Towards complete proteome quantitation
Matthias Mann
Max-Planck-Institute Martinsried, German
Despite tremendous progress in mass spectrometry-based proteomics, identification of a complete proteome has not yet been reported. Here we use a combination of advanced instrumentation (LTQ-Orbitrap), sample preparation and computational strategies to identify essentially all proteins expressed in normally growing yeast. Furthermore, we employed the Stable Isotope Labeling by Amino Acids in Cell culture (SILAC) technology to quantify the proteomes of two cellular states against each other. Haploid yeast can mate, whereas diploid yeast cannot, consequently we found drastic changes in the expression of the yeast mating pathway between these two cell types. We also compared the proteomic data against a microarray data set and found low correlation between transcriptome and proteome in general. Members of the mating pathway, however, did show concordant changes, as biologically expected. Several other examples of large scale proteome quantitation will be discussed as well.
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