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 - 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 -