Proteogenomics uses an integrated approach by combining genomics, proteomics, and transcriptomics.
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 [1] has been referred to as single-cell proteogenomics,[2][3][4] 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.[5]
^"Proteona ESCAPE RNA Sequencing". 11 December 2018.
^"Proteona Driving Adoption of Immune Profiling Platform for CAR-T, Multiple Myeloma Research". Precision Oncology News. 2021-05-07. Retrieved 2021-05-15.
^"TotalSeq eBook". BioLegend. Retrieved November 23, 2020.
^"Proteona releases ESCAPE™ RNA sequencing for measuring protein and RNA in single cells with a focus on clinical questions". Proteona. Retrieved November 23, 2020.
^"Method of the Year 2019: Single-cell multimodal omics". Nature Methods. 17 (1): 1. January 2020. doi:10.1038/s41592-019-0703-5. ISSN 1548-7105. PMID 31907477.
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approximately 12,000–14,000 pseudogenes in the human genome. A 2016 proteogenomics analysis using mass spectrometry of peptides identified at least 19...
in protein folding studies. In what is now commonly referred to as proteogenomics, peptides identified with mass spectrometry are used for improving gene...
Uses proteomics mass spectrometry data for protein expression studies Proteogenomics: An emerging field of biological research at the intersection of proteomics...
(also Community Proteomics, Environmental Proteomics, or Community Proteogenomics) is an umbrella term for experimental approaches to study all proteins...
endosymbionts of Riftia pachyptila and Tevnia jerichonana revealed by proteogenomics. (2011, October 20). Retrieved June 1, 2015, from http://www.nature...
fluid mechanics engineer and university professor 賴義雄博士 Yu-Ju Chen, proteogenomics researcher 陳玉如 David Ho, medical researcher 何大一 Henry Lee*, forensic...
to determine if polypeptides are, in fact, translated from a sORF. Proteogenomics combines proteomics, genomics, and transciptomics. This is important...
approaches, such as metagenomics, metatranscriptomics, proteomics and proteogenomics, are rapidly advancing, at least for the microbial world. Metaphenomics...
frameshifts and translation initiation factors. To solve this problem, proteogenomics based approaches are employed, which utilize information from expressed...
Jackson ER, Vitanza NA, Cain JE, et al. (January 2022). "Pharmaco-proteogenomic profiling of pediatric diffuse midline glioma to inform future treatment...
1093/nar/gks1193. PMC 3531084. PMID 23193258. Ahn, Jung-Mo; et al. (Nov 2013). "Proteogenomic Analysis of Human Chromosome 9-Encoded Genes from Human Samples and...
Cancer Clinical Proteomics Research". "Mount Sinai Designated as National Cancer Institute Proteogenomics Data Analysis Center | Mount Sinai - New York"....
an avalanche of overlapping genes and ORFs within numerous genomes. Proteogenomic methods have been essential in discovering numerous overlapping genes...
Leeuwenhoek 101(3): 551-560 Delmotte, N., et al. (2009). "Community proteogenomics reveals insights into the physiology of phyllosphere bacteria." Proc...
Chaffron S, Innerebner G, Roschitzki B, et al. (2009). "Community proteogenomics reveals insights into the physiology of phyllosphere bacteria" (PDF)...
Studer (born 1957), ornithologist and environmentalist Yu-Ju Chen, proteogenomics researcher Chung-Pei Ma (born 1966), astrophysicist, now in the United...
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