Proteogenomics

Proteogenomics combines genomic and proteomic data to identify proteins, study gene expression, and improve genome annotation.

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Mass spectrometry: An analytical technique that identifies molecules by measuring the mass-to-charge ratios of their ions. It supplies peptide measurements that proteogenomic analyses compare with predicted protein sequences.
Genome: The complete set of genetic material in an organism or cell. Its sequence provides the potential coding regions that proteogenomic evidence can test.
Genome annotation: The identification and description of genes and other functional features in a genome sequence. Protein evidence can refine coding boundaries, splice forms, and translated regions.
Shotgun proteomics: A proteomics strategy that identifies proteins by analyzing peptides from a complex sample. It can identify proteins using existing databases without revising genome-derived sequences.
Tandem mass spectrometry: Mass spectrometry that fragments selected ions to produce spectra revealing molecular structure. Fragmentation spectra help distinguish peptide sequences in genome-informed protein searches.
Transcriptome: The complete set of RNA transcripts produced in a cell or organism under specified conditions. RNA evidence helps locate expressed genes and interpret protein-coding regions.
Alternative splicing: The production of different RNA transcripts from one gene by joining exons in distinct combinations. Peptides spanning particular exon combinations can support specific protein isoforms.
RNA sequencing: A sequencing method that measures RNA molecules in a biological sample. It reveals transcription, while proteogenomics adds direct evidence about translated proteins.
Database search: A computational method that compares experimental data with entries in a reference database. Proteogenomics searches peptide spectra against protein sequences translated from genomic regions.
Proteome: The complete set of proteins expressed by a cell, tissue, or organism under specified conditions. Proteomic measurements reveal which gene products are present in the sampled material.