Supplementary Data and Source Code:

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, and Leonid Kruglyak


All of the raw mass spectra analyzed in this manuscript are available for download here. We have also deposited the data in the repository. It is availible for download via the following accession hash: Yp24/w2UjJ8Qp1WDknjf5IZoJWGTN0zKbFpm9XLz7CGAg1xRx32TUV1njJPzRdQ4t/YiTo5YA5nj+ex5CcdqnWpe3UIAAAAAAAAEuw==

Replicate 1

hybrid (15N) vs. S. cerevisiae (14N)
hybrid (15N) vs. S. bayanus (14N)

Replicate 2

hybrid (15N) vs. S. cerevisiae (14N)
hybrid (15N) vs. S. bayanus (14N)

Control Experiment

sythetic hybrid (15N) vs. Scer and synthetic hybrid (15N) Sbay (YPA)
Scer (15N) vs. Sbay (14N)

Instructions for PVIEW analysis of the LC-MS data:

Note that we provide the output of PVIEW with the analysis scripts below so these steps are optional.

  1. Download one pair of the two technical replicates above.
  2. Unzip each of the files, keeping the directory structure
  3. Run PVIEW which can be downloaded here.
  4. Choose "File > Open... and select the directory containing the .mzXML file for the hybrid vs. S. cervisiae comparison.
  5. Make sure the quantification mode is set to "stable isotope pairing (H/L)"
  6. Under the "Isotope" tab, make sure "Use 15N metabolic labeling" is checked.
  7. Switch to the MS2 tab and make sure that 1 missed cleavage is allowed, the enzyme is trypsin, and the mass error is 10 ppms.
  8. Click "Load data..."
  9. When processing is complete, select the menu item Isotope Pairs > Save Tab Delimited.
  10. Save the data as the file Scer_techrepX.txt in the directory containing the proteins.R script replacing X with technical replicate number (1 or 2).
  11. Repeat the last 7 steps for the hybrid vs. S. bayanus data set, but save the output as Sbay_techrepX.txt replacing X with technical replicate number (1 or 2).

For additional information on PVIEW, please visit the Princeton LC-MS/MS Data Viewer and Analyzer (PVIEW) web page.

Requirements for Analysis Scripts

In order to generate the allele specific measurements, we rely on a script that uses the R statistical package. The script uses the plyr library from ggplot2. You'll need install ggplot2 before following the instructions below.

Scripts for the Analysis

We have provided all of the scripts and additional data necessary to replicate the analysis in the manuscript.

You can download the scripts and data by clicking here:

  1. Launch the R statistical package.
  2. Run source("run_all.R").
  3. The script should generate PDF files of the figures in the manuscript.