Tuesday, November 14, 2017

*** protein abundance in cells, yeast, paxdb

protein abundnace


From W Dang,  " a common control protein sample is mixed in the same quantity with all protein samples. Each mass spec peak is compared between the sample and the control, producing a ratio of sample/control for each protein".  Does this "common control protein sample" refers to BY4741 young cells? 

So, if we choose the protein abundance measurement from database, such as https://pax-db.org/species/4932, we can use the ratios of "NR1 O/Y" to estimate the protein levels of "NR1 old cells" as: 
    NR1-old-cell-protein-levels = "NR1 O/Y" X BY4741-protein-levels

Likewise, we can use "CR1 O/Y" X BY4741-protein-levels = protein-levels-of-CR1-old cells ? 

Do these make sense? 


  1. This database is cool! The dataset with "WHOLE_ORGANISM" integrates published data and gives an estimation of the average abundance of all proteins in the cell. However, it assumes that the molecules keep a (quasi-)static distribution in the cell, which is not realistic. The spatial (e.g., in different organelles) and temporal (e.g., Tu et al. Nature 2005, 310:1152) variations of the protein distributions in the cell, especially under stresses including aging or dietary restriction, are not reflected in this dataset. It may serve as a controlling reference. -- HB