Journal of Proteome Research, 1535-3893

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  2. Biology/Disease-Driven Initiative on Protein-Aggregation Diseases of the Human Proteome Project: Goals and Progress to Date

    Boersema, P. J., Melnik, A., Hazenberg, B. P. C., Melinda Rezeli, György Marko-Varga, Kamiie, J., Portelius, E., Blennow, K., Zubarev, R. A., Polymenidou, M. & Picotti, P., 2018 Dec 7, In : Journal of Proteome Research. 17, 12, p. 4072-4084

    Research output: Contribution to journalArticle

  3. 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

  4. Blood Metabolic Signatures of Body Mass Index: A Targeted Metabolomics Study in the EPIC Cohort

    Carayol, M., Leitzmann, M. F., Ferrari, P., Zamora-Ros, R., Achaintre, D., Stepien, M., Schmidt, J. A., Travis, R. C., Overvad, K., Tjønneland, A., Hansen, L., Kaaks, R., Kühn, T., Boeing, H., Bachlechner, U., Trichopoulou, A., Bamia, C., Palli, D., Agnoli, C., Tumino, R. & 18 othersVineis, P., Panico, S., Quirós, J. R., Sánchez-Cantalejo, E., Huerta, J. M., Ardanaz, E., Arriola, L., Agudo, A., Nilsson, J., Olle Melander, Bueno de Mesquita, B., Peeters, P. H., Wareham, N., Khaw, K-T., Jenab, M., Key, T. J., Scalbert, A. & Rinaldi, S., 2017 Sep 1, In : Journal of Proteome Research. 16, 9, p. 3137-3146 10 p.

    Research output: Contribution to journalArticle

  5. Improvements in Mass Spectrometry Assay Library Generation for Targeted Proteomics

    Teleman, J., Hauri, S. & Johan Malmström, 2017 Jul 7, In : Journal of Proteome Research. 16, 7, p. 2384-2392 9 p.

    Research output: Contribution to journalArticle

  6. Identification of a Novel Autoimmune Peptide Epitope of Prostein in Prostate Cancer

    Pin, E., Henjes, F., Hong, M. G., Wiklund, F., Magnusson, P., Anders Bjartell, Uhlén, M., Nilsson, P. & Schwenk, J. M., 2017 Jan 6, In : Journal of Proteome Research. 16, 1, p. 204-216 13 p.

    Research output: Contribution to journalArticle

  7. FK506, an Immunosuppressive Drug, Induces Autophagy by Binding to the V-ATPase Catalytic Subunit A in Neuronal Cells

    Kim, D., Hwang, H. Y., Kim, Y. J., Lee, J. Y., Yoo, J. S., György Marko-Varga & Kwon, H. J., 2017 Jan 6, In : Journal of Proteome Research. 16, 1, p. 55-64 10 p.

    Research output: Contribution to journalArticle

  8. Dinosaur: A Refined Open-Source Peptide MS Feature Detector

    Teleman, J., Chawade, A., Sandin, M., Fredrik Levander & Johan Malmström, 2016 Jul 1, In : Journal of Proteome Research. 15, 7, p. 2143-2151 9 p.

    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. Elucidating the Molecular Composition of Cartilage by Proteomics

    Hsueh, M. F., Khabut, A., Sven Kjellström, Patrik Önnerfjord & Kraus, V. B., 2016 Feb 5, In : Journal of Proteome Research. 15, 2, p. 374-388 15 p.

    Research output: Contribution to journalArticle

  11. 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

  12. Integrated Transcriptomic and Glycomic Profiling of Glioma Stem Cell Xenografts

    Wildburger, N. C., Zhou, S., Zacharias, L. G., Kroes, R. A., Moskal, J. R., Schmidt, M., Mirzaei, P., Gumin, J., Lang, F., Mechref, Y. & Carol Nilsson, 2015 Sep 4, In : Journal of Proteome Research. 14, 9, p. 3932-9 8 p.

    Research output: Contribution to journalArticle

  13. ESI-MS/MS and MALDI-IMS Localization Reveal Alterations in Phosphatidic Acid, Diacylglycerol, and DHA in Glioma Stem Cell Xenografts

    Wildburger, N. C., Wood, P. L., Gumin, J., Lichti, C. F., Emmett, M. R., Lang, F. & Carol L Nilsson, 2015 Jun 5, In : Journal of Proteome Research. 14, 6, p. 2511-9 9 p.

    Research output: Contribution to journalArticle

  14. Data Processing Has Major Impact on the Outcome of Quantitative Label-Free LC-MS Analysis

    Chawade, A., Sandin, M., Teleman, J., Johan Malmström & Fredrik Levander, 2015, In : Journal of Proteome Research. 14, 2, p. 676-687

    Research output: Contribution to journalArticle

  15. Integration of Proteomics and Transcriptomics Data Sets for the Analysis of a Lymphoma B-Cell Line in the Context of the Chromosome-Centric Human Proteome Project

    Diez, P., Droste, C., Degano, R. M., Gonzalez-Munoz, M., Ibarrola, N., Perez-Andres, M., Garin-Muga, A., Segura, V., György Marko-Varga, LaBaer, J., Orfao, A., Corrales, F. J., De Las Rivas, J. & Fuentes, M., 2015, In : Journal of Proteome Research. 14, 9, p. 3530-3540

    Research output: Contribution to journalArticle

  16. 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

  17. 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 othersCasal, 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

  18. An Integrated Workflow for Multiplex CSF Proteomics and Peptidomics-Identification of Candidate Cerebrospinal Fluid Biomarkers of Alzheimer's Disease

    Holtta, M., Lennart Minthon, Oskar Hansson, Holmen-Larsson, J., Pike, I., Ward, M., Kuhn, K., Ruetschi, U., Zetterberg, H., Blennow, K. & Gobom, J., 2015, In : Journal of Proteome Research. 14, 2, p. 654-663

    Research output: Contribution to journalArticle

  19. 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 othersMoskal, J., Berven, F., Fehniger, T. & György Marko-Varga, 2015, In : Journal of Proteome Research. 14, 2, p. 603-608

    Research output: Contribution to journalArticle

  20. A Combined Shotgun and Targeted Mass Spectrometry Strategy for Breast Cancer Biomarker Discovery

    Martin Sjöström, Ossola, R., Breslin, T., Rinner, O., Malmstroem, L., Schmidt, A., Aebersold, R., Johan Malmström & Emma Niméus, 2015, In : Journal of Proteome Research. 14, 7, p. 2807-2818

    Research output: Contribution to journalArticle

  21. 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

  22. In vitro Transcription/Translation System: A Versatile Tool in the Search for Missing Proteins

    Horvatovich, P., Végvári, Á., Saul, J., Park, J., Qiu, J., Syring, M., Pirrotte, P., Petritis, K., Tegeler, T., Aziz, M., Fuentes, M., Diez, P., Gonzalez-Gonzalez, M., Ibarrola, N., Droste, C., De Las Rivas, J., Gil, C., Clemente, F., Hernaez, M. L., Corrales, F. & 6 othersNilsson, C., Berven, F., Bischoff, R., Fehniger, T., LaBaer, J. & György Marko-Varga, 2015, In : Journal of Proteome Research. 14, 9, p. 3441-3451

    Research output: Contribution to journalArticle

  23. Development of Phage-Based Antibody Fragment Reagents for Affinity Enrichment of Bacterial Immunoglobulin G Binding Proteins.

    Säll, A., Sjöholm, K., Waldemarson, S., Lotta Happonen, Christofer Karlsson, Persson, H. & Johan Malmström, 2015, In : Journal of Proteome Research. 14, 11, p. 4704-4713

    Research output: Contribution to journalArticle

  24. 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

  25. AFFIRM – a multiplexed immunoaffinity platform that combines recombinant antibody fragments and LC-SRM analysis

    Säll, A., Carlsson, F., Olsson, N., Christer Wingren, Mats Ohlin, Persson, H. & Waldemarson, S., 2014, In : Journal of Proteome Research. 13, 12, p. 5837-5847

    Research output: Contribution to journalArticle

  26. 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

  27. Integrated Chromosome 19 Transcriptomic and Proteomic Datasets Derived from Six Glioma-Derived Cancer Stem Cell Lines

    Lichti, C., Liu, H., Shavkunov, A. S., Mostovenko, E., Sulman, E. P., Ezhilarasan, R., Wang, Q., Kroes, R., Moskal, J. C., Fenyö, D., Oksuz, B. A., Conrad, C. A., Lang, F. F., Berven, F. S., Végvári, Á., Melinda Rezeli, György Marko-Varga, Hober, S. & Nilsson, C. L., 2014, In : Journal of Proteome Research. 13, 1, p. 191-199

    Research output: Contribution to journalArticle

  28. Assessment of Peptide Chemical Modifications on the Development of an Accurate and Precise Multiplex Selected Reaction Monitoring Assay for Apolipoprotein E Isoforms

    Martinez-Morillo, E., Nielsen, H., Batruch, I., Drabovich, A. P., Begcevic, I., Lopez, M. F., Lennart Minthon, Bu, G., Mattsson, N., Portelius, E., Oskar Hansson & Diamandis, E. P., 2014, In : Journal of Proteome Research. 13, 2, p. 1077-1087

    Research output: Contribution to journalArticle

  29. 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

  30. Confirmation of Protein Biomarkers of Corticosteroids Treatment in Veal Calves Sampled under Field Conditions

    Stella, R., Arrigoni, G., Biancotto, G., Krogh, M., Vascellari, M., Lega, F., Pozza, G., Angeletti, R., Andrighetto, I. & Peter James, 2014, In : Journal of Proteome Research. 13, 4, p. 1794-1799

    Research output: Contribution to journalArticle

  31. 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

  32. A modified database search strategy leads to improved identification of in vitro brominated peptides spiked into a complex proteomic sample

    Liu, H., Lichti, C. F., Mirfattah, B., Frahm, J. & Carol L Nilsson, 2013 Sep 6, In : Journal of Proteome Research. 12, 9, p. 4248-54 7 p.

    Research output: Contribution to journalArticle

  33. A First Step Toward Completion of a Genome-Wide Characterization of the Human Proteome.

    György Marko-Varga, Omenn, G. S., Paik, Y-K. & Hancock, W. S., 2013, In : Journal of Proteome Research. 12, 1, p. 1-5

    Research output: Contribution to journalArticle

  34. Blood Plasma Reference Material – A Global Resource for Proteomic Research

    Johan Malm, Danmyr, P., Nilsson, R., Roger Appelqvist, Végvári, Á. & György Marko-Varga, 2013, In : Journal of Proteome Research. 12, 7, p. 3087-3092

    Research output: Contribution to journalArticle

  35. Experimental Models to Study Drug Distributions in Tissue Using MALDI Mass Spectrometry

    Végvári, Á., Fehniger, T. E., Melinda Rezeli, Thomas Laurell, Döme, B., Jansson, B., Charlotte Welinder & György Marko-Varga, 2013, In : Journal of Proteome Research. 12, 12, p. 5626-5633

    Research output: Contribution to journalArticle

  36. 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

  37. 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

  38. Determination of Phosphorylation Sites in the DivIVA Cytoskeletal Protein of Streptomyces coelicolor by Targeted LC-MS/MS

    Saalbach, G., Hempel, A. M., Vigouroux, M., Klas Flärdh, Buttner, M. J. & Naldrett, M. J., 2013, In : Journal of Proteome Research. 12, 9, p. 4187-4192

    Research output: Contribution to journalArticle

  39. 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

  40. Chromosome 19 Annotations with Disease Speciation - A First Report from the Global Research Consortium

    Nilsson, C. L., Berven, F., Selheim, F., Liu, H., Moskal, J. F., Kroes, R. A., Sulman, E. P., Conrad, C. A., Lang, F. F., Andrén, P. E., Nilsson, A., Carlsohn, E., Lilja, H., Malm, J., Fenyö, D., Subramaniyam, D., Wang, X., Gonzales-Gonzales, M., Dasilva, N., Diez, P. & 11 othersFuentes, M., Végvári, Á., Sjödin, K., Charlotte Welinder, Thomas Laurell, Fehniger, T., Henrik Lindberg, Melinda Rezeli, Edula, G., Hober, S. & György Marko-Varga, 2013, In : Journal of Proteome Research. 12, 1, p. 135-150

    Research output: Contribution to journalArticle

  41. 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

  42. Contribution of Antibody-based Protein Profiling to the Human Chromosome-centric Proteome Project (C-HPP)

    Fagerberg, L., Oksvold, P., Skogs, M., Algenas, C., Lundberg, E., Ponten, F., Sivertsson, A., Odeberg, J., Klevebring, D., Kampf, C., Asplund, A., Sjostedt, E., Szigyarto, C. A-K., Edqvist, P-H., Olsson, I., Rydberg, U., Hudson, P., Takanen, J. O., Berling, H., Bjorling, L. & 12 othersTegel, H., Rockberg, J., Nilsson, P., Navani, S., Karin Jirström, Mulder, J., Schwenk, J. M., Zwahlen, M., Hober, S., Forsberg, M., von Feilitzen, K. & Uhlen, M., 2013, In : Journal of Proteome Research. 12, 6, p. 2439-2448

    Research output: Contribution to journalArticle

  43. Automated Workflow for Large-Scale Selected Reaction Monitoring Experiments

    Malmstrom, L., Johan Malmström, Selevsek, N., Rosenberger, G. & Aebersold, R., 2012, In : Journal of Proteome Research. 11, 3, p. 1644-1653

    Research output: Contribution to journalArticle

  44. 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 othersBergeron, J., Salekdeh, G. H. & Hancock, W. S., 2012, In : Journal of Proteome Research. 11, 4, p. 2005-2013

    Research output: Contribution to journalArticle

  45. Critical Comparison of Multidimensional Separation Methods for Increasing Protein Expression Coverage

    Antberg, L., Cifani, P., Sandin, M., Fredrik Levander & Peter James, 2012, In : Journal of Proteome Research. 11, 5, p. 2644-2652

    Research output: Contribution to journalArticle

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