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Related Concept Videos

Proteomics01:33

Proteomics

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...
Protein Families02:47

Protein Families

Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism.   Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members.   If these new proteins contain similar amino acids in key locations, protein...
Tagging and Fusion Proteins01:24

Tagging and Fusion Proteins

Proteins are involved in several cellular processes and biochemical reactions. Analyzing a specific protein of interest requires it to be isolated from the other proteins in the cell. This is achieved by overexpressing the specific gene in a suitable host to produce large quantities of the target protein. A tag or label is recombined with the gene to produce a fusion protein containing the target protein and the tag. The tags on these fusion proteins can then be used for easy detection and...
Ribosome Profiling02:24

Ribosome 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...
Genome Annotation and Assembly03:36

Genome 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.
Globular and Fibrous Proteins02:21

Globular and Fibrous Proteins

Many proteins can be classified into two distinct subtypes - globular or fibrous. These two types differ in their shapes and solubilities.
Globular proteins are also known as spheroproteins and typically are approximately round in shape. They contain a mix of amino acid types and contain differing sequences in their primary structures. Globular proteins have many different functions, such as enzymes, cellular messengers, and molecular transporters. These roles often require the proteins to be...

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Updated: Jul 5, 2026

Mass Spectrometry-Based Proteomics Analyses Using the OpenProt Database to Unveil Novel Proteins Translated from Non-Canonical Open Reading Frames
07:38

Mass Spectrometry-Based Proteomics Analyses Using the OpenProt Database to Unveil Novel Proteins Translated from Non-Canonical Open Reading Frames

Published on: April 11, 2019

Proteomics FASTA archive and reference resource.

Jayson A Falkner1, James A Hill, Philip C Andrews

  • 1Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA.

Proteomics
|April 30, 2008
PubMed
Summary
This summary is machine-generated.

A new FASTA file archive and reference resource is now available on ProteomeCommons.org. This resource facilitates citing and archiving FASTA files, supporting the Human Proteome Organization

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Last Updated: Jul 5, 2026

Mass Spectrometry-Based Proteomics Analyses Using the OpenProt Database to Unveil Novel Proteins Translated from Non-Canonical Open Reading Frames
07:38

Mass Spectrometry-Based Proteomics Analyses Using the OpenProt Database to Unveil Novel Proteins Translated from Non-Canonical Open Reading Frames

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14:51

Comprehensive Workflow of Mass Spectrometry-based Shotgun Proteomics of Tissue Samples

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Navigating the Mass Spectrometry-Based Proteomic Data Using Free Computational Tools
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Navigating the Mass Spectrometry-Based Proteomic Data Using Free Computational Tools

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Area of Science:

  • Proteomics
  • Bioinformatics
  • Data Archiving

Background:

  • The Human Proteome Organization's Proteomics Standards Initiative (HUPO-PSI) has standardized FASTA file formats.
  • There is a lack of standardized methods for citing and accessing FASTA files in scientific publications.
  • Proteomics research relies heavily on FASTA files for sequence data.

Purpose of the Study:

  • To introduce a new FASTA file archive and reference resource on ProteomeCommons.org.
  • To address the need for standardized FASTA file citation and public accessibility.
  • To support the adoption of HUPO-PSI standards in proteomics research.

Main Methods:

  • Developed an extension to the Tranche data sharing network.
  • Integrated web pages, documentation, and tools for FASTA file management.
  • Implemented features for FASTA file conversion to HUPO-PSI format, citation, and archiving.

Main Results:

  • A new, free, and publicly accessible FASTA archive is now available at http://www.proteomecommons.org/data/fasta/.
  • Tools for FASTA file conversion, citation, and archiving are provided.
  • Source-code for related tools is available under the BSD license.

Conclusions:

  • The new resource provides a centralized solution for managing FASTA files in proteomics studies.
  • This initiative promotes data reproducibility and accessibility in the scientific community.
  • The resource supports the HUPO-PSI standards, enhancing data interoperability.