title: MAPA distinguishes genotype-specific variability of highly similar regulatory protein isoforms in potato tuber.
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.
authors.affiliation: Department of Molecular Systems Biology, University of Vienna, Faculty of Life Sciences, Althanstrasse 14, A-1090, Vienna, Austria. wolfgang.hoehenwarter@univie.ac.at
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Hoehenwarter
authors.forename: Abdelhalim
authors.initials: A
authors.lastname: Larhlimi
authors.forename: Jan
authors.initials: J
authors.lastname: Hummel
authors.forename: Volker
authors.initials: V
authors.lastname: Egelhofer
authors.forename: Joachim
authors.initials: J
authors.lastname: Selbig
authors.forename: Joost T
authors.initials: JT
authors.lastname: van Dongen
authors.forename: Stefanie
authors.initials: S
authors.lastname: Wienkoop
authors.forename: Wolfram
authors.initials: W
authors.lastname: Weckwerth
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D002265:Carboxylic Ester Hydrolases / Q000235:genetics / Q000378:metabolism; D002853:Chromatography, Liquid; D016000:Cluster Analysis; D015853:Cysteine Proteinase Inhibitors / Q000235:genetics / Q000378:metabolism; D015180:Electrophoresis, Gel, Two-Dimensional; D056726:Genetic Association Studies; D014644:Genetic Variation; D005838:Genotype; D008084:Lipoxygenase / Q000235:genetics / Q000378:metabolism; D008969:Molecular Sequence Data; D015999:Multivariate Analysis; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D035281:Plant Tubers / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D020033:Protein Isoforms / Q000235:genetics* / Q000378:metabolism; D020543:Proteome / Q000235:genetics* / Q000378:metabolism; D040901:Proteomics / Q000379:methods*; D011198:Solanum tuberosum / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D053719:Tandem Mass Spectrometry; D057891:Tetraploidy
chemical_list: D015853:Cysteine Proteinase Inhibitors; D010940:Plant Proteins; D020033:Protein Isoforms; D020543:Proteome; C043222:patatin protein, Solanum tuberosum; D008084:Lipoxygenase; D002265:Carboxylic Ester Hydrolases