Journal of Proteomics & Bioinformatics
Open Access

David R Goodlett

Publications

• Research Article
  Systematic Analysis of Yeast Proteome Reveals Peptide Detectability Factors for Mass Spectrometry
  Author(s): Sunhee Jung, Samuel A Danziger, Alexandre Panchaud, Priska von Haller, John D Aitchison and David R GoodlettSunhee Jung, Samuel A Danziger, Alexandre Panchaud, Priska von Haller, John D Aitchison and David R Goodlett
  
  Here we used a data-independent acquisition (DIA) method, Precursor Acquisition Independent from Ion Count (PAcIFIC), to systematically profile the S. cerevisiae proteome. Direct PAcIFIC analysis of a yeast whole cell lysate (WCL) yielded 90% reproducibility between replicates and detected approximately 2000 proteins. When combined with sub-cellular fractionation, reproducibility was equally high and the number of detected yeast proteins approached 5000. As noted previously, this unbiased DIA approach identified so-called “orphan” peptides that could only be detected by tandem mass spectra because there was no detectable precursor ion. Using this unique dataset we examined features associated with peptide detectability and demonstrated that orphans were more likely to arise from low copy number proteins than proteins with median or high copy number. Finally, an investigati.. View More»
  DOI: 10.4172/jpb.1000374

  Abstract PDF

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