1. Integration of proteomics and transcriptomics data to model the dynamics of gene expression The processes that drive gene transcription and translation remain poorly understood, as is evident from long non-coding RNAs (lncRNAs), small open reading frames (sORFs), and complex correlations between protein and mRNA abundances. We will therefore endeavor to develop integrative strategies to explore these issues in more detail.
PROTEOFORMS -aided by genomics/transcriptomics/ translatomics -unravel proteome complexity -novel sequencing technologies: PacBio (SMRT-seq) and Oxford Nanopore (MinION) -lncRNAs, sORFs, uORFs, SAAV… Issues - Opportunities: DBsize+++, matching cross-omics datasets, feed public resources
(RE-)ANNOTATION -non-model (micro)organisms -rescan public repos ( key topic 2 ), stringent workflow to reannotate novel events -PRIDE - Ensembl integration (ProteoAnnotator) -Identify novelty in the proteome: reannotate GENCODE, Ensembl, UCSC - completely novel coding gene - novel isoform - new CDS in non-coding Issues - Opportunities: metadata, stringent filter for FP , robust workflows
QUANTIFICATION -compare NGS (semi-)quantitative measures to MS measures (spectral, label or intensity based, SRM, DIA) -longitudinal studies -systems biology / personalized medicine -asses post-transcriptional or -translational regulation Issues - Opportunities: robust implementations for integration
IMMUNOPEPTIDOMICS -MHC HLA class I and II immunopeptidome -HUPO-HIPP Issues - Opportunities: create and update atlasses (e.g. systemMHC, create standards for reporting, improve detection of immunopeptidome
CustomProDB Quilts SpliceDB Derived NGS mapping sofware NGS other tools Experimental data redundancy removal/filtering Public repositories TOOL DEVELOPMENT 1. DB creation Specialized DB 3. Peptide identi fj cation Automated Pipelines DB-search Tag-based, hybrid search TISdb TIS based on RIBOseq De novo or homology search PROTEOFORMER ChimerDB - dbCRID - ChiTaRS Fusion, chimeric - uses RIBOseq dbSNP - CanProVar - COSMIC Variation - includes isoform, expression, TIS, variant SearchGUI interface to: Tag-based search: DenovoGUI interface to: HaltORF Alternative ORF info X!tandem InSpect PepNovo+ sORFdb Small ORF - Galaxy + command line interface (CLI) MyriMatch GenoMS DirecTag UTRdb Untranslated Regions MS Amanda uORF Translated upstream ORF CustomProDB MS-GF+ Tag-based search & UniNovo dbRES -DARNED RNA-editing sites - uses RNAseq OMSSA homology match: LNCiPedia Long non-coding RNA - includes expression, variant, junction info Comet Spider MS-Blast Animal Toxin Annotation Venoms, Toxins - Bioconductor - R language Tide TagRecon MS-Homology OMIM Human Genes/Disorders Quilts Galaxy implementations - uses RNAseq - includes junction, variant, fusion info 4. Validation & interpretation PROTEOFORMER + SearchGUI/Peptide - - web interface and CLI Known/Derived Protein DB Shaker PeptideShaker - RIBOseq + proteomics integration SpliceDB - genome-centric visualization - uses RNAseq - Combined PEP/FDR estimation for RIBOseq-derived DB Known - includes variant, junction info SAP-db/SPLICE-db/REDUCED-db + (1RF translation) and reference protein DB (Crappé et al., protein UniProtKB, RefSeq, - CLI SearchGUI/PeptideShaker 2015 & Menschaert et al., 2013) Ensembl - RNAseq + proteomics integration genome 6 RF translation SAP-db, SPLICE-db, REDUCED-db - Multistage PEP/FDR estimation using the follow-up analysis EST 3 RF translation - uses RNAseq Multiple multi-omics tools are available for RNAseq-derived DB (3RF translation) and reference - includes variant, junction and expression - see examples in (Boekel et al., 2015) protein DB (Nesvizhskii, 2014) Derived info Custom DB creation NGS - Galaxy Other stand-alone platforms - Event calling (e.g. novel TIS, novel coding region ...) Experimental or publicly availabe (NCBI-SRA, EBI-ENA) exome-, RNAseq 3 RF translation PEPPY (Eukaryotes) MSMSpdbb (prokaryotic genomes) - Annotation analysis (STRING, QuickGO, DAVID, ...) RIBOseq 1 RF translation GenoSuite , bacterial-proteogenom - - uses genome sequence - CLI ic-pipeline (Prokaryotes) - GO enrichment analysis (Ensembl-GO) - 6RF genome translation NGS mapping sofware Complete proteogenomics pipeline - MS-based proteomics integration PIT Bowtie Non-splice aware mapper Peptide/ProteinProphet - visualization - uses RNAseq BWA - STAR - TopHat Splice aware alignment - Galaxy and CLI - within the Trans-Proteomic Pipeline (TPP) ENOSI NGS other tools - 6RF + RNAseq (using SpliceDB tool) GATK Variation calling - peptide identification samtools/mpileup - visualization + annotation 5. Mapping & visualization PGTools Tools aiding the mapping and covisualization of proteomics - RNAseq or Ensembl-derived 2. MS/MS data - peptide identification and NGS data (genome-centric) Customized DB - visualization + (onco-)annotation Mapping Visualization PMT peptide_to_gff Experimental data ProteoAnnotator Sequence redundancy removal/filtering based on: PGx iPiG - gene (re-)annotation using MS proteomics PepLine MIMOMICs Public repositories - using HUPO PSI standard: MSIdentML Gene Prediction EST overlap IggyPep PG Nexus using IGV PRIDE Homology-based RNAseq/RIBOseq overlap Other workflow solutions PeptideAtlas proBAMr Protter Splice Graph GENCODE annotation MassIVE VESPA Tag-based chromosome-centric (C-HPP) Taverna, KNIME, Yabi, bioKepler m/z ProteomicsDB Tool aiding the multi-omics visualization of protein interaction Chorus networks: Retention Time (HiRief) CPTAC Circos Cytoscape SearchGUI PROTEOFORMER + SearchGUI/Peptide Shaker SearchGUI/PeptideShaker multi-omics tools GenoSuite bacterial-proteogenom ic-pipeline - peptide identification PGTools - peptide identification Mapping Visualization Other workflow solutions Taverna, KNIME, Yabi, bioKepler
TOOLS Integration Genomic coordinates - with genomics/transcriptomics Coverage Junction proBAM =>PSI: proBed / proBAM Alignment Gene structure collapsed view expanded view proBed - quantitative: => 2D annotation enrichment/Perseus - with NXTSEQ tools: => BioConda + Galaxy, Knime ( key topic 4 )
TOOLS Statistics & Machine Learning - FDR calcul for expanding custom DBs ( key topic 3 ) -predictive models for ORF detection, proteogenomics applications
TOOLS Visualization - reporting -Cytoscape (plugins), Gephi, GraphViz for proteogenomics visual integration of ShotgunMS, NtermMS, RNAseq, RIBOseq and RRBS viral response (GO- annotation) based on PI network or pathway
Proteoforms - Proteome Complexity (Re-)Annotation Quantification Immunopeptidome Tool Development
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