TY - JOUR A1 - Hummel, Jan A1 - Keshvari, N. A1 - Weckwerth, Wolfram A1 - Selbig, Joachim T1 - Species-specific analysis of protein sequence motifs using mutual information N2 - Background: Protein sequence motifs are by definition short fragments of conserved amino acids, often associated with a specific function. Accordingly protein sequence profiles derived from multiple sequence alignments provide an alternative description of functional motifs characterizing families of related sequences. Such profiles conveniently reflect functional necessities by pointing out proximity at conserved sequence positions as well as depicting distances at variable positions. Discovering significant conservation characteristics within the variable positions of profiles mirrors group-specific and, in particular, evolutionary features of the underlying sequences. Results: We describe the tool PROfile analysis based on Mutual Information (PROMI) that enables comparative analysis of user-classified protein sequences. PROMI is implemented as a web service using Perl and R as well as other publicly available packages and tools on the server-side. On the client-side platform-independence is achieved by generally applied internet delivery standards. As one possible application analysis of the zinc finger C2H2-type protein domain is introduced to illustrate the functionality of the tool. Conclusion: The web service PROMI should assist researchers to detect evolutionary correlations in protein profiles of defined biological sequences. It is available at http:// promi.mpimpgolm. mpg.de where additional documentation can be found Y1 - 2005 SN - 1471-2105 ER - TY - JOUR A1 - Kempa, Stefan A1 - Hummel, Jan A1 - Schwemmer, Thorsten A1 - Pietzke, Matthias A1 - Strehmel, Nadine A1 - Wienkoop, Stefanie A1 - Kopka, Joachim A1 - Weckwerth, Wolfram T1 - 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 N2 - 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. Y1 - 2009 UR - http://www3.interscience.wiley.com/cgi-bin/jhome/5007687 U6 - https://doi.org/10.1002/jobm.200800337 SN - 0233-111X ER - TY - THES A1 - Hummel, Jan Vitus T1 - Knowledge discovery from mass spectroscopy data Y1 - 2010 CY - Potsdam ER - TY - JOUR A1 - Höhenwarter, Wolfgang A1 - Larhlimi, Abdelhalim A1 - Hummel, Jan A1 - Egelhofer, Volker A1 - Selbig, Joachim A1 - van Dongen, Joost T. A1 - Wienkoop, Stefanie A1 - Weckwerth, Wolfram T1 - MAPA Distinguishes genotype-specific variability of highly similar regulatory protein isoforms in potato tuber JF - Journal of proteome research N2 - 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. KW - comparative proteomics KW - mass accuracy KW - protein isoforms KW - potato tuber KW - lipoxygenase KW - protease inhibitor KW - phenotype KW - genetic variability Y1 - 2011 U6 - https://doi.org/10.1021/pr101109a SN - 1535-3893 VL - 10 IS - 7 SP - 2979 EP - 2991 PB - American Chemical Society CY - Washington ER - TY - JOUR A1 - Steinfath, Matthias A1 - Strehmel, Nadine A1 - Peters, Rolf A1 - Schauer, Nicolas A1 - Groth, Detlef A1 - Hummel, Jan A1 - Steup, Martin A1 - Selbig, Joachim A1 - Kopka, Joachim A1 - Geigenberger, Peter A1 - Dongen, Joost T. van T1 - Discovering plant metabolic biomarkers for phenotype prediction using an untargeted approach N2 - Biomarkers are used to predict phenotypical properties before these features become apparent and, therefore, are valuable tools for both fundamental and applied research. Diagnostic biomarkers have been discovered in medicine many decades ago and are now commonly applied. While this is routine in the field of medicine, it is of surprise that in agriculture this approach has never been investigated. Up to now, the prediction of phenotypes in plants was based on growing plants and assaying the organs of interest in a time intensive process. For the first time, we demonstrate in this study the application of metabolomics to predict agronomic important phenotypes of a crop plant that was grown in different environments. Our procedure consists of established techniques to screen untargeted for a large amount of metabolites in parallel, in combination with machine learning methods. By using this combination of metabolomics and biomathematical tools metabolites were identified that can be used as biomarkers to improve the prediction of traits. The predictive metabolites can be selected and used subsequently to develop fast, targeted and low-cost diagnostic biomarker assays that can be implemented in breeding programs or quality assessment analysis. The identified metabolic biomarkers allow for the prediction of crop product quality. Furthermore, marker-assisted selection can benefit from the discovery of metabolic biomarkers when other molecular markers come to its limitation. The described marker selection method was developed for potato tubers, but is generally applicable to any crop and trait as it functions independently of genomic information. Y1 - 2010 UR - http://www3.interscience.wiley.com/cgi-bin/issn?DESCRIPTOR=PRINTISSN&VALUE=1467-7644 U6 - https://doi.org/10.1111/j.1467-7652.2010.00516.x SN - 1467-7644 ER - TY - JOUR A1 - Aichert, Ingrid A1 - Staiger, Anja A1 - Schulte-Mäter, Anne A1 - Becker-Redding, Ulrike A1 - Stahn, Corinna A1 - Peschke, Claudia A1 - Heide, Judith A1 - Ott, Susan A1 - Herrmann, Heike A1 - Völsch, Juliane A1 - Mayer, Jörg A1 - Rohnke, Lucie A1 - Frank, Ulrike A1 - Stadie, Nicole A1 - Jentsch, Nadine A1 - Blech, Anke A1 - Kurtenbach, Stephanie A1 - Thieke, Johanna A1 - Schröder, Astrid A1 - Stahn, Corinna A1 - Hörnig, Robin A1 - Burchert, Frank A1 - De Bleser, Ria A1 - Heister, Julian A1 - Bartels, Luise A1 - Würzner, Kay-Michael A1 - Böhme, Romy A1 - Burmester, Juliane A1 - Krajewski, Melanie A1 - Nager, Wido A1 - Jungehülsing, Gerhard Jan A1 - Wartenburger, Isabell A1 - Jöbges, Michael A1 - Schwilling, Eleonore A1 - Lidzba, Karen A1 - Winkler, Susanne A1 - Konietzko, Andreas A1 - Krägeloh-Mann, Ingeborg A1 - Rilling, Eva A1 - Wilken, Rainer A1 - Wismann, Kathrin A1 - Glandorf, Birte A1 - Hoffmann, Hannah A1 - Hinnenkamp, Christiane A1 - Rohlmann, Insa A1 - Ludewigt, Jacqueline A1 - Bittner, Christian A1 - Orlov, Tatjana A1 - Claus, Katrin A1 - Ehemann, Christine A1 - Winnecken, Andreas A1 - Hummel, Katja A1 - Breitenstein, Sarah ED - Wahl, Michael ED - Stahn, Corinna ED - Hanne, Sandra ED - Fritzsche, Tom T1 - Spektrum Patholinguistik = Schwerpunktthema: Von der Programmierung zur Artikulation : Sprechapraxie bei Kindern und Erwachsenen N2 - Das 3. Herbsttreffen Patholinguistik fand am 21. November 2009 an der Universität Potsdam statt. Der vorliegende Tagungsband enthält die drei Hauptvorträge zum Schwerpunktthema „Von der Programmierung zu Artikulation: Sprechapraxie bei Kindern und Erwachsenen“. Darüber hinaus enthält der Band die Beiträge aus dem Spektrum Patholinguistik, sowie die Abstracts der Posterpräsentationen. N2 - The 3rd Herbsttreffen Patholinguistik was held on November 21st, 2009 at the University of Potsdam. These proceedings contain the three main lectures of the central topic „From programming to articulation: Apraxia of speech of children and adults “. Additionally this volume contains the contributions of Spektrum Patholinguistik, as well as the abstracts of the poster presentations. T3 - Spektrum Patholinguistik - 3 KW - Patholinguistik KW - Sprechapraxie KW - Sprachtherapie KW - patholinguistics KW - apraxia of speech KW - speech and language therapy Y1 - 2010 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-45470 SN - 978-3-86956-079-3 SN - 1869-3822 SN - 1866-9433 IS - 3 PB - Universitätsverlag Potsdam CY - Potsdam ER -