Peter James

Summary

Affiliation: Lund University
Country: Sweden

Publications

  1. ncbi request reprint Chips for proteomics: a new tool or just hype?
    Peter James
    Lund University, Lund, Sweden
    Biotechniques . 2002
  2. ncbi request reprint Methods for the detection and analysis of protein-protein interactions
    Tord Berggard
    Department of Biophysical Chemistry, Lund University, Lund, Sweden
    Proteomics 7:2833-42. 2007
  3. pmc Protein expression analysis: from "tip of the iceberg" to a global method
    P James
    Wallenberg Laboratory II, Lund University, P O Box 7031, SE 220 07 Lund, Sweden
    Dis Markers 17:235-46. 2001
  4. pmc Automated selected reaction monitoring software for accurate label-free protein quantification
    Johan Teleman
    Protein Technology, Department of Immunotechnology, Lund University, BMC D13, 22184 Lund, Sweden
    J Proteome Res 11:3766-73. 2012
  5. ncbi request reprint Analysis of DIGE data using a linear mixed model allowing for protein-specific dye effects
    Morten Krogh
    Computational Biology and Biological Physics, Department of Theoretical Physics, Lund University, Lund, Sweden
    Proteomics 7:4235-44. 2007
  6. doi request reprint Quantification of membrane proteins using nonspecific protease digestions
    Maria Bendz
    Protein Technology, Department of Immunotechnology, CREATE Health, Lund University, Sweden
    J Proteome Res 8:5666-73. 2009
  7. ncbi request reprint Metabolomic and proteomic analysis of a clonal insulin-producing beta-cell line (INS-1 832/13)
    Celine Fernandez
    Unit of Molecular Endocrinology, Department of Experimental Medical Science, Lund University, Sweden
    J Proteome Res 7:400-11. 2008
  8. doi request reprint Protein expression changes in ovarian cancer during the transition from benign to malignant
    Sofia Waldemarson
    Department of Immunotechnology, Lund University, BMC D13, 221 84 Lund, Sweden
    J Proteome Res 11:2876-89. 2012
  9. pmc Epitope-specificity of recombinant antibodies reveals promiscuous peptide-binding properties
    Niclas Olsson
    Department of Immunotechnology, Lund University, Lund, Sweden
    Protein Sci 21:1897-910. 2012
  10. pmc Proteomic analysis and discovery using affinity proteomics and mass spectrometry
    Niclas Olsson
    Department of Immunotechnology, Lund University, Lund, Sweden, and CREATE Health, BMC D13, Lund, Sweden
    Mol Cell Proteomics 10:M110.003962. 2011

Detail Information

Publications46

  1. ncbi request reprint Chips for proteomics: a new tool or just hype?
    Peter James
    Lund University, Lund, Sweden
    Biotechniques . 2002
  2. ncbi request reprint Methods for the detection and analysis of protein-protein interactions
    Tord Berggard
    Department of Biophysical Chemistry, Lund University, Lund, Sweden
    Proteomics 7:2833-42. 2007
    ..Throughout the review we focus particularly on the advantages and limitations of each method...
  3. pmc Protein expression analysis: from "tip of the iceberg" to a global method
    P James
    Wallenberg Laboratory II, Lund University, P O Box 7031, SE 220 07 Lund, Sweden
    Dis Markers 17:235-46. 2001
    ....
  4. pmc Automated selected reaction monitoring software for accurate label-free protein quantification
    Johan Teleman
    Protein Technology, Department of Immunotechnology, Lund University, BMC D13, 22184 Lund, Sweden
    J Proteome Res 11:3766-73. 2012
    ..Our results show that the label-free SRM workflow with automated data analysis is feasible for large-scale biological studies, opening up new possibilities for quantitative proteomics and systems biology...
  5. ncbi request reprint Analysis of DIGE data using a linear mixed model allowing for protein-specific dye effects
    Morten Krogh
    Computational Biology and Biological Physics, Department of Theoretical Physics, Lund University, Lund, Sweden
    Proteomics 7:4235-44. 2007
    ..The maximal dye effect was a seven-fold change. The dye effects of spots corresponding to the same protein tend to be similar within each of the three experiments, and to a smaller degree across experiments...
  6. doi request reprint Quantification of membrane proteins using nonspecific protease digestions
    Maria Bendz
    Protein Technology, Department of Immunotechnology, CREATE Health, Lund University, Sweden
    J Proteome Res 8:5666-73. 2009
    ..The resulting peptides are modified with a fragmentation-directing isotope labeled tag. We apply the method to quantify differences in membrane protein expression of Bacillus subtilis grown in the presence or absence of glucose...
  7. ncbi request reprint Metabolomic and proteomic analysis of a clonal insulin-producing beta-cell line (INS-1 832/13)
    Celine Fernandez
    Unit of Molecular Endocrinology, Department of Experimental Medical Science, Lund University, Sweden
    J Proteome Res 7:400-11. 2008
    ..This suggests that substrate availability, allosteric regulation, and/or post-translational modifications are more important determinants of metabolite levels than enzyme expression at the protein level...
  8. doi request reprint Protein expression changes in ovarian cancer during the transition from benign to malignant
    Sofia Waldemarson
    Department of Immunotechnology, Lund University, BMC D13, 221 84 Lund, Sweden
    J Proteome Res 11:2876-89. 2012
    ..This work demonstrates the utility of using a shotgun approach to filter out a signature of a few proteins only that discriminates between the different sample groups...
  9. pmc Epitope-specificity of recombinant antibodies reveals promiscuous peptide-binding properties
    Niclas Olsson
    Department of Immunotechnology, Lund University, Lund, Sweden
    Protein Sci 21:1897-910. 2012
    ....
  10. pmc Proteomic analysis and discovery using affinity proteomics and mass spectrometry
    Niclas Olsson
    Department of Immunotechnology, Lund University, Lund, Sweden, and CREATE Health, BMC D13, Lund, Sweden
    Mol Cell Proteomics 10:M110.003962. 2011
    ..In this study, we profiled extracts from human colon tissue, yeast cells lysate, and mouse liver tissue to demonstrate proof-of-concept...
  11. doi request reprint Parallel post-source decay for increasing protein identification confidence levels from 2-D gels
    Asa Wahlander
    Department of Protein Technology, Lund University, Lund, Sweden
    Proteomics 8:1771-9. 2008
    ..We also investigated the use of a charge-directed fragmentation modification reagent to improve the identification rate and confidence levels...
  12. pmc Quantitative proteomics targeting classes of motif-containing peptides using immunoaffinity-based mass spectrometry
    Niclas Olsson
    Department of Immunotechnology, Lund University, Lund, Sweden
    Mol Cell Proteomics 11:342-54. 2012
    ..Taken together, the study demonstrated the potential of our immunoaffinity-based mass spectrometry platform for reproducible quantitative proteomics targeting classes of motif-containing peptides...
  13. doi request reprint Critical comparison of multidimensional separation methods for increasing protein expression coverage
    Linn Antberg
    Protein Technology, Department of Immunotechnology, CREATE Health, Lund University, Sweden
    J Proteome Res 11:2644-52. 2012
    ..We find that the most critical parameters are the data accumulation time, which defines the level of under-sampling and the avoidance of peptides from high expression level proteins eluting over the entire gradient...
  14. pmc Grading breast cancer tissues using molecular portraits
    Niclas Olsson
    Department of Immunotechnology and CREATE Health, Lund University, Medicon Village, SE 223 81 Lund, Sweden
    Mol Cell Proteomics 12:3612-23. 2013
    ..Taken together, these molecular portraits could pave the way for improved classification and prognostication of breast cancer. ..
  15. ncbi request reprint Multisite phosphorylation of adipocyte and hepatocyte phosphodiesterase 3B
    Rebecka Lindh
    Department of Experimental Medical Sciences, Division for Diabetes, Metabolism and Endocrinology, Lund University, Lund, Sweden
    Biochim Biophys Acta 1773:584-92. 2007
    ..Several of the sites were phosphorylated by insulin as well as cAMP-increasing hormones indicating integration of the two signalling pathways upstream of PDE3B, maybe at the level of protein kinase B...
  16. ncbi request reprint A probabilistic treatment of the missing spot problem in 2D gel electrophoresis experiments
    Morten Krogh
    Computational Biology and Biological Physics, Department of Theoretical Physics, Lund University, Sweden
    J Proteome Res 6:3335-43. 2007
    ..We have evaluated this approach in two different gel data sets of different biological origin. An R-program, implementing the algorithm, is freely available at http://bioinfo.thep .lu.se/MissingValues2Dgels.html...
  17. doi request reprint Hunting for protein markers of hypoxia by combining plasma membrane enrichment with a new approach to membrane protein analysis
    Paolo Cifani
    Department of Immunotechnology, CREATE Health, Lund University, Sweden
    J Proteome Res 10:1645-56. 2011
    ..We present previously undescribed membrane proteins expressed under hypoxic conditions that are candidates for evaluation as biomarkers...
  18. ncbi request reprint The protein expression of Streptococcus pyogenes is significantly influenced by human plasma
    Björn P Johansson
    Department of Clinical Sciences, Lund University, Lund, Sweden
    J Proteome Res 4:2302-11. 2005
    ..The pronounced effect of plasma on protein expression, suggests this is an important adaptive mechanism with implications for S. pyogenes pathogenicity...
  19. ncbi request reprint Development of reagents for differential protein quantitation by subtractive parent (precursor) ion scanning
    Asa Wahlander
    Department of Protein Technology, Lund University, Sweden
    J Proteome Res 6:1101-13. 2007
    ..Using the ion-pair ratio, we show that it is possible to select only BSA peptides (with a 3:1 light heavy isotope ratio) for MS/MS when spiked in a whole yeast extract using Parent (precursor) Ion Quantitation Scanning (PIQS) for MS/MS...
  20. ncbi request reprint Automated reporting from gel-based proteomics experiments using the open source Proteios database application
    Fredrik Levander
    Protein Technology, Lund University, BMC D13, Lund, Sweden
    Proteomics 7:668-74. 2007
    ....
  21. doi request reprint Omics analyses reveal a potential link between hormone-sensitive lipase and polyamine metabolism
    Celine Fernandez
    Department of Experimental Medical Science and Lund University Diabetes Center, Lund University, Lund, Sweden
    J Proteome Res 8:5008-19. 2009
    ..The present work also describes a limited correlation between mRNA, protein and metabolite levels, thus, underscoring the importance of integrated approaches...
  22. pmc Altered desaturation and elongation of fatty acids in hormone-sensitive lipase null mice
    Celine Fernandez
    Department of Experimental Medical Science, Lund University, Lund, Sweden
    PLoS ONE 6:e21603. 2011
    ..The aim of this study was to define lipid profiles in plasma, white adipose tissue (WAT) and liver of HSL null mice, in order to better understand the role of this multifunctional enzyme...
  23. ncbi request reprint Large-scale proteomics analysis of human ovarian cancer for biomarkers
    Sofia Bengtsson
    Department of Protein Technology, Lund University, 221 84 Lund, Sweden
    J Proteome Res 6:1440-50. 2007
    ..Currently, we have validated 5 of these antibodies for use in immunohistochemical analysis using tissue microarrays of healthy and diseased ovarian, as well as other, human tissues...
  24. ncbi request reprint Proteomic analysis of striatal proteins in the rat model of L-DOPA-induced dyskinesia
    Barbara Valastro
    Basal Ganglia Pathophysiology Unit, Department of Experimental Medical Science, Lund University, Lund, Sweden
    J Neurochem 102:1395-409. 2007
    ..In conclusion, this study provides new insights into the protein changes occurring in LID...
  25. ncbi request reprint Automated protein identification by the combination of MALDI MS and MS/MS spectra from different instruments
    Fredrik Levander
    Department of Protein Technology, Electrical Measurements, Lund University, Lund, Sweden
    J Proteome Res 4:71-4. 2005
    ..AP-MALDI-IT MS/MS spectra were in general less effective than the MALDI-TOF spectra for protein identification, but the combination of the two methods clearly enhanced the confidence in protein identification...
  26. pmc Binding of calcium ions and SNAP-25 to the hexa EF-hand protein secretagogin
    Annika Rogstam
    Department of Biophysical Chemistry, Lund University, P O Box 124, SE 221 00 Lund, Sweden
    Biochem J 401:353-63. 2007
    ..The comparatively low Ca2+ affinity for secretagogin and the fact that it undergoes Ca2+-induced conformational changes and interacts with SNAP-25 raise the possibility that secretagogin may link Ca2+ signalling to exocytotic processes...
  27. ncbi request reprint Comparison of MS/MS methods for protein identification from 2D-PAGE
    Giorgio Arrigoni
    Department of Protein Technology, Lund University, Sweden
    J Proteome Res 5:2294-300. 2006
    ..The results obtained using the MALDI-MS/MS system are comparable to those from the LC-MS/MS system in terms of accuracy, but less low-level proteins are identified while the time required for the analysis is dramatically reduced...
  28. doi request reprint Strategy for surveying the proteome using affinity proteomics and mass spectrometry
    Christer Wingren
    Department of Immunotechnology, Lund University, Lund, Sweden
    Proteomics 9:1511-7. 2009
    ..The biological sample is digested, exposed to these immobilized antibodies, whereby motif-containing peptides are specifically captured, enriched and subsequently detected and identified using MS...
  29. ncbi request reprint Membrane protein identification: N-terminal labeling of nontryptic membrane protein peptides facilitates database searching
    Maria Jansson
    Department of Protein Technology, BMC D13, Lund University, Lund SE 221 84, Sweden
    J Proteome Res 7:659-65. 2008
    ....
  30. pmc Plasma lipid composition and risk of developing cardiovascular disease
    Celine Fernandez
    Department of Clinical Sciences, Lund University, Malmo, Sweden
    PLoS ONE 8:e71846. 2013
    ....
  31. ncbi request reprint Automating MALDI sample plate loading
    Tomas Andersson
    Divisions of Robotics and Protein Technology, Lund University, SE 221 84 Lund, Sweden
    J Proteome Res 6:894-6. 2007
    ..The soft- and hardware aspects are described together with the various safety issues that need to be addressed. The automation increases throughput by a factor of between 5- and 80-fold...
  32. ncbi request reprint 140 mouse brain proteins identified by Ca2+-calmodulin affinity chromatography and tandem mass spectrometry
    Tord Berggard
    Department of Protein Technology, Lund University, Sölvegatan 33, Wallenberglaboratoriet, SE 221 00 Lund, Sweden
    J Proteome Res 5:669-87. 2006
    ..This study provides a functional framework for studies on these previously uncharacterized proteins...
  33. ncbi request reprint Automated prescan function for scanning fluorescently stained 2D-PAGE gels
    Peter Bäck
    Protein Technology, Wallenberg Laboratory II, Lund University, P O Box 7031, SE 220 07 Lund, Sweden
    J Proteome Res 4:1511-5. 2005
    ..In this work, we describe the implementation and effectiveness of a pre-scan function in a robotic solution for the automation of 2D gel scanning...
  34. pmc WNT5A-mediated β-catenin-independent signalling is a novel regulator of cancer cell metabolism
    Victoria Sherwood
    Cell and Experimental Pathology, Department of Laboratory Medicine, Lund University, Clinical Research Centre, Skane University Hospital, SE 20502 Malmo, Sweden
    Carcinogenesis 35:784-94. 2014
    ..These findings support a new role for WNT5A in the metabolic reprogramming of cancer cells that is a context- dependent event. ..
  35. doi request reprint The International Proteomics Tutorial Programme (IPTP): a teaching tool box for the proteomics community
    Peter James
    Lund University, Lund, Sweden
    Proteomics 11:3596-7. 2011
    ..The programme is being led by Peter James (Sweden), Thierry Rabilloud (France) and Kazuyuki Nakamura (Japan)...
  36. ncbi request reprint Report. Proteomics education, an important challenge for the scientific community: report on the activities of the EuPA Education Committee
    Peter James
    Department of Protein Technology, Lund University, Lund, Sweden
    Proteomics 6:77-81. 2006
    ..These activities include courses (basic and advanced courses and a summer school), workshops, laboratory networking and tutorials...
  37. ncbi request reprint Chemical derivatization of phosphoserine and phosphothreonine containing peptides to increase sensitivity for MALDI-based analysis and for selectivity of MS/MS analysis
    Giorgio Arrigoni
    Department of Protein Technology, Lund University, Lund, Sweden
    Proteomics 6:757-66. 2006
    ..The optimisation of the approach is described for a standard model peptide and protein and then applied to phosphorylation analysis in two biologically derived proteins purified from different experimental systems...
  38. ncbi request reprint Acidic proteome of growing and resting Lactococcus lactis metabolizing maltose
    Johan Palmfeldt
    Applied Microbiology, Lund University, Sweden
    Proteomics 4:3881-98. 2004
    ..lactis is auxotrophic for. L. lactis conserves the protein profile to a high extent, even after prolonged amino acid starvation, so that the protein expression profile of the bacterium remains almost invariant...
  39. doi request reprint Human Proteinpedia enables sharing of human protein data
    Suresh Mathivanan
    Nat Biotechnol 26:164-7. 2008
  40. ncbi request reprint Somatostatin effects on the proteome of the LNCaP cell-line
    Zhaoxu Liu
    Department of Oncology and Pathology, Karolinska Institute, Stockholm, Sweden
    Int J Oncol 30:1173-9. 2007
    ..This could indicate important pathways on which smsdx might be able to curb the progression of HRPC. The results encourage a pending clinical phase II study...
  41. ncbi request reprint Altered chaperone and protein turnover regulators expression in cultured skin fibroblasts from type 1 diabetes mellitus with nephropathy
    Paolo Tessari
    Department of Clinical and Experimental Medicine, Chair of Metabolism, University of Padova, Padova, Italy
    J Proteome Res 6:976-86. 2007
    ..These changes of chaperone-like proteins in fibroblasts may highlight those of the kidney and be patho-physiologically related to the development of nephropathy in T1DM...
  42. ncbi request reprint Promoting proteomics knowledge in Europe: report on the activities of the EuPA Education Committee 2006-2007
    Juan Pablo Albar
    ProteoRed, Centro Nacional de Biotecnologia, Madrid, Spain
    Proteomics 7:90-4. 2007
    ..Another important event has been the merger of the EuPA and HUPO (Human Proteome Organisation) Education Committees into a single one in order to combine ideas and ef for ts that will favour global education in proteomics...
  43. ncbi request reprint Automated methods for improved protein identification by peptide mass fingerprinting
    Fredrik Levander
    Department of Protein Technology, Lund University, Sweden
    Proteomics 4:2594-601. 2004
    ..The results indicate that identification of especially small and low-abundance proteins could be significantly improved after sequential digestions with two enzymes...
  44. ncbi request reprint Biomarker discovery: a proteomic approach for brain cancer profiling
    Ashraf A Khalil
    Department of Protein Technology, Mubarak City for Scientific Research, Alexandria 21934, Egypt
    Cancer Sci 98:201-13. 2007
    ..These differentially expressed proteins provided novel information on the differences existing between normal brain and gliomas, and thus might prove to be useful molecular indicators of diagnostic or prognostic value...
  45. ncbi request reprint Automating gel image acquisition
    Peter Bäck
    Division of Robotics, Lund University, Lund, Sweden
    J Proteome Res 2:662-4. 2003
    ..We describe the design and implementation of a robotic solution to automate the acquisition of gel images. The soft- and hardware aspects are outlined together with the various safety aspects that need to be addressed...
  46. ncbi request reprint [From genome to proteome--aim of human proteomics]
    Kazuyuki Nakamura
    Department of Biochemistry and Biomolecular Recognition, Fatulty of Medicine, Yamaguchi University, 1 1 1 Minami kogushi, Ube, Yamaguchi 755 8505, Japan
    Seikagaku 76:1271-4. 2004