PROBE Publications

2012 (5)

Koehler CJ, Arntzen MO, Treumann A, Thiede B: Comparison of data analysis parameters and MS/MS fragmentation techniques for quantitative proteome analysis using isobaric peptide termini labeling (IPTL). Anal Bioanal Chem. (in press) *

Oveland E, Wergeland L, Hovland R, Lorens JB, Gjertsen BT, Fladmark KE: Ectopic expression of Flt3 kinase inhibits proliferation and promotes cell death in different human cancer cell lines. Cell Biol Toxicol. (in press)

Aye, Thin Thin; Low, Teck; Bjørlykke, Yngvild; Barsnes, Harald; Heck, Albert; Berven, Frode: Stable isotope dimethyl labeling coupled to selected reaction monitoring enhances throughput by multiplexing relative quantitation of targeted proteins. Analytical Chemistry. (in press)

Sandvig K and Llorente A: Proteomic analysis of microvesicles released by the human prostate cancer cell line PC-3. Mol Cell Proteomics. (in press) *

Mjaavatten O, Nygaard G, Berven F and Selheim F: Minimization of side reactions during Lys Tag derivatization of C-terminal lysine peptides. Analytica Chimica Acta. 2012 Jan 27;712:101-7.

2011 (20)

Kamil A, Falk K, Sharma A, Raae A, Berven FS, Koppang EO, Hordvik I.: A monoclonal antibody distinguishes between two IgM heavy chain isotypes in Atlantic salmon and brown trout: Protein characterization, 3D modeling and epitope mapping. Mol Immunol. 2011 Sep;48(15-16):1859-67.

Colaert N., Barsnes H., Vaudel M., Helsens K., Timmerman E., Sickmann A., Gevaert K., Martens L.: thermo-msf-parser: an open source java library to parse and visualize Thermo Proteome Discoverer msf files. J Proteome Res. 2011 Aug 5;10(8):3840-3.

Teunissen C., Tumani H., Bennett J., Berven F.S., et al.: Consensus guidelines for CSF and blood biobanking for CNS biomarker studies. Multiple Sclerosis International, Volume 2011 (2011), Article ID 246412, 9 pages, doi:10.1155/2011/246412.

Fridén V, Oveland E, Tenstad O, Ebefors K, Nyström J, Nilsson UA, Haraldsson B: The glomerular endothelial cell coat is essential for glomerular filtration. Kidney Int. 2011 Jun;79(12):1322-30.

Berle, M; Kroksveen, AC; Haaland, ØA; Aye, TT; Opsahl, JA; Oveland, E; Wester, K; Ulvik, RJ; Helland, CA; Berven, FS: Protein profiling reveals inter-individual protein homogeneity of arachnoid cyst fluid and high qualitative similarity to cerebrospinal fluid. Fluids Barriers CNS. 2011 May 20;8(1):19.

Herfindal L, Myhren L, Kleppe R, Krakstad C, Selheim F, Jokela J, Sivonen K, Døskeland SO: Nostocyclopeptide-M1: A Potent, Nontoxic Inhibitor of the Hepatocyte Drug Transporters OATP1B3 and OATP1B1. Mol Pharm. 2011 Apr 4;8(2):360-7.

Barsnes, H.; Vaudel, M.; Colaert, N.; Helsens, K.; Sickmann, A.; Berven, F.S.; Martens, L.: compomics-utilities: an open-source Java library for computational proteomics. BMC Bioinformatics. 2011 Mar 8;12(1):70.

Barsnes, H.; Eidhammer I.; Martens L.: A global analysis of peptide fragmentation variability. Proteomics. 2011 Mar;11(6):1181-8.

Vaudel M.; Barsnes, H., Berven, F.S.; Sickmann, A; Martens, L.: SearchGUI: An open-source graphical user interface for simultaneous OMSSA and X!Tandem searches. Proteomics 2011. 11(5):996-9.

Arntzen, M.; Koehler, C.; Barsnes, H.; Berven, F; Treumann, A.; Thiede, B.: IsobariQ: software for isobaric quantitative proteomics using IPTL, iTRAQ and TMT. J Proteome Res. 2011 Feb 4;10(2):913-20.

Calvo, A.C.; Pey, A.L.; Miranda-Vizuete, A.; Døskeland, A.P.; Martinez, A.: Divergence in enzyme regulation between C. elegans and human tyrosine hydroxylase, the key enzyme in the synthesis of dopamine. Biochem J. 2011 Jan 27;434(1):133-41.

Jensen, B.O, Kleppe R, Kopperud R, Nygard G, Døskeland S.O, Holmsen H and Selheim F: Dipyramidole synergizes with nitric oxide to prfolong inhibition of thrombin-induced platelet shape change in a PKG-independent manner. Platelets 2011;22(1):7-18.

Aurélia E Lewis, Lilly Sommer, Magnus Ø Arntzen, Yvan Strahm, Nicolas A. Morrice, Nullin Divecha and Clive S D’Santos. Identification of nuclear phosphatidylinositol 4,5-bisphosphate-interacting proteins by neomycin extraction. Mol Cell Proteomics 2011 Feb;10(2):M110.003376.

Kroksveen A.C.; Opsahl, J.A.; Aye T.T.; Ulvik R.J.; Berven F.S.: Proteomics of human cerebrospinal fluid. Discovery and verification of disease biomarker candidates in neurodegenerative diseases using quantitative proteomics. J Proteomics. 2011 Apr 1;74(4):371-88.

Odd Andre Karlsen, Frode S. Berven, June Iren Bagstevold, Øivind Larsen, and Harald B. Jensen: Methylococcus capsulatus (Bath): From Genome to protein function, and vice versa. Methods Enzymol. 2011;495:63-79.

Odd A. Karlsen, Frode S. Berven, Harald B. Jensen and Anne Fjellbirkeland: Methanotroph outer membrane preparation. Methods Enzymol. 2011;495:167-76.

Kleppe R, Krakstad C, Selheim F, Kopperud R, and Døskeland SO: The cAMP-dependent protein kinase pathway as therapeutic target – possibilities and pitfalls. Curr Top Med Chem. 2011;11(11):1393-405.

Oftedal L, Skjærven KH, Coyne RT, Edvardsen B, Rohrlack T, Skulberg OM, Døskeland SO, Herfindal L: The apoptosis-inducing activity towards leukemia and lymphoma cells in a cyanobacterial culture collection is not associated with mouse bioassay toxicity. J Ind Microbiol Biotechnol. 2011 Apr;38(4):489-501. *

de Souza GA, Arntzen MO, Fortuin S, Schürch AC, Målen H, McEvoy CR, van Soolingen D, Thiede B, Warren RM, Wiker HG: Proteogenomic analysis of polymorphisms and gene annotation divergences in prokaryotes using a clustered mass spectrometry-friendly database. Mol Cell Proteomics. 2011 Jan;10(1):M110.002527.

Ardawatia VV, Masià-Balagué M, Krakstad BF, Johansson BB, Kreitzburg KM, Spriet E, Lewis AE, Meigs TE, Aragay AM: Gα(12) binds to the N-terminal regulatory domain of p120(ctn), and downregulates p120(ctn) tyrosine phosphorylation induced by Src family kinases via a RhoA independent mechanism. Exp Cell Res. 2011 Feb 1;317(3):293-306.

2010 (13)

de Souza GA, Fortuin S, Aguilar D, Pando RH, McEvoy CR, van Helden PD, Koehler CJ, Thiede B, Warren RM and Wiker, HG: Using a label-free proteomic method to identify differentially abundant proteins in closely related hypo- and hyper-virulent clinical Mycobacterium tuberculosis Beijingi solates. Mol Cell Proteomics. 2010 Nov; 9(11):2414-23.

Målen, H.; Pathak, S., Søfteland, T.; de Souza, G.A. and Wiker, H.G.: Definition of novel cell envelope associated proteins in Triton X-114 extracts of Mycobacterium tuberculosis H37Rv. BMC Microbiol. 2010 Apr 29;10:132.

Jokela J, Herfindal L, Wahlsten M, Permi P, Selheim F, Vasconçelos V, Døskeland SO, Sivonen K.: A novel cyanobacterial nostocyclopeptide is a potent antitoxin against microcystins. Chembiochem. 2010 Jul 26;11(11):1594-9.

Berle M, Wester KG, Ulvik RJ, Kroksveen AC, Haaland OA, Amiry-Moghaddam M, Berven FS, Helland CA: Arachnoid cysts do not contain cerebrospinal fluid: A comparative chemical analysis of arachnoid cyst fluid and cerebrospinal fluid in adults. Cerebrospinal Fluid Res. 2010 Jun 10;7:8.

Rajalahti T, Kroksveen AC, Arneberg R, Berven FS, Vedeler CA, Myhr KM, Kvalheim OM: A multivariate approach to reveal biomarker signatures for disease classification: application to mass spectral profiles of cerebrospinal fluid from patients with multiple sclerosis. J Proteome Res. 2010 Jul 2;9(7):3608-20.

Opsahl JA, Hjørnevik LV, Bull VH, Fismen L, Frøyset AK, Gromyko D, Solstad T, Fladmark KE: Increased interaction between DJ-1 and the Mi-2/ nucleosome remodelling and deacetylase complex during cellular stress. Proteomics. 2010 10,1494-504.

de Souza, G.A.; Arntzen, M.O. and Wiker, H.G. MSMSpdbb: Providing protein databases of closely related organisms to improve proteomic characterization of prokaryotic microbes. Bioinformatics 2010, 26(5), p 698-9, 2010.

Tomazella, G.G.; da Silva, I; Thome, C.H.; Greene, L.J.; Koehler, C.J.; Thiede, B.; Wiker, H.G. and de Souza, G.A.: Analysis of detergent-insoluble and whole cell lysate fractions of resting neutrophils using high-resolution mass spectrometry. J Proteome Res 9(4), p 2030-6, 2010.

Carpenter, J.E.; Jackson, W.; de Souza, G.A.; Haarr, L. and Grose, C.: Insulin degrading enzyme binds to the nonglycosylated precursor of varicella zoster virus gE protein found in the endoplasmic reticulum. J Virology 84(2), p 857-55, 2010.

de Souza, G.A. and Wiker, H.G.: Proteomic approaches to study immunity in infection. Invited as part of book chapter in Methods in Microbiology 37, Eds Dietrich Kabelitz and Stefan Kaufmann. Elsevier p 101-114, 2010.

Aumo L, Rusten M, Mellgren G, Bakke M, Lewis AE: Functional roles of protein kinase A (PKA) and exchange protein directly activated by 3',5'-cyclic adenosine 5'-monophosphate (cAMP) 2 (EPAC2) in cAMP-mediated actions in adrenocortical cells. Endocrinology. 2010 May;151(5):2151-61.

Hoivik EA, Lewis AE, Aumo L, Bakke M: Molecular aspects of steroidogenic factor 1 (SF-1). Mol Cell Endocrinol. 2010 Feb 5;315(1-2):27-39.

Linn Oftedal, Frode Selheim, Matti Wahlsten, Kaarina Sivonen, Stein Ove Døskeland, and Lars Herfindal: Marine Benthic Cyanobacteria Contain Apoptosis-Inducing Activity Synergizing with Daunorubicin to Kill Leukemia Cells, but not Cardiomyocytes. Mar. Drugs 2010, 8(10), 2659-2672. 

2009 (9)

Prestegard SK, Oftedal L, Coyne RT, Nygaard G, Skjaerven KH, Knutsen G, Døskeland SO, Herfindal L: Marine benthic diatoms contain compounds able to induce leukemia cell death and modulate blood platelet activity. Mar Drugs. 2009 Nov 18;7(4):605-23.

Birkeland E, Nygaard G, Oveland E, Mjaavatten O, Ljones M, Doskeland SO, Krakstad C and Selheim F.: Epac-induced Alterations in the Proteome of Human SH-SY5Y Neuroblastoma Cells. J Proteomics Bioinform 2009 June 8: 244-254.

Oveland E, Gjertsen BT, Wergeland L, Selheim F, Fladmark KE, Hovland R.: Ligand-induced Flt3-downregulation modulates cell death associated proteins and enhances chemosensitivity to idarubicin in THP-1 acute myeloid leukemia cells. Leuk Res. 2009 Feb;33(2):276-87

Kellmann R, Schaffner CA, Grønset TA, Satake M, Ziegler M, Fladmark KE.: Proteomic response of human neuroblastoma cells to azaspiracid-1. J Proteomics. 2009 May 2;72(4):695-707.

Tomazella GG, da Silva I, Laure HJ, Rosa JC, Chammas R, Wiker HG, de Souza GA, Greene LJ.: Proteomic analysis of total cellular proteins of human neutrophils. Proteome Sci. 2009 Aug 31;7(1):32.

Pathak S, De Souza GA, Salte T, Wiker HG, Asjö B.: HIV induces both a down-regulation of IRAK-4 that impairs TLR signalling and an up-regulation of the antibiotic peptide dermcidin in monocytic cells. Scand J Immunol. 2009 Sep;70(3):264-76.

de Souza GA, Søfteland T, Koehler CJ, Thiede B, Wiker HG.: Validating divergent ORF annotation of the Mycobacterium leprae genome through a full translation data set and peptide identification by tandem mass spectrometry. Proteomics. 2009 Jun;9(12):3233-43.

Leversen NA, de Souza GA, Målen H, Prasad S, Jonassen I, Wiker HG.: Evaluation of signal peptide prediction algorithms for identification of mycobacterial signal peptides using sequence data from proteomic methods. Microbiology. 2009 Jul;155(Pt 7):2375-83.

Arntzen  MØ, Osland CL, Rasch-Olsen Raa  C, Kopperud R, Doskeland  SO, Lewis AE, and D’Santos CS: POSTMan (POST-translational Modification analysis); a software application for PTM discovery. Proteomics (2009), 9: 1400–1406. 

2008 (7)

Gausdal G, Gjertsen BT, McCormack E, Van Damme P, Hovland R, Krakstad C, Bruserud Ø, Gevaert K, Vandekerckhove J, Døskeland SO: Abolition of stress-induced protein synthesis sensitizes leukemia cells to anthracycline-induced death. Blood. 2008 Mar 1;111(5):2866-77. Epub 2008 Jan 8.

Solstad T, Fismen L, Garberg H, Fladmark KE.: Identification of a novel phosphorylation site of acyl-CoA binding protein (ACBP) in nodularin-induced apoptotic hepatocytes. Exp Cell Res. 2008 Jun 10;314(10):2141-9.

Malen H, Berven FS, Softeland T, Arntzen MØ, D’Santos CS, De Souza G and Wiker H.: Membrane- and membrane associated proteins in Triton X-114 extracts of Mycobacterium bovis BCG identified using a combination of gel-based and gel-free fractionation strategies. Proteomics (2008) 8:1859-70.

Winge I, McKinney JA, Ying M, D'Santos CS, Kleppe R, Knappskog PM and Haavik J.: Activation and stabilization of human tryptophan hydroxylase 2 by phosphorylation and 14-3-3 binding. Biochemistry Journal. (2008) 410:195-204.

Chekenya M, Krakstad C, Svendsen A, Netland IA, Staalesen V, Tysnes BB, Selheim F, Wang J et al.: The progenitor cell marker NG2/MPG promotes chemoresistance by activation of integrin-dependent PI3K/Akt signaling. Oncogene. 2008 Sep 4;27(39):5182-94.

de Souza GA, Målen H, Søfteland T, Saelensminde G, Prasad S, Jonassen I, Wiker HG.: High accuracy mass spectrometry analysis as a tool to verify and improve gene annotation using Mycobacterium tuberculosis as an example. BMC Genomics. 2008 Jul 2;9:316.

Målen H, Søfteland T, Wiker HG.: Antigen analysis of Mycobacterium tuberculosis H37Rv culture filtrate proteins. Scand J Immunol. 2008 Mar;67(3):245-52. Epub 2008 Jan 16. 

2007 (7)

Flikka K, Meukens J, Helsens K, Vandekerckhove J, Eidhammer I, Gevaert K, Martens L: Implementation and application of a versatile clustering tool for tandem mass spectrometry data. Proteomics. 2007 Sep;7(18):3245-58.

Tait SW, de Vries E, Maas C, Keller AM, D'Santos CS and Borst J.: Apoptosis induction by Bid requires unconventional ubiquitination and degradation of its N-terminal fragment. J Cell Biol. (2007) 179:1453-66.

Kool J, Reubsaet L, Wesseldijk F,  Maravilha RT, Pinkse MW, D’Santos CS, van Hilten R, Zijlstra FJ, and Heck AJ.: Suction blister fluid as a potential biological matrix for biomarker proteins. Proteomics. (2007)  7: 3638-50.

Arneberg R, Rajalahti T, Flikka K, Berven FS, Kroksveen AC, Berle M, Myhr KM, Vedeler CA, Ulvik RJ, Kvalheim OM.: Pretreatment of mass spectral profiles: application to proteomic data. Anal Chem. 2007 Sep 15;79(18):7014-26.

Målen H, Berven FS, Fladmark KE, Wiker HG.: Comprehensive analysis of exported proteins from Mycobacterium tuberculosis H37Rv. Proteomics. 2007 May;7(10):1702-18.

Aukrust I, Evensen L, Hollås H, Berven F, Atkinson RA, Travé G, Flatmark T, Vedeler A.: Engineering, biophysical characterisation and binding properties of a soluble mutant form of annexin A2 domain IV that adopts a partially folded conformation. J Mol Biol. 2006 Oct 20;363(2):469-81.

Berven FS, Kroksveen AC, Berle M, Rajalahti T, Flikka K, Arneberg R, Myhr KM, Vedeler C, Kvalheim OM, Ulvik RJ: Pre-analytical influence on the low molecular weight cerebrospinal fluid proteome. Proteomics Clin Appl Volume 1 Issue 7, Pages 699 - 711. 

2006 (15)

Sjøholt, G., Bedringaas, S.L., Døskeland, A.P. and Gjertsen, B.T.: Proteomic Strategies for Individualizing Therapy of Acute Myeloid Leukemia (AML). Curr. Pharm. Biotechnol. 2006; 7:159-170.

Døskeland, A.P.: A method for simple identification of signature peptides derived from polyUb-K48 and K63 by MALDI-TOF MS and chemically assisted MS/MS fragmentation. Amino Acids 2006; 30, 99-103.

Krakstad C, Herfindal L, Gjertsen BT, Bøe R, Vintermyr OK, Fladmark KE, Døskeland SO: CaM-kinaseII-dependent commitment to microcystin-induced apoptosis is coupled to cell budding, but not to shrinkage or chromatin hypercondensation. Cell Death Differ. 2006 Jul;13(7):1191-202. Epub 2005 Nov 25.

Solstad T, Fladmark KE: Algal toxins as guidance to identify phosphoproteins with key roles in apoptotic cell death. Curr Pharm Biotechnol. 2006 Jun;7(3):209-15.

Oveland E, Fladmark KE, Wergeland L, Gjertsen BT, Hovland R: Proteomics approaches to elucidate oncogenic tyrosine kinase signaling in myeloid malignancies.  Curr Pharm Biotechnol. 2006 Jun;7(3):185-98.

Flikka K, Martens L, Vandekerckhove J, Gevaert K, Eidhammer I. Improving the reliability and throughput of mass spectrometry-based proteomics by spectrum quality filtering. Proteomics. 2006 Apr;6(7):2086-94. 

Halstead J, van Rheenen J, Snel M, Meeuws S, Mohammed S, D'Santos CS, Heck AJ, Jalink K and Divecha N.: A Role for PtdIns(4,5)P2 and PIP5K? in Regulating Stress-Induced Apoptosis. Current Biology, (2006) 16: 1850-1856.

Jones D, Bultsma Y, Keune W, Halstead J, Elouarrat D, Mohammed S, Heck AJ, D'Santos CS, and Divecha N.: Nuclear PtdIns5P as a Transducer of Stress Signaling: An In Vivo Role for PIP4Kbeta. Molecular Cell, (2006)  23: 685-695.

Ånensen N, Haaland I, D’Santos CS, Van Belle W, and Gjertsen BT.: Proteomics of p53 in diagnostics and therapy of Acute Myeloid Leukemia. Current Pharmaceutical Biotechnology (2006) 7: 199-207.

Herfindal L and Selheim F.: Microcystin produces disparate effects on liver cells in a dose dependent manner. Mini Rev Med Chem. 2006 Mar;6(3):279-85.

Fladmark  K.E. and Selheim F.: PROBE – nasjonal platform for proteomikk. NBS – nytt 3/2006: 32-35. (without per-reviewer) .

Selheim F.: Proteomic Technologies in Translational medicine. Curr Pharm Biotechnol. 2006 Jun;7(3): (Editorial) 133.

Kleppe R, Kjarland E and Selheim F.: Proteomic and computational methods in systems modeling of cellular signaling. Curr Pharm Biotechnol. 2006 Jun;7(3):135-45.

Berven FS, Flikka K, Berle M, Vedeler C, Ulvik RJ.: Proteomic-based biomarker discovery with emphasis on cerebrospinal fluid and multiple sclerosis. Curr Pharm Biotechnol. 2006 Jun;7(3):147-58.

Berven FS, Karlsen OA, Straume AH, Flikka K, Murrell JC, Fjellbirkeland A, Lillehaug JR, Eidhammer I, Jensen HB.: Analysing the outer membrane subproteome of Methylococcus capsulatus (Bath) using proteomics and novel biocomputing tools. Arch Microbiol. 2006 Feb;184(6):362-77. 

2005 (2)

Herfindal L, Oftedal L, Selheim F, Wahlsten M, Sivonen K, Doskeland SO.: A high proportion of Baltic Sea benthic cyanobacterial Isolates contain apoptogens able to induce rapid death of isolated rat hepatocytes. Toxicon 2005 Sep 1;46(3):252-60.

Selheim F, Herfindal L, Martins R, Vasconcelos V, Døskeland SO.: Neuro-apoptogenic and blood platelet targeting toxins in benthic marine cyanobacteria from the Portuguese coast. Aquat Toxicol. 2005 Sep 30;74(4):294-306.

Koehler CJ, Arntzen MO, Treumann A, Thiede B: Comparison of data analysis parameters and MS/MS fragmentation techniques for quantitative proteome analysis using isobaric peptide termini labeling (IPTL). Anal Bioanal Chem. (in press).*