title: PGx: Putting Peptides to BED.
abstract: Every molecular player in the cast of biology's central dogma is being sequenced and quantified with increasing ease and coverage. To bring the resulting genomic, transcriptomic, and proteomic data sets into coherence, tools must be developed that do not constrain data acquisition and analytics in any way but rather provide simple links across previously acquired data sets with minimal preprocessing and hassle. Here we present such a tool: PGx, which supports proteogenomic integration of mass spectrometry proteomics data with next-generation sequencing by mapping identified peptides onto their putative genomic coordinates.
authors.affiliation: Biomedical Hosting LLC, 33 Lewis Avenue, Arlington, Massachusetts 02474, United States.
authors.forename: Manor
authors.initials: M
authors.lastname: Askenazi
authors.affiliation: NYU Langone Medical Center , 227 East 30th Street, New York, New York 10016, United States.
authors.forename: Kelly V
authors.initials: KV
authors.lastname: Ruggles
authors.affiliation: NYU Langone Medical Center , 227 East 30th Street, New York, New York 10016, United States.
authors.forename: David
authors.initials: D
authors.lastname: Fenyö
mesh_terms: D030562:Databases, Protein; D020869:Gene Expression Profiling; D023281:Genomics / Q000379:methods*; D006801:Humans; D013058:Mass Spectrometry; D009363:Neoplasm Proteins / Q000235:genetics; D010449:Peptide Mapping; D040901:Proteomics / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*
chemical_list: D009363:Neoplasm Proteins
keywords: proteogenomic mapping; proteogenomics; proteomics