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dc.contributor.authorSchlaffner, CN
dc.contributor.authorPirklbauer, GJ
dc.contributor.authorBender, A
dc.contributor.authorSteen, JAJ
dc.contributor.authorChoudhary, JS
dc.date.accessioned2019-02-25T16:36:08Z
dc.date.issued2018-05-22
dc.identifier.citationJournal of visualized experiments : JoVE, 2018, (135)
dc.identifier.issn1940-087X
dc.identifier.urihttps://repository.icr.ac.uk/handle/internal/3094
dc.identifier.eissn1940-087X
dc.identifier.doi10.3791/57633
dc.description.abstractCross-talk between genes, transcripts, and proteins is the key to cellular responses; hence, analysis of molecular levels as distinct entities is slowly being extended to integrative studies to enhance the understanding of molecular dynamics within cells. Current tools for the visualization and integration of proteomics with other omics datasets are inadequate for large-scale studies. Furthermore, they only capture basic sequence identify, discarding post-translational modifications and quantitation. To address these issues, we developed PoGo to map peptides with associated post-translational modifications and quantification to reference genome annotation. In addition, the tool was developed to enable the mapping of peptides identified from customized sequence databases incorporating single amino acid variants. While PoGo is a command line tool, the graphical interface PoGoGUI enables non-bioinformatics researchers to easily map peptides to 25 species supported by Ensembl genome annotation. The generated output borrows file formats from the genomics field and, therefore, visualization is supported in most genome browsers. For large-scale studies, PoGo is supported by TrackHubGenerator to create web-accessible repositories of data mapped to genomes that also enable an easy sharing of proteogenomics data. With little effort, this tool can map millions of peptides to reference genomes within only a few minutes, outperforming other available sequence-identity based tools. This protocol demonstrates the best approaches for proteogenomics mapping through PoGo with publicly available datasets of quantitative and phosphoproteomics, as well as large-scale studies.
dc.formatElectronic
dc.languageeng
dc.language.isoeng
dc.rights.urihttps://creativecommons.org/licenses/by/4.0
dc.subjectPeptides
dc.subjectProteomics
dc.subjectGenomics
dc.subjectProtein Processing, Post-Translational
dc.subjectGenome
dc.titleA Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes.
dc.typeJournal Article
dcterms.dateAccepted2018-05-22
rioxxterms.versionofrecord10.3791/57633
rioxxterms.licenseref.urihttps://creativecommons.org/licenses/by/4.0
rioxxterms.licenseref.startdate2018-05-22
rioxxterms.typeJournal Article/Review
dc.relation.isPartOfJournal of visualized experiments : JoVE
pubs.issue135
pubs.notesNot known
pubs.organisational-group/ICR
pubs.organisational-group/ICR
pubs.publication-statusPublished
pubs.embargo.termsNot known
dc.contributor.icrauthorChoudhary, Jyotien


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