Related Experiment Video
Updated: May 13, 2026
09:10
A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes
Published on: May 22, 2018
Whole human genome proteogenomic mapping for ENCODE cell line data: identifying protein-coding regions.
Jainab Khatun1, Yanbao Yu, John A Wrobel
1College of Arts and Sciences, Boise State University, Boise, ID, USA. jainabkhatun@boisestate.edu
BMC Genomics
|March 2, 2013
Summary
Proteogenomic mapping using mass spectrometry identified novel protein-coding regions in the human genome. This approach complements existing genome annotation methods by revealing regions outside current gene models.
Area of Science:
- Genomics
- Proteomics
- Bioinformatics
Background:
- Proteogenomic mapping leverages mass spectrometry data to identify protein-coding genes.
- This method aids in discovering novel translational regions within the human genome.
- The study integrated with the Encyclopedia of DNA Elements (ENCODE) project.
Purpose of the Study:
- To apply proteogenomic mapping to identify potential protein-coding regions missing from the human genome.
- To generate proteogenomic tracks for the UCSC Genome Browser.
Main Methods:
- Generated approximately 1 million tandem mass (MS/MS) spectra from K562 and GM12878 cell lines.
- Mapped spectra against the UCSC hg19 human genome and GENCODE V7 annotations.
- Compared results from protein, transcript, and whole-genome searches to enhance confidence in novel findings.
Main Results:
- Identified 481 unique peptides solely through whole-genome proteogenomic mapping.
- At a 1% false discovery rate, identified 26,472 peptides from protein, 24,406 from transcript, and 13,128 from whole-genome searches.
- Discovered that approximately 4% of uniquely mapped peptides fell outside GENCODE V7 annotated exons.
Conclusions:
- Whole-genome proteogenomic mapping is a valuable complementary technique for genome annotation.
- This approach identified 15% more spectra compared to protein database searches alone.
- The proteogenomic mapping data are publicly available on the UCSC Genome Browser.
Related Concept Videos
02:24Ribosome Profiling
Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique helps...
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique helps...
01:33Proteomics
A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term proteomics...
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term proteomics...
00:58Genomic DNA in Eukaryotes
Eukaryotes have large genomes compared to prokaryotes. To fit their genomes into a cell, eukaryotic DNA is packaged extraordinarily tightly inside the nucleus. To achieve this, DNA is tightly wound around proteins called histones, which are packaged into nucleosomes that are joined by linker DNA and coil into chromatin fibers. Additional fibrous proteins further compact the chromatin, which is recognizable as chromosomes during certain phases of cell division.
03:36Genome Annotation and Assembly
The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
02:02Genomics
Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
00:46Genomic DNA in Prokaryotes
The genome of most prokaryotic organisms consists of double-stranded DNA organized into one circular chromosome in a region of cytoplasm called the nucleoid. The chromosome is tightly wound, or supercoiled, for efficient storage. Prokaryotes also contain other circular pieces of DNA called plasmids. These plasmids are smaller than the chromosome and often carry genes that confer adaptive functions, such as antibiotic resistance.
Genomic Diversity in Bacteria
Although bacterial genomes are much...
Genomic Diversity in Bacteria
Although bacterial genomes are much...