NextSearch: A Search Engine for Mass Spectrometry Data against a Compact Nucleotide Exon Graph

Proteogenomics
research has been using six-frame translation of
the whole genome or amino acid exon graphs to overcome the limitations
of reference protein sequence database; however, six-frame translation
is not suitable for annotating genes that span over multiple exons,
and amino acid exon graphs are not convenient to represent novel splice
variants and exon skipping events between exons of incompatible reading
frames. We propose a proteogenomic pipeline NextSearch (Nucleotide
EXon-graph Transcriptome Search) that is based on a nucleotide exon
graph. This pipeline consists of constructing a compact nucleotide
exon graph that systematically incorporates novel splice variations
and a search tool that identifies peptides by directly searching the
nucleotide exon graph against tandem mass spectra. Because our exon
graph stores nucleotide sequences, it can easily represent novel splice
variations and exon skipping events between incompatible reading frame
exons. Searching for peptide identification is performed against this
nucleotide exon graph, without converting it into a protein sequence
in FASTA format, achieving an order of magnitude reduction in the
size of the sequence database storage. NextSearch outputs the proteome-genome/transcriptome
mapping results in a general feature format (GFF) file, which can
be visualized by public tools such as the UCSC Genome Browser.