers, F. & Andreasson, E., 2014, In : Journal of Proteome Research. 13, 4, p. 1848-1859

    Research output: Contribution to journalArticle

  20. Quantitation of 87 Proteins by nLC-MRM/MS in Human Plasma: Workflow for Large-Scale Analysis of Biobank Samples

    Melinda Rezeli, Sjödin, K., Henrik Lindberg, Olof Gidlöf, Lindahl, B., Jernberg, T., Spaak, J., David Erlinge & György Marko-Varga, 2017 Sep 1, In : Journal of Proteome Research. 16, 9, p. 3242-3254 13 p.

    Research output: Contribution to journalArticle

  21. Quantification of Membrane Proteins Using Nonspecific Protease Digestions

    Bendz, M., Carlsson Möller, M., Arrigoni, G., Wåhlander, Å., Stella, R., Cappadona, S., Fredrik Levander, Lars Hederstedt & Peter James, 2009, In : Journal of Proteome Research. 8, 12, p. 5666-5673

    Research output: Contribution to journalArticle

  22. Quantification of Human Kallikrein-2 in Clinical Samples by Selected Reaction Monitoring

    Végvári, Á., Sjödin, K., Melinda Rezeli & György Marko-Varga, 2013, In : Journal of Proteome Research. 12, 10, p. 4612-4616

    Research output: Contribution to journalArticle

  23. Proteomic variation is as large within as between strawberry varieties

    Alm, R., Ekefjard, A., Krogh, M., Jari Häkkinen & Cecilia Emanuelsson, 2007, In : Journal of Proteome Research. 6, 8, p. 3011-3020

    Research output: Contribution to journalArticle

  24. Proteomics and leukocytes: an approach to understanding potential molecular mechanisms of inflammatory responses.

    Wang, X., Zhao, H. & Roland Andersson, 2004, In : Journal of Proteome Research. 3, 5, p. 921-929

    Research output: Contribution to journalReview article

  25. Proteomics and disease - The challenges for technology and discovery

    György Marko-Varga & Fehniger, TE., 2004, In : Journal of Proteome Research. 3, 2, p. 167-178

    Research output: Contribution to journalArticle

  26. Proteomic profiling of plasma in Huntington's disease reveals neuroinflammatory activation and biomarker candidates

    Dalrymple, A., Wild, E. J., Joubert, R., Sathasivam, K., Bjorkqvist, M., Åsa Petersén, Jackson, G. S., Isaacs, J. D., Kristiansen, M., Bates, G. P., Leavitt, B. R., Keir, G., Ward, M. & Tabrizi, S. J., 2007, In : Journal of Proteome Research. 6, 7, p. 2833-2840

    Research output: Contribution to journalArticle

  27. Proteomic investigation of glioblastoma cell lines treated with wild-type p53 and cytotoxic chemotherapy demonstrates an association between galectin-1 and p53 expression

    Puchades, M., Carol L Nilsson, Emmett, M. R., Aldape, K. D., Ji, Y., Lang, F., Liu, T-J. & Conrad, C. A., 2007 Feb, In : Journal of Proteome Research. 6, 2, p. 869-75 7 p.

    Research output: Contribution to journalArticle

  28. Proteome annotations and identifications of the human pulmonary fibroblast.

    Johan Malmström, Larsen, K., Lars Malmström, Ellen Tufvesson, Parker, K., Marchese, J., Williamson, B., Hattan, S., Patterson, D., Martin, S., Graber, A., Juhasz, H. P., Gunilla Westergren-Thorsson & György Marko-Varga, 2004, In : Journal of Proteome Research. 3, 3, p. 525-537

    Research output: Contribution to journalArticle

  29. Protein Expression Profiling of Formalin-Fixed Paraffin-Embedded Tissue Using Recombinant Antibody Microarrays

    Pauly, F., Dexlin Mellby, L., Sara Ek, Mats Ohlin, Olsson, N., Karin Jirström, Michael Dictor, Schoenmakers, S., Carl Borrebaeck & Christer Wingren, 2013, In : Journal of Proteome Research. 12, 12, p. 5943-5953

    Research output: Contribution to journalArticle

  30. Protein Expression Changes in Skeletal Muscle in Response to Growth Promoter Abuse in Beef Cattle

    Stella, R., Biancotto, G., Krogh, M., Angeletti, R., Pozza, G., Sorgato, M. C., Peter James & Andrighetto, I., 2011, In : Journal of Proteome Research. 10, 6, p. 2744-2757

    Research output: Contribution to journalArticle

  31. Protein Expression Changes in Ovarian Cancer during the Transition from Benign to Malignant.

    Waldemarson, S., Krogh, M., Alaiya, A., Kirik, U., Schedvins, K., Auer, G., Hansson, K. M., Ossola, R., Aebersold, R., Lee, H., Johan Malmström & Peter James, 2012, In : Journal of Proteome Research. 11, 5, p. 2876-2889

    Research output: Contribution to journalArticle

  32. Prefractionation of cerebrospinal fluid to enhance glycoprotein concentration prior to structural determination with FT-ICR mass spectrometry

    Sihlbom, C., Davidsson, P. & Carol L Nilsson, 2005 Dec 13, In : Journal of Proteome Research. 4, 6, p. 2294-301 8 p.

    Research output: Contribution to journalArticle

  33. Optimized peptide separation and identification for mass spectrometry based proteomics via free-flow electrophoresis

    Johan Malmström, Lee, H., Nesvizhskii, A. I., Shteynberg, D., Mohanty, S., Brunner, E., Ye, M., Weber, G., Eckerskorn, C. & Aebersold, R., 2006 Sep, In : Journal of Proteome Research. 5, 9, p. 2241-9 9 p.

    Research output: Contribution to journalArticle

  34. Omics Analyses Reveal a Potential Link between Hormone-Sensitive Lipase and Polyamine Metabolism.

    Fernandez, C., Krogh, M., Wårell, K., Alm, K., Stina Oredsson, Lo Persson, Peter James & Cecilia Holm, 2009, In : Journal of Proteome Research. 8, p. 5008-5019

    Research output: Contribution to journalArticle

  35. Normalyzer: A Tool for Rapid Evaluation of Normalization Methods for Omics Data Sets

    Chawade, A., Alexandersson, E. & Fredrik Levander, 2014, In : Journal of Proteome Research. 13, 6, p. 3114-3120

    Research output: Contribution to journalArticle

  36. Multimodel Pathway Enrichment Methods for Functional Evaluation of Expression Regulation.

    Kirik, U., Cifani, P., Albrekt, A-S., Malin Lindstedt, Anders Heyden & Fredrik Levander, 2012, In : Journal of Proteome Research. 11, 5, p. 2955-2967

    Research output: Contribution to journalArticle

  37. Molecular Portrait of Breast-Cancer-Derived Cell Lines Reveals Poor Similarity with Tumors.

    Cifani, P., Kirik, U., Waldemarson, S. & Peter James, 2015, In : Journal of Proteome Research. 14, 7, p. 2819-2827

    Research output: Contribution to journalArticle

  38. Mining the Proteome Associated with Rheumatic and Autoimmune Diseases

    Ruiz-Romero, C., Lam, M. P. Y., Nilsson, P., Patrik Önnerfjord, Utz, P. J., Van Eyk, J. E., Venkatraman, V., Fert-Bober, J., Watt, F. E. & Blanco, F. J., 2019 Oct 10, In : Journal of Proteome Research.

    Research output: Contribution to journalArticle

  39. Metabolomic and proteomic analysis of a clonal insulin-producing beta-cell line (INS-1 832/13).

    Celine Fernandez, Krus, U., Hallgard, E., Peter Spégel, Cecilia Holm, Krogh, M., Wårell, K., Peter James & Hindrik Mulder, 2008, In : Journal of Proteome Research. 7, 1, p. 400-411

    Research output: Contribution to journalArticle

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