title: Heat-Treatment-Responsive Proteins in Different Developmental Stages of Tomato Pollen Detected by Targeted Mass Accuracy Precursor Alignment (tMAPA).
abstract: Recently, we have developed a quantitative shotgun proteomics strategy called mass accuracy precursor alignment (MAPA). The MAPA algorithm uses high mass accuracy to bin mass-to-charge (m/z) ratios of precursor ions from LC-MS analyses, determines their intensities, and extracts a quantitative sample versus m/z ratio data alignment matrix from a multitude of samples. Here, we introduce a novel feature of this algorithm that allows the extraction and alignment of proteotypic peptide precursor ions or any other target peptide from complex shotgun proteomics data for accurate quantification of unique proteins. This strategy circumvents the problem of confusing the quantification of proteins due to indistinguishable protein isoforms by a typical shotgun proteomics approach. We applied this strategy to a comparison of control and heat-treated tomato pollen grains at two developmental stages, post-meiotic and mature. Pollen is a temperature-sensitive tissue involved in the reproductive cycle of plants and plays a major role in fruit setting and yield. By LC-MS-based shotgun proteomics, we identified more than 2000 proteins in total for all different tissues. By applying the targeted MAPA data-processing strategy, 51 unique proteins were identified as heat-treatment-responsive protein candidates. The potential function of the identified candidates in a specific developmental stage is discussed.
authors.affiliation: Department of Ecogenomics and Systems Biology, Faculty of Sciences, University of Vienna , Althanstrasse 14, A-1090 Vienna, Austria.
authors.forename: Palak
authors.initials: P
authors.lastname: Chaturvedi
authors.affiliation: Department of Ecogenomics and Systems Biology, Faculty of Sciences, University of Vienna , Althanstrasse 14, A-1090 Vienna, Austria.
authors.forename: Hannes
authors.initials: H
authors.lastname: Doerfler
authors.affiliation: Department of Vegetable Research, Institute of Plant Sciences, The Volcani Centre, Agricultural Research Organization , Bet Dagan, 50250, Israel.
authors.forename: Sridharan
authors.initials: S
authors.lastname: Jegadeesan
authors.affiliation: Department of Ecogenomics and Systems Biology, Faculty of Sciences, University of Vienna , Althanstrasse 14, A-1090 Vienna, Austria.|School of Biotechnology and Bioinformatics, D.Y. Patil University , Sector 15, CBD Belapur, Navi Mumbai, Maharashtra 400614, India.
authors.forename: Arindam
authors.initials: A
authors.lastname: Ghatak
authors.affiliation: Department of Vegetable Research, Institute of Plant Sciences, The Volcani Centre, Agricultural Research Organization , Bet Dagan, 50250, Israel.
authors.forename: Etan
authors.initials: E
authors.lastname: Pressman
authors.affiliation: Department of Ecogenomics and Systems Biology, Faculty of Sciences, University of Vienna , Althanstrasse 14, A-1090 Vienna, Austria.
authors.forename: Maria Angeles
authors.initials: MA
authors.lastname: Castillejo
authors.affiliation: Department of Ecogenomics and Systems Biology, Faculty of Sciences, University of Vienna , Althanstrasse 14, A-1090 Vienna, Austria.
authors.forename: Stefanie
authors.initials: S
authors.lastname: Wienkoop
authors.affiliation: Department of Ecogenomics and Systems Biology, Faculty of Sciences, University of Vienna , Althanstrasse 14, A-1090 Vienna, Austria.
authors.forename: Volker
authors.initials: V
authors.lastname: Egelhofer
authors.affiliation: Department of Vegetable Research, Institute of Plant Sciences, The Volcani Centre, Agricultural Research Organization , Bet Dagan, 50250, Israel.
authors.forename: Nurit
authors.initials: N
authors.lastname: Firon
authors.affiliation: Department of Ecogenomics and Systems Biology, Faculty of Sciences, University of Vienna , Althanstrasse 14, A-1090 Vienna, Austria.
authors.forename: Wolfram
authors.initials: W
authors.lastname: Weckwerth
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics; D000465:Algorithms; D000595:Amino Acid Sequence; D002853:Chromatography, Liquid; D018507:Gene Expression Regulation, Developmental; D018506:Gene Expression Regulation, Plant; D006358:Hot Temperature; D018551:Solanum lycopersicum / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism; D013058:Mass Spectrometry / Q000706:statistics & numerical data; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D010455:Peptides / Q000737:chemistry / Q000302:isolation & purification*; D010940:Plant Proteins / Q000235:genetics / Q000302:isolation & purification* / Q000378:metabolism; D011058:Pollen / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism; D025341:Principal Component Analysis; D059748:Proteolysis; D020543:Proteome / Q000235:genetics / Q000302:isolation & purification* / Q000378:metabolism; D040901:Proteomics / Q000379:methods
chemical_list: D010455:Peptides; D010940:Plant Proteins; D020543:Proteome
keywords: Protmax; climate change; developmental priming; heat treatment; plant productivity; pollen development; proteotypic peptide; tMAPA; tomato