Mass-Spectrometry-Based Near-Complete Draft of the Saccharomyces cerevisiae Proteome

Proteomics approaches designed to
catalogue all open reading frames
(ORFs) under a defined set of growth conditions of an organism have
flourished in recent years. However, no proteome has been sequenced
completely so far. Here, we generate the largest yeast proteome data
set, including 5610 identified proteins, using a strategy based on
optimized sample preparation and high-resolution mass spectrometry.
Among the 5610 identified proteins, 94.1% are core proteins, which
achieves near-complete coverage of the yeast ORFs. Comprehensive analysis
of missing proteins showed that proteins are missed mainly due to
physical properties. A review of protein abundance shows that our
proteome encompasses a uniquely broad dynamic range. Additionally,
these values highly correlate with mRNA abundance, implying a high
level of accuracy, sensitivity, and precision. We present examples
of how the data could be used, including reannotating gene localization,
providing expression evidence of pseudogenes. Our near-complete yeast
proteome data set will be a useful and important resource for further
systematic studies.