Using proteomics to mine genome sequences

Journal of Proteome Research
Jonathan W Arthur, Marc R Wilkins

Abstract

We present a method for mining unannotated or annotated genome sequences with proteomic data to identify open reading frames. The region of a genome coding for a protein sequence is identified by using information from the analysis of proteins and peptides with MALDI-TOF mass spectrometry. The raw genome sequence or any unassembled contigs of an organism are theoretically cleaved into a number of equal sized but overlapping fragments, and these are then translated in all six frames into a series of virtual proteins. Each virtual protein is then subjected to a theoretical enzymatic digestion. Standard proteomic sample preparation methods are used to separate, array, and digest the proteins of interest to peptides. The masses of the resulting peptides are measured using mass spectrometry and compared to the theoretical peptide masses of the virtual proteins. The region of the genome responsible for coding for a particular protein can then be identified when there are a large number of hits between peptides from the protein and peptides from the virtual protein. The method makes no assumptions about the location of a protein in a particular gene sequence or the positions or types of start and stop codons. To illustrate this approa...Continue Reading

References

Aug 31, 1993·Biochemical and Biophysical Research Communications·P JamesG Gonnet
Jun 1, 1993·Proceedings of the National Academy of Sciences of the United States of America·W J HenzelC Watanabe
Jun 15, 1996·Genomics·M Burset, R Guigó
Jul 13, 2000·Electrophoresis·E J BreenM R Wilkins
May 5, 2001·Genome Research·S RogicF B Ouellette
Oct 27, 2001·Proteomics·J S ChoudharyJ S Cottrell
Oct 5, 2002·Nucleic Acids Research·Catherine MathéPierre Rouzé
Jan 10, 2003·Nucleic Acids Research·David L WheelerLukas Wagner
Jan 10, 2003·Nucleic Acids Research·Brigitte BoeckmannMichel Schneider
Jun 20, 2003·Journal of Proteome Research·Susanne K PedersenBen R Herbert

❮ Previous
Next ❯

Citations

Aug 30, 2008·Nature Chemical Biology·Ben GoldCarl Nathan
Jan 21, 2006·BMC Bioinformatics·Bradford C Powell, Clyde A Hutchison
Oct 31, 2006·BMC Bioinformatics·Kosaku ShinodaMasaru Tomita
May 9, 2008·PLoS Computational Biology·Leo McHugh, Jonathan W Arthur
Oct 18, 2006·Proteomics·Sandrine Palcy, Eric Chevet
Apr 4, 2006·Drug Discovery Today·Anne S De Groot
Apr 30, 2019·Expert Review of Proteomics·Deepa BishtVivek Kumar Gupta
Feb 15, 2005·Journal of Proteome Research·Jacques ColingeLydie Bougueleret
Nov 4, 2006·Journal of Proteome Research·Alon SavidorW Hayes McDonald

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.

Related Papers

Proceedings of the National Academy of Sciences of the United States of America
Michael C GiddingsBarry Moore
Proceedings of the National Academy of Sciences of the United States of America
Siu Kwan SzeFred W McLafferty
© 2022 Meta ULC. All rights reserved