@article{BaesslerWeissWienkoopetal.2009,
  author    = {Baessler, Olivia Y. and Weiss, Julia and Wienkoop, Stefanie and Lehmann, Karola and Scheler, Christian and Doelle, Sabine and Schwarz, Dietmar and Franken, Philipp and George, Eckhard and Worm, Margitta and Weckwerth, Wolfram},
  title     = {Evidence for novel tomato seed allergens : IgE-reactive legumin and vicilin proteins identified by multidimensional protein fractionation-mass spectrometry and in silico epitope modeling},
  issn      = {1535-3893},
  doi       = {10.1021/Pr800186d},
  year      = {2009},
  abstract  = {Tomato fruit and seed allergens were detected by IgE-immunoblotting using sera from 18 adult tomato-sensitized patients selected based on a positive history skin prick test (SPT) and specific Immunglobulin (Ig) E-levels. Isolated tomato seed total protein showed high SPT activity comparable or even higher than tomato fruit protein. For the molecular characterization of tomato seed allergens, a multidimensional protein fractionation strategy and LC-MS/MS was used. Two legumin- and vicilin-proteins were purified and showed strong IgE-reactivity in immunoblots. Individual patient sera exhibited varying IgE-sensitivity against the purified proteins. In silico structural modeling indicates high homology between epitopes of known walnut allergens and the detected IgE-crossreactive tomato proteins.},
  language  = {en}
}
@article{HoehenwarterLarhlimiHummeletal.2011,
  author    = {H{\"o}henwarter, Wolfgang and Larhlimi, Abdelhalim and Hummel, Jan and Egelhofer, Volker and Selbig, Joachim and van Dongen, Joost T. and Wienkoop, Stefanie and Weckwerth, Wolfram},
  title     = {MAPA Distinguishes genotype-specific variability of highly similar regulatory protein isoforms in potato tuber},
  series = {Journal of proteome research},
  volume    = {10},
  journal   = {Journal of proteome research},
  number    = {7},
  publisher = {American Chemical Society},
  address   = {Washington},
  issn      = {1535-3893},
  doi       = {10.1021/pr101109a},
  pages     = {2979 -- 2991},
  year      = {2011},
  abstract  = {Mass Accuracy Precursor Alignment is a fast and flexible method for comparative proteome analysis that allows the comparison of unprecedented numbers of shotgun proteomics analyses on a personal computer in a matter of hours. We compared 183 LC-MS analyses and more than 2 million MS/MS spectra and could define and separate the proteomic phenotypes of field grown tubers of 12 tetraploid cultivars of the crop plant Solanum tuberosum. Protein isoforms of patatin as well as other major gene families such as lipoxygenase and cysteine protease inhibitor that regulate tuber development were found to be the primary source of variability between the cultivars. This suggests that differentially expressed protein isoforms modulate genotype specific tuber development and the plant phenotype. We properly assigned the measured abundance of tryptic peptides to different protein isoforms that share extensive stretches of primary structure and thus inferred their abundance. Peptides unique to different protein isoforms were used to classify the remaining peptides assigned to the entire subset of isoforms based on a common abundance profile using multivariate statistical procedures. We identified nearly 4000,proteins which we used for quantitative functional annotation making this the most extensive study of the tuber proteome to date.},
  language  = {en}
}
@article{KempaHummelSchwemmeretal.2009,
  author    = {Kempa, Stefan and Hummel, Jan and Schwemmer, Thorsten and Pietzke, Matthias and Strehmel, Nadine and Wienkoop, Stefanie and Kopka, Joachim and Weckwerth, Wolfram},
  title     = {An automated GCxGC-TOF-MS protocol for batch-wise extraction and alignment of mass isotopomer matrixes from differential C-13-labelling experiments : a case study for photoautotrophic-mixotrophic grown Chlamydomonas reinhardtii cells},
  issn      = {0233-111X},
  doi       = {10.1002/jobm.200800337},
  year      = {2009},
  abstract  = {Two dimensional gas chromatography coupled to time-of-flight mass spectrometry (GCxGC-TOF-MS) is a promising technique to overcome limits of complex metabolome analysis using one dimensional GC-TOF-MS. Especially at the stage of data export and data mining, however, convenient procedures to cope with the complexity of GCxGC-TOF-MS data are still in development. Here, we present a high sample throughput protocol exploiting first and second retention index for spectral library search and subsequent construction of a high dimensional data matrix useful for statistical analysis. The method was applied to the analysis of 13 C-labelling experiments in the unicellular green alga Chlamydomonas reinhardtii. We developed a rapid sampling and extraction procedure for Chlamydomonas reinhardtii laboratory strain (CC503), a cell wall deficient mutant. By testing all published quenching protocols we observed dramatic metabolite leakage rates for certain metabolites. To circumvent metabolite leakage, samples were directly quenched and analyzed without separation of the medium. The growth medium was adapted to this rapid sampling protocol to avoid interference with GCxGC-TOF-MS analysis. To analyse batches of samples a new software tool, MetMax, was implemented which extracts the isotopomer matrix from stable isotope labelling experiments together with the first and second retention index (RI1 and RI2). To exploit RI1 and RI2 for metabolite identification we used the Golm metabolome database (GMD [1] with RI1/ RI2-reference spectra and new search algorithms. Using those techniques we analysed the dynamics of (CO2)-C-13 and C-13- acetate uptake in Chlamydomonas reinhardtii cells in two different steady states namely photoautotrophic and mixotrophic growth conditions.},
  language  = {en}
}
@article{WinckKwasniewskiWienkoopetal.2011,
  author    = {Winck, Flavia Vischi and Kwasniewski, Miroslaw and Wienkoop, Stefanie and M{\"u}ller-R{\"o}ber, Bernd},
  title     = {An optimized method for the isolation of nuclei from chlamydomas Reinhardtii (Chlorophyceae)},
  series = {Journal of phycology},
  volume    = {47},
  journal   = {Journal of phycology},
  number    = {2},
  publisher = {Wiley-Blackwell},
  address   = {Malden},
  issn      = {0022-3646},
  doi       = {10.1111/j.1529-8817.2011.00967.x},
  pages     = {333 -- 340},
  year      = {2011},
  abstract  = {The cell nucleus harbors a large number of proteins involved in transcription, RNA processing, chromatin remodeling, nuclear signaling, and ribosome assembly. The nuclear genome of the model alga Chlamydomonas reinhardtii P. A. Dang. was recently sequenced, and many genes encoding nuclear proteins, including transcription factors and transcription regulators, have been identified through computational discovery tools. However, elucidating the specific biological roles of nuclear proteins will require support from biochemical and proteomics data. Cellular preparations with enriched nuclei are important to assist in such analyses. Here, we describe a simple protocol for the isolation of nuclei from Chlamydomonas, based on a commercially available kit. The modifications done in the original protocol mainly include alterations of the differential centrifugation parameters and detergent-based cell lysis. The nuclei-enriched fractions obtained with the optimized protocol show low contamination with mitochondrial and plastid proteins. The protocol can be concluded within only 3 h, and the proteins extracted can be used for gel-based and non-gel-based proteomic approaches.},
  language  = {en}
}