Peptide Selection for Targeted Protein Quantitation

Targeted proteomics methods in their
different flavors rely on
the use of a few peptides as proxies for protein quantitation, which
need to be specified either prior to or after data acquisition. However,
in contrast with discovery methods that use all identified peptides
for a given protein to estimate its abundance, targeted proteomics
methods are limited in the number of peptides that are used for protein
quantitation. Because only a few peptides per protein are acquired
or extracted in targeted experiments, the selection of peptides that
are used for targeted protein quantitation becomes crucial. Several
rules have been proposed to guide peptide selection for targeted proteomics
studies, which have generally been based on the amino acidic composition
of the peptide sequences. However, the compliance of these rules does
not imply that not-conformed peptides are not reproducibly generated
nor do they guarantee that the selected peptides correctly represent
the behavior of the protein abundance under different conditions.