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  - Winck, Flavia Vischi
A1  - Kwasniewski, Miroslaw
A1  - Wienkoop, Stefanie
A1  - Müller-Röber, Bernd
T1  - An optimized method for the isolation of nuclei from chlamydomas Reinhardtii (Chlorophyceae)
JF  - Journal of phycology
N2  - 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.
KW  - 2D gel electrophoresis
KW  - algae
KW  - Chlamydomonas
KW  - nuclear proteins
KW  - nucleus
KW  - proteomics
Y1  - 2011
U6  - https://doi.org/10.1111/j.1529-8817.2011.00967.x
SN  - 0022-3646
VL  - 47
IS  - 2
SP  - 333
EP  - 340
PB  - Wiley-Blackwell
CY  - Malden
ER  -