RT Journal
A1 Grobei, Monica A.
A1 Qeli, Ermir
A1 Brunner, Erich
A1 Rehrauer, Hubert
A1 Zhang, Runxuan
A1 Roschitzki, Bernd
A1 Basler, Konrad
A1 Ahrens, Christian H.
A1 Grossniklaus, Ueli
T1 Deterministic protein inference for shotgun proteomics data provides new insights into Arabidopsis pollen development and function
JF Genome Research 
JO Genome Research 
YR 2009 
FD October 01 
VO 19 
IS 10 
SP 1786 
OP 1800 
DO 10.1101/gr.089060.108 
UL http://genome.cshlp.org/content/19/10/1786.abstract 
AB Pollen, the male gametophyte of flowering plants, represents an ideal biological system to study developmental processes, such as cell polarity, tip growth, and morphogenesis. Upon hydration, the metabolically quiescent pollen rapidly switches to an active state, exhibiting extremely fast growth. This rapid switch requires relevant proteins to be stored in the mature pollen, where they have to retain functionality in a desiccated environment. Using a shotgun proteomics approach, we unambiguously identified ∼3500 proteins in Arabidopsis pollen, including 537 proteins that were not identified in genetic or transcriptomic studies. To generate this comprehensive reference data set, which extends the previously reported pollen proteome by a factor of 13, we developed a novel deterministic peptide classification scheme for protein inference. This generally applicable approach considers the gene model–protein sequence–protein accession relationships. It allowed us to classify and eliminate ambiguities inherently associated with any shotgun proteomics data set, to report a conservative list of protein identifications, and to seamlessly integrate data from previous transcriptomics studies. Manual validation of proteins unambiguously identified by a single, information-rich peptide enabled us to significantly reduce the false discovery rate, while keeping valuable identifications of shorter and lower abundant proteins. Bioinformatic analyses revealed a higher stability of pollen proteins compared to those of other tissues and implied a protein family of previously unknown function in vesicle trafficking. Interestingly, the pollen proteome is most similar to that of seeds, indicating physiological similarities between these developmentally distinct tissues.