Corporate Banner
Satellite Banner
Proteomics
Scientific Community
 
Become a Member | Sign in
Home>News>This Article
  News
Return

The HUPO Proteomics Standards Initiative- Mass Spectrometry Controlled Vocabulary

Published: Monday, March 25, 2013
Last Updated: Wednesday, March 27, 2013
Bookmark and Share
In this article, researchers describe the overall structure of the controlled vocabularies, the process by which it has been developed and is maintained and the dependencies on other ontologies.

Abstract
Controlled vocabularies (CVs), i.e. a collection of predefined terms describing a modeling domain, used for the semantic annotation of data, and ontologies are used in structured data formats and databases to avoid inconsistencies in annotation, to have a unique (and preferably short) accession number and to give researchers and computer algorithms the possibility for more expressive semantic annotation of data. The Human Proteome Organization (HUPO)-Proteomics Standards Initiative (PSI) makes extensive use of ontologies/CVs in their data formats. The PSI-Mass Spectrometry (MS) CV contains all the terms used in the PSI MS-related data standards. The CV contains a logical hierarchical structure to ensure ease of maintenance and the development of software that makes use of complex semantics. The CV contains terms required for a complete description of an MS analysis pipeline used in proteomics, including sample labeling, digestion enzymes, instrumentation parts and parameters, software used for identification and quantification of peptides/proteins and the parameters and scores used to determine their significance. Owing to the range of topics covered by the CV, collaborative development across several PSI working groups, including proteomics research groups, instrument manufacturers and software vendors, was necessary. 

The article is published online in Database: The journal of biological databases and curation and is free to access.


Further Information

Join For Free

Access to this exclusive content is for Technology Networks Premium members only.

Join Technology Networks Premium for free access to:

  • Exclusive articles
  • Presentations from international conferences
  • Over 3,100+ scientific posters on ePosters
  • More than 4,500+ scientific videos on LabTube
  • 35 community eNewsletters


Sign In



Forgotten your details? Click Here
If you are not a member you can join here

*Please note: By logging into TechnologyNetworks.com you agree to accept the use of cookies. To find out more about the cookies we use and how to delete them, see our privacy policy.

Related Content

Proteomics for Systems Toxicology
MS-based proteomics is maturing into a robust technology for the measurement of proteome-wide exposure effects.
Monday, November 24, 2014
Identification of Psoriatic Arthritis Mediators in Synovial Fluid
This study represents the most comprehensive proteomic analysis of psoriatic arthritis synovial fluid, to date.
Friday, August 08, 2014
The Role of Mass Spectrometry in the "Omics" Era
The tremendous developments of the MS technology and concurrent gene sequencing efforts have made the “-omic” revolution possible.
Tuesday, February 18, 2014
Predictors of Obesity: The "Power" of the Omics
Diet and nutrient biomarkers should provide objective measures of dietary intake and nutritional status, as well as an integrated measure of intake, absorption and metabolism.
Friday, October 25, 2013
Label-free MS Proteome Quantification of Human Embryonic Kidney Cells Following 24 Hours of Sialic Acid Overproduction
Researchers have identified 1802 distinct proteins of which 105 proteins showed reliable expression changes.
Tuesday, August 13, 2013
Solid-Phase Glycan Isolation for Glycomics Analysis
In this article researchers from John Hopkins University reviewed current glycomics technologies for glycan purification, isolation, separation, and detection.
Thursday, June 27, 2013
A Nano LC-MALDI Mass Spectrometry Droplet Interface for the Analysis of Complex Protein Samples
In this article researchers from ETH Zürich have demonstrated a novel droplet-based interface between Nano–liquid chromatography and matrix assisted laser desorption ionisation mass spectrometry.
Thursday, June 06, 2013
Whole Gel Processing Procedure for GeLC-MS/MS Based Proteomics
The procedure will enable clinical proteomics for which GeLC-MS/MS is a popular workflow and sample numbers are relatively high.
Tuesday, May 14, 2013
Mass Spectrometry-Based Proteomics in Molecular Diagnostics: Discovery of Cancer Biomarkers Using Tissue Culture
Rapid development of MS-based proteomic techniques in the last decade that has immensely helped researchers in candidate biomarker discovery.
Monday, May 13, 2013
MultiAlign: A Multiple LC-MS Analysis Tool for Targeted Omics Analysis
This article demonstrates how two dissimilar LC-MS feature maps could be analyzed using MultiAlign’s MS/MS traceback and spectral clustering capability.
Tuesday, April 30, 2013
Identification of Plasma Lipid Biomarkers for Prostate Cancer by Lipidomics and Bioinformatics
This study explores a new approach to seeking biomarkers for prostate cancer and other diseases.
Monday, April 08, 2013
Development and Characterization of a Novel Plug and Play LC-MS Source
This article reports the development and characterization of a novel, vendor neutral, ultra-high pressure compatible (~10,000 psi) LC-MS source.
Tuesday, March 12, 2013
'Omics' Approaches to Understanding Interstitial Cystitis/Painful Bladder Syndrome/Bladder Pain Syndrome
This review describes the current state of 'omics' studies and available data sets relevant to IC/PBS/BPS.
Monday, March 11, 2013
Optimal Precursor Ion Selection for LC-MALDI MS/MS
Researchers present two algorithms for inclusion list creation that formulate precursor ion selection as an optimization problem.
Tuesday, February 26, 2013
Systems Biology Approaches and Applications in Obesity, Diabetes, and Cardiovascular Diseases
This article summarizes systems biology methodologies that can produce novel mechanistic insights, identify disease biomarkers, and uncover potential therapeutic targets from a combination of omics datasets.
Thursday, February 21, 2013
Scientific News
Structure of Essential Digestive Enzyme Uncovered
Using a powerful combination of techniques from biophysics to mathematics, researchers have revealed new insights into the mechanism of a liver enzyme that is critical for human health.
Getting a Better Look at How HIV Infects and Takes Over its Host Cells
A new approach, developed by a team of researchers led by The Rockefeller University and The Aaron Diamond AIDS Research Center (ADARC), offers an unprecedented view of how a virus infects and appropriates a host cell, step by step.
Untangling Disease-Related Protein Misfolding
Work advances understanding of genetic forms of thrombosis, emphysema, cirrhosis of the liver, neurodegenerative diseases and inflammation, among others.
Scientists Find Evidence That Cancer Can Arise Changes
Researchers at Rockefeller University have found a mutation that affects the proteins that package DNA without changing the DNA itself can cause a rare form of cancer.
US-India Collab Finds Molecular Signatures of Severe Malaria
Study may be a significant advancement in understanding the causes of severe malaria.
Triple-Negative Breast Cancer Target Is Found
Researchers at UC Berkeley discover a target that drives cancer metabolism in triple-negative breast cancer.
Crucial Reaction for Vision Revealed
Scientists have tracked the reaction of a protein responding to light, paving the way for a new understanding of life's essential reactions.
Cancer Can Arise from Histone Mutations
A mutation that affects the proteins that package DNA—without changing the DNA itself—can cause a rare form of cancer.
Mimicking Evolution to Create Novel Proteins
A study by researchers in the Kuhlman lab offers a new route to design the 'cellular machines' needed to understand and battle diseases.
Can Gender Play A Role In Determining Cancer Treatment Choices?
MD Anderson study reveals “sex-biased” gene signatures in review of 13 cancer types.
Scroll Up
Scroll Down
SELECTBIO

Skyscraper Banner
Go to LabTube
Go to eposters
 
Access to the latest scientific news
Exclusive articles
Upload and share your posters on ePosters
Latest presentations and webinars
View a library of 1,800+ scientific and medical posters
3,100+ scientific and medical posters
A library of 2,500+ scientific videos on LabTube
4,500+ scientific videos
Close
Premium CrownJOIN TECHNOLOGY NETWORKS PREMIUM FOR FREE!