title: Lights and shadows of proteomic technologies for the study of protein species including isoforms, splicing variants and protein post-translational modifications.
abstract: Recent reviews pinpointed the enormous diversity of proteins found in living organisms, especially in higher eukaryotes. Protein diversity is driven through three main processes: first, at deoxyribonucleic acid (DNA) level (i.e. gene polymorphisms), second, at precursor messenger ribonucleic acid (pre-mRNA) or messenger ribonucleic acid (mRNA) level (i.e. alternative splicing, also termed as differential splicing) and, finally, at the protein level (i.e. PTM). Current proteomic technologies allow the identification, characterization and quantitation of up to several thousands of proteins in a single experiment. Nevertheless, the identification and characterization of protein species using these technologies are still hampered. Here, we review the use of the terms "protein species" and "protein isoform." We evidence that the appropriate selection of the database used for searches can impede or facilitate the identification of protein species. We also describe examples where protein identification search engines systematically fail in the attribution of protein species. We briefly review the characterization of protein species using proteomic technologies including gel-based, gel-free, bottom-up and top-down analysis and discuss their limitations. As an example, we discuss the theoretical characterization of the two human choline kinase species, α-1 and α-2, sharing the same catalytic activity but generated by alternative splicing on CHKA gene.
authors.affiliation: Instituto de Investigaciones Biomédicas Alberto Sols, Spanish National Research Council (CSIC), Madrid, Spain. jcasado@iib.uam.es
authors.forename: Juan
authors.initials: J
authors.lastname: Casado-Vela
authors.forename: Arancha
authors.initials: A
authors.lastname: Cebrián
authors.forename: Maria Teresa
authors.initials: MT
authors.lastname: Gómez del Pulgar
authors.forename: Elsa
authors.initials: E
authors.lastname: Sánchez-López
authors.forename: Marta
authors.initials: M
authors.lastname: Vilaseca
authors.forename: Laura
authors.initials: L
authors.lastname: Menchén
authors.forename: Claudia
authors.initials: C
authors.lastname: Diema
authors.forename: Susana
authors.initials: S
authors.lastname: Sellés-Marchart
authors.forename: María José
authors.initials: MJ
authors.lastname: Martínez-Esteso
authors.forename: Noemí
authors.initials: N
authors.lastname: Yubero
authors.forename: Roque
authors.initials: R
authors.lastname: Bru-Martínez
authors.forename: Juan Carlos
authors.initials: JC
authors.lastname: Lacal
authors.forename: Juan Caelos
authors.initials: JC
authors.lastname: Lacal
mesh_terms: D000818:Animals; D006801:Humans; D020033:Protein Isoforms; D011499:Protein Processing, Post-Translational; D011506:Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D040901:Proteomics / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods
chemical_list: D020033:Protein Isoforms; D011506:Proteins