Quantitative measurement of allele-specific protein expression in a diploid yeast hybrid by LC-MS

Zia Khan, Joshua S. Bloom, Sasan Amini, Mona Singh, David H. Perlman, Amy A. Caudy, Leonid Kruglyak

Research output: Contribution to journalArticlepeer-review

26 Scopus citations


Understanding the genetic basis of gene regulatory variation is a key goal of evolutionary and medical genetics. Regulatory variation can act in an allele-specific manner (cis-acting) or it can affect both alleles of a gene (trans-acting). Differential allele-specific expression (ASE), in which the expression of one allele differs from another in a diploid, implies the presence of cis-acting regulatory variation. While microarrays and high-throughput sequencing have enabled genome-wide measurements of transcriptional ASE, methods for measurement of protein ASE (pASE) have lagged far behind. We describe a flexible, accurate, and scalable strategy for measurement of pASE by liquid chromatography-coupled mass spectrometry (LC-MS). We apply this approach to a hybrid between the yeast species Saccharomyces cerevisiae and Saccharomyces bayanus. Our results provide the first analysis of the relative contribution of cis-acting and trans-acting regulatory differences to protein expression divergence between yeast species.

Original languageEnglish (US)
Article number602
JournalMolecular Systems Biology
StatePublished - 2012

All Science Journal Classification (ASJC) codes

  • General Agricultural and Biological Sciences
  • Applied Mathematics
  • General Biochemistry, Genetics and Molecular Biology
  • General Immunology and Microbiology


  • allele specific
  • divergence
  • mass spectrometry
  • protein expression
  • proteomics


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