title: SpliceProt: a protein sequence repository of predicted human splice variants.
abstract: The mechanism of alternative splicing in the transcriptome may increase the proteome diversity in eukaryotes. In proteomics, several studies aim to use protein sequence repositories to annotate MS experiments or to detect differentially expressed proteins. However, the available protein sequence repositories are not designed to fully detect protein isoforms derived from mRNA splice variants. To foster knowledge for the field, here we introduce SpliceProt, a new protein sequence repository of transcriptome experimental data used to investigate for putative splice variants in human proteomes. Current version of SpliceProt contains 159 719 non-redundant putative polypeptide sequences. The assessment of the potential of SpliceProt in detecting new protein isoforms resulting from alternative splicing was performed by using publicly available proteomics data. We detected 173 peptides hypothetically derived from splice variants, which 54 of them are not present in UniprotKB/TrEMBL sequence repository. In comparison to other protein sequence repositories, SpliceProt contains a greater number of unique peptides and is able to detect more splice variants. Therefore, SpliceProt provides a solution for the annotation of proteomics experiments regarding splice isofoms. The repository files containing the translated sequences of the predicted splice variants and a visualization tool are freely available at http://lbbc.inca.gov.br/spliceprot.
authors.affiliation: Bioinformatics Unit, Clinical Research Coordination, Instituto Nacional de Câncer (INCA), Rio de Janeiro, Brazil.
authors.forename: Raphael
authors.initials: R
authors.lastname: Tavares
authors.forename: Nicole
authors.initials: N
authors.lastname: de Miranda Scherer
authors.forename: Bianca Alves
authors.initials: BA
authors.lastname: Pauletti
authors.forename: Elói
authors.initials: E
authors.lastname: Araújo
authors.forename: Edson Luiz
authors.initials: EL
authors.lastname: Folador
authors.forename: Gabriel
authors.initials: G
authors.lastname: Espindola
authors.forename: Carlos Gil
authors.initials: CG
authors.lastname: Ferreira
authors.forename: Adriana Franco
authors.initials: AF
authors.lastname: Paes Leme
authors.forename: Paulo Sergio Lopes
authors.initials: PS
authors.lastname: de Oliveira
authors.forename: Fabio
authors.initials: F
authors.lastname: Passetti
mesh_terms: D017398:Alternative Splicing; D000595:Amino Acid Sequence; D000818:Animals; D003198:Computer Simulation; D030562:Databases, Protein; D006801:Humans; D010455:Peptides / Q000737:chemistry* / Q000235:genetics; D020033:Protein Isoforms / Q000737:chemistry* / Q000235:genetics; D040901:Proteomics / Q000379:methods*
chemical_list: D010455:Peptides; D020033:Protein Isoforms
keywords: Alternative splicing; Bioinformatics