title: Peptide Selection for Targeted Protein Quantitation.
abstract: 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.
authors.affiliation: Proteomics Unit, Centre de Regulació Genòmica (CRG), Barcelona Institute of Science and Technology (BIST) , Dr. Aiguader 88, 08003 Barcelona, Spain.|Universitat Pompeu Fabra (UPF) , Dr. Aiguader 88, 08003 Barcelona, Spain.
authors.forename: Cristina
authors.initials: C
authors.lastname: Chiva
authors.affiliation: Proteomics Unit, Centre de Regulació Genòmica (CRG), Barcelona Institute of Science and Technology (BIST) , Dr. Aiguader 88, 08003 Barcelona, Spain.|Universitat Pompeu Fabra (UPF) , Dr. Aiguader 88, 08003 Barcelona, Spain.
authors.forename: Eduard
authors.identifier: 0000-0001-6506-7714
authors.initials: E
authors.lastname: Sabidó
mesh_terms: D001426:Bacterial Proteins / Q000032:analysis; D030562:Databases, Protein; D004926:Escherichia coli / Q000737:chemistry; D058990:Molecular Targeted Therapy; D010455:Peptides / Q000302:isolation & purification*; D011506:Proteins / Q000032:analysis*; D040901:Proteomics / Q000379:methods*
chemical_list: D001426:Bacterial Proteins; D010455:Peptides; D011506:Proteins