The Proteogenomic Mapping Tool

Abstract

BackgroundHigh-throughput mass spectrometry (MS) proteomics data is increasingly being used to complement traditional structural genome annotation methods. To keep pace with the high speed of experimental data generation and to aid in structural genome annotation, experimentally observed peptides need to be mapped back to their source genome location quickly and exactly. Previously, the tools to do this have been limited to custom scripts designed by individual research groups to analyze their own data, are generally not widely available, and do not scale well with large eukaryotic genomes.ResultsThe Proteogenomic Mapping Tool includes a Java implementation of the Aho-Corasick string searching algorithm which takes as input standardized file types and rapidly searches experimentally observed peptides against a given genome translated in all 6 reading frames for exact matches. The Java implementation allows the application to scale well with larger eukaryotic genomes while providing cross-platform functionality.ConclusionsThe Proteogenomic Mapping Tool provides a standalone application for mapping peptides back to their source genome on a number of operating system platforms with standard desktop computer hardware and executes very rapidly for a variety of datasets. Allowing the selection of different genetic codes for different organisms allows researchers to easily customize the tool to their own research interests and is recommended for anyone working to structurally annotate genomes using MS derived proteomics data.

Comprehensive annotation of Glossina pallidipes salivary gland hypertrophy virus from Ethiopian tsetse flies: a proteogenomics approach

“…TRS9, 11 and 13, and 10, 12 and 14 shared w80 % sequence identities amongst each other. Occurrence of repeat sequences at multiple locations along the genomes has been reported in baculoviruses (Cochran & Faulkner, 1983), nudiviruses (Wang et al, 2011) and whispovirus (Syed Musthaq et al, 2006). Potentially, the repetitive elements may serve as regulators of viral gene expression (Schnitzler et al, 1987).…”

“…For the transcript mapping, the transcripts were mapped on to the virus genome sequence translated into all six reading frames using BioEdit local BLAST alignment. For proteogenomic mapping, the validated unique peptides derived from the LC-MS/MS spectral matches were mapped back to the virus genome (translated in all six reading frames) using the Proteogenomic Mapping Pipeline (PMP) (Sanders et al, 2011). Briefly, three files were inputted into the PMP: a FASTA file containing validated unique MS/MS peptides, a FASTA file of the GpSGHV genome and a text file containing the National Center for Biotechnology Information (NCBI) genetic code (genetic_code_table).…”

“…Briefly, three files were inputted into the PMP: a FASTA file containing validated unique MS/MS peptides, a FASTA file of the GpSGHV genome and a text file containing the National Center for Biotechnology Information (NCBI) genetic code (genetic_code_table). The output file was used to analyse the expressed protein sequence tags created after the peptides had mapped to the virus nucleotide sequence (Sanders et al, 2011). Gene ontology annotation of the predicted ORFs was performed using Blast2GO version 3.0.4 (Conesa et al, 2005).…”

Proteogenomics of rare taxonomic phyla: A prospective treasure trove of protein coding genes

“…However, de novo approaches are considered erroneous and less sensitive and thus are not widely utilized in proteogenomic studies. The Proteogenomic Mapping Tool rapidly maps the identified peptide onto the translated genome database but does not search MS/MS spectra [67]. A recently developed analysis pipeline GenoSuite is the first automated and complete prokaryotic proteogenomic solution [30].…”

Resolution of the type material of the Asian elephant, Elephas maximus Linnaeus, 1758 (Proboscidea, Elephantidae)

“…To identify more genus-diagnostic tryptic peptides, we adopted a proteogenomics approach (Sanders et al, 2011) that: (1) extracted, from the L. africana genome (loxAfr3.67 downloaded from Ensembl Genome Browser, www.ensembl.org), the DNA sequences coding for the tryptic peptides confidently identified by matching the spectra from the Seba elephant against the African elephant reference proteome; (2) extended for 120 bases each of the ends of the identified coding regions; (3) assembled, if possible, the DNA sequences previously generated into short contigs, to obtain the coding DNA sequence for the ancient proteins identified on the basis of several contiguous peptides; (4) mapped a set of shotgun Illumina DNA reads, generated at the Roslin Institute from two modern Asian elephants, against the L. africana DNA extended reads and short contigs coding the peptides identified in the Seba foetus; and (5) filtered to retain alternate, homozygous, nonsynonymous single nucleotide polymorphisms (SNPs) in the positions coding for the ancient foetus tryptic peptides, allowing us to identify which of the peptides identified in the ancient sample had genusdiagnostic potential. Detailed description of this procedure is reported as Supporting Information S3.…”