Selection of reference peptides for absolute quantification of budding yeast proteome

Absolute quantification of proteome is one of the most important tasks in proteomic research. The aim in this analysis is selection of reference tryptic peptides used for stable isotope-labeled standard, based on their spectral peak intensities. Approximate abundance is also calculated by label-free quantitative method, in which identification frequency (counts of peptide spectral matchings) in each protein is normalized by observability of peptide ions to calculate relative copy number of proteins. For proteins with higher relative copy number, peptide ions that fulfill following criteria — 2- or 3-charge state, without methionine residues and well known post-translational modification sites — are selected as reference tryptic peptides.