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.

Quantitative comparison of CrkL-SH3 binding proteins from embryonic murine brain and liver: Implications for developmental signaling and the quantification of protein species variants in bottom-up proteomics

“…We anticipate that our inability to detect additional splice variants was due to a low sample abundance issue in addition to the fact that some splice junctions will simply not be amenable to detection using trypsin. This approach is helpful in identifying splice variants in both large-scale and single protein analyses as a companion to searches that make use of important splice variant databases [20, 21]. …”

Splice variants in the proteome: a promising and challenging field to targeted drug discovery

“…Following a similar strategy of concatenating peptide sequences to reference sequence databases, Tavares et al [9] designed a customized database (SpliceProt) comprising a reference database (Uniprot/SwissProt) and peptide sequences from dbEST, RefSeq, and RNA-Seq data. Using the same proteomic data and statistical assignment presented by Sheynkman et al [8], the usage of the SpliceProt sequence repository yielded the identification of 54 novel peptides that were not present in the UniprotKB/TrEMBL data set.…”

“…For example, RNA-Seq enabled the discovery of new potential splice isoforms [8,9] and the analysis of transcript expression levels [10] in different cell types and conditions. The methods of sequencing and the assembly of reads have been compared [11] and improved over the past few years, promoting new perspectives in transcriptomics [12], including noncoding RNAs (reviewed in [13]).…”

Proteogenomics: Integrating Next-Generation Sequencing and Mass Spectrometry to Characterize Human Proteomic Variation

“…Beyond standard proteomic databases, several specialized databases have been created that focus on a particular variation type, such as SNPs (61–67), splice variants (68–70), or chimeric transcripts (47, 71). In many cases, these databases were designed so that the relevant amino acid sequences corresponding to the variation could be downloaded in a format amenable to MS database searching.…”

“…To identify protein isoforms, the generic protein database must include the relevant isoform sequences. In the case where an isoform is not in the database, one can use a comprehensive splice database such as ECGene or SpliceProt (68, 70) to identify peptides corresponding to novel isoforms specific to a sample or relevant to a disease (68–70, 105, 127). However, though the number and size of splice-specific databases is high, RNA-Seq data collected on hundreds of sample types have shown that the catalog of human isoforms is still incomplete (128).…”