title: Deep proteomics of the Xenopus laevis egg using an mRNA-derived reference database.
abstract: BACKGROUND
  Mass spectrometry-based proteomics enables the global identification and quantification of proteins and their posttranslational modifications in complex biological samples. However, proteomic analysis requires a complete and accurate reference set of proteins and is therefore largely restricted to model organisms with sequenced genomes.
  
  
  RESULTS
  Here, we demonstrate the feasibility of deep genome-free proteomics by using a reference proteome derived from heterogeneous mRNA data. We identify more than 11,000 proteins with 99% confidence from the unfertilized Xenopus laevis egg and estimate protein abundance with approximately 2-fold precision. Our reference database outperforms the provisional gene models based on genomic DNA sequencing and references generated by other methods. Surprisingly, we find that many proteins in the egg lack mRNA support and that many of these proteins are found in blood or liver, suggesting that they are taken up from the blood plasma, together with yolk, during oocyte growth and maturation, potentially contributing to early embryogenesis.
  
  
  CONCLUSIONS
  To facilitate proteomics in nonmodel organisms, we make our platform available as an online resource that converts heterogeneous mRNA data into a protein reference set. Thus, we demonstrate the feasibility and power of genome-free proteomics while shedding new light on embryogenesis in vertebrates.
authors: Department of Systems Biology, Harvard Medical School, 02115 Boston, MA, USA.|Department of Cell Biology, Harvard Medical School, 02115 Boston, MA, USA.
authors: Martin
authors: M
authors: Wühr
authors: Department of Systems Biology, Harvard Medical School, 02115 Boston, MA, USA.
authors: Robert M
authors: RM
authors: Freeman
authors: Department of Systems Biology, Harvard Medical School, 02115 Boston, MA, USA.
authors: Marc
authors: M
authors: Presler
authors: Bell Center for Regenerative Biology and Tissue Engineering and National Xenopus Resource, Marine Biological Laboratory, Woods Hole, MA 02543, USA.
authors: Marko E
authors: ME
authors: Horb
authors: Department of Systems Biology, Harvard Medical School, 02115 Boston, MA, USA.
authors: Leonid
authors: L
authors: Peshkin
authors: Department of Cell Biology, Harvard Medical School, 02115 Boston, MA, USA.
authors: Steven
authors: S
authors: Gygi
authors: Department of Systems Biology, Harvard Medical School, 02115 Boston, MA, USA.
authors: Marc W
authors: MW
authors: Kirschner
mesh_terms: D000818:Animals; D019295:Computational Biology; D030562:Databases, Protein; D018507:Gene Expression Regulation, Developmental / Q000235:genetics*; D020407:Internet; D013058:Mass Spectrometry; D010063:Ovum / Q000378:metabolism*; D011506:Proteins / Q000378:metabolism*; D040901:Proteomics / Q000379:methods*; D012333:RNA, Messenger / Q000378:metabolism*; D014982:Xenopus laevis / Q000235:genetics*
chemical_list: D011506:Proteins; D012333:RNA, Messenger