Proteogenomics

rdf:langString Proteogenomics

rdf:langString Proteogenomics is a field of biological research that utilizes a combination of proteomics, genomics, and transcriptomics to aid in the discovery and identification of peptides. Proteogenomics is used to identify new peptides by comparing MS/MS spectra against a protein database that has been derived from genomic and transcriptomic information. Proteogenomics often refers to studies that use proteomic information, often derived from mass spectrometry, to improve gene annotations. The utilization of both proteomics and genomics data alongside advances in the availability and power of spectrographic and chromatographic technology led to the emergence of proteogenomics as its own field in 2004. Proteomics deals with proteins in the same way that Genomics studies the genetic code of entire organisms, while Transcriptomics deals with the study of RNA sequencing and transcripts. While all three fields might use forms of mass spectrometry and chromatography to identify and study the functions of DNA, RNA, and proteins, proteomics relies on the assumption that current gene models are correct and that all relevant protein sequences can be found in a reference database such as the Proteomics Identifications Database. Proteogenomics helps eliminate this reliance on existing, limited genetic models by combining datasets from multiple fields in order to produce a database of proteins or genetic markers. In addition, the emergence of novel protein sequences due to mutations often cannot be accounted for in traditional proteomic databases, but can be predicted and studied using a synthesis of genomic and transcriptomic data. The resulting research has applications in improving gene annotations, studying mutations, and understanding the effects of genetic manipulation. More recently, the joint profiling of surface proteins and mRNA transcripts from single cells by methods such as CITE-Seq and ESCAPE has been referred to as single-cell proteogenomics, although the goals of these studies are not related to peptide identification. Since 2019 these methods are more commonly referred to as multimodal omics or multi-omics.