Shotgun proteonomics

CREATED: 200808140219 Speaker: Christian von Mering

** Proteonomics workflow

peptide sequencing

** Spectral counting: quantitative information of protein abundance

convectional methods relay on peptide labeling, measure relative changes
spectral counting: directly from shotgun data, no need for peptide labels
problem: not all peptides are produced at cleavage points, not all peptides are detected by the machine
very short/long peptides are not observed
$a = (\sum_i count(p_i) \times length(p_i))/(\sum_j length(q_j) \times f(q_j))$
p = identified peptides, q = tryptic peptides, f(q) = peptide length correction factor
comparison of worm with yeast
genes which are part of operons in C. elegans are more abundant and more easily detected
operons are probably not cause for abundance, because orthologous genes in fly are also more abundant

** Comparative analysis

orthologous protein pairs in worm and fly
correlation of 0.79 between abundance of orthologs in worm and fly (2691 pairs of orthologs)
breakdown of correlation of abundance levels according to functional categories
protein abundance have better correlation compared to comparison of transcript abundance => mRNA can drift
protein vs transcript within an organism

** Future work