SLIDE 7 TOOL DEVELOPMENT
Specialized DB Customized DB
Sequence redundancy removal/filtering based on: EST overlap RNAseq/RIBOseq overlap GENCODE annotation chromosome-centric (C-HPP) Retention Time (HiRief)
Known/Derived Protein DB
Known protein genome EST Derived NGS Experimental or publicly availabe (NCBI-SRA, EBI-ENA) exome-, RNAseq RIBOseq NGS mapping sofware Bowtie BWA - STAR - TopHat NGS other tools GATK samtools/mpileup
Custom DB creation
Automated Pipelines
PROTEOFORMER
- uses RIBOseq
- includes isoform, expression, TIS, variant
info
- Galaxy + command line interface (CLI)
CustomProDB
- uses RNAseq
- includes expression, variant, junction info
- Bioconductor - R language
Quilts
- uses RNAseq
- includes junction, variant, fusion info
- web interface and CLI
SpliceDB
- uses RNAseq
- includes variant, junction info
- CLI
SAP-db, SPLICE-db, REDUCED-db
- uses RNAseq
- includes variant, junction and expression
info
MSMSpdbb (prokaryotic genomes)
PIT
- uses RNAseq
- Galaxy and CLI
- 1. DB creation
- 2. MS/MS data
Experimental data Public repositories PRIDE PeptideAtlas MassIVE ProteomicsDB Chorus CPTAC
m/z
SearchGUI PROTEOFORMER + SearchGUI/Peptide Shaker SearchGUI/PeptideShaker multi-omics tools GenoSuite bacterial-proteogenom ic-pipeline
PGTools
Other workflow solutions
Taverna, KNIME, Yabi, bioKepler Mapping Visualization TISdb ChimerDB - dbCRID - ChiTaRS dbSNP - CanProVar - COSMIC HaltORF sORFdb UTRdb uORF dbRES -DARNED LNCiPedia Animal Toxin Annotation OMIM TIS based on RIBOseq Fusion, chimeric Variation Alternative ORF Small ORF Untranslated Regions Translated upstream ORF RNA-editing sites Long non-coding RNA Venoms, Toxins Human Genes/Disorders UniProtKB, RefSeq, Ensembl 6 RF translation 3 RF translation 3 RF translation 1 RF translation Non-splice aware mapper Splice aware alignment Variation calling Gene Prediction Homology-based Splice Graph Tag-based redundancy removal/filtering Derived NGS mapping sofware NGS other tools CustomProDB Quilts SpliceDB
- 3. Peptide identifjcation
- 4. Validation & interpretation
- 5. Mapping & visualization
Complete proteogenomics pipeline
Experimental data Public repositories
DB-search Tag-based, hybrid search De novo or homology search
SearchGUI interface to: X!tandem MyriMatch MS Amanda MS-GF+ OMSSA Comet Tide Tag-based search: InSpect GenoMS Tag-based search & homology match: Spider TagRecon DenovoGUI interface to: PepNovo+ DirecTag UniNovo MS-Blast MS-Homology Tools aiding the mapping and covisualization of proteomics and NGS data (genome-centric)
Galaxy implementations
PROTEOFORMER + SearchGUI/Peptide- Shaker
- RIBOseq + proteomics integration
- genome-centric visualization
SAP-db/SPLICE-db/REDUCED-db + SearchGUI/PeptideShaker
- RNAseq + proteomics integration
Multiple multi-omics tools are available
- see examples in (Boekel et al., 2015)
Other stand-alone platforms
PEPPY (Eukaryotes) GenoSuite, bacterial-proteogenom- ic-pipeline (Prokaryotes)
- 6RF genome translation
- MS-based proteomics integration
- visualization
ENOSI
- 6RF + RNAseq (using SpliceDB tool)
- peptide identification
- visualization + annotation
PGTools
- RNAseq or Ensembl-derived
- peptide identification
- visualization + (onco-)annotation
ProteoAnnotator
- gene (re-)annotation using MS proteomics
- using HUPO PSI standard: MSIdentML
Other workflow solutions
Taverna, KNIME, Yabi, bioKepler Mapping PMT PGx PepLine IggyPep proBAMr Visualization peptide_to_gff iPiG MIMOMICs PG Nexus using IGV Protter VESPA
PeptideShaker
- Combined PEP/FDR estimation for RIBOseq-derived DB
(1RF translation) and reference protein DB (Crappé et al., 2015 & Menschaert et al., 2013)
- Multistage PEP/FDR estimation using the follow-up analysis
for RNAseq-derived DB (3RF translation) and reference protein DB (Nesvizhskii, 2014)
- Event calling (e.g. novel TIS, novel coding region ...)
- Annotation analysis (STRING, QuickGO, DAVID, ...)
- GO enrichment analysis (Ensembl-GO)
Peptide/ProteinProphet
- within the Trans-Proteomic Pipeline (TPP)
Tool aiding the multi-omics visualization of protein interaction networks: Circos Cytoscape
