Computational advances in the label-free quantification of cancer proteomics data

December 27, 2018

In recent years, proteomics research has become a popular method for characterizing the functional proteins driving the transformation of malignancy, tracing the large-scale protein alterations induced by anti-cancer drug, as well as discovering the innovative targets and first-in-class drugs for oncologic disorders. Proteomics became popular due to its ability to provide quantitative and dynamic information on tumor genesis and development by directly profiling protein expression. Label-free Quantification (LFQ) is an important method for quantifying protein expression in cancer proteomics. However, the main challenge in using this method for discovering anti-cancer targets and drugs is the low precision, poor reproducibility, and inaccuracy of the LFQ of proteomics data.

This paper presents a review of the recent advances and the computational development of LFQ in cancer proteomics. PubMed and Web of Science databases were searched for label-free quantification approaches, cancer proteomics, and computational advances. A number of experiments including popular acquisition techniques and state-of-the-art quantification tools are critically analyzed and discussed. Following this, the processing approaches which included transformation, normalization, filtering, and imputation were discussed and their impacts on improving LFQ performance of cancer proteomics were evaluated.

The authors also discuss the future direction for enhancing the computation-based quantification technique for cancer proteomics. The dramatic increase in the use of LFQ approaches in cancer proteomics can lead to the enhancement of quantification strategies for studying cancer proteomics in the future once its limitations are accounted for.
-end-
The article is Open Access till 31st December, 2018. To obtain the article, please visit: http://www.eurekaselect.com/166976

Bentham Science Publishers

Related Proteomics Articles from Brightsurf:

Recipe for success -- interaction proteomics become a household item
A research team from University of Helsinki introduces a new optimised and integrated interaction proteomics protocol that combines two state-of-the art methods to allow rapid identification of protein-protein interactions and more.

New technology CF LINK for protein bioconjugation and structural proteomics
CF Plus Chemicals, a spin-off of ETH Zurich, IOCB Prague, and IMIC have developed a new technology called CF LINK for site-selective bioconjugation of proteins and also their structural characterization.

New proteomics technique gives insights into ubiquitin signalling
Australian researchers are among the first in the world to have access to a new approach to understand intricate changes that control how proteins function in our cells in health and disease.

Computational advances in the label-free quantification of cancer proteomics data
In this paper, the recent advances and development in the computational perspective of LFQ in cancer proteomics were systematically reviewed and analyzed.

Proteomics studies on the basic biology of Alzheimer's, cancer and listeriosis
Recent articles in the journal Molecular & Cellular Proteomics investigate metabolic quirks of cancer cells, the effects of inhibiting the enzyme that generates amyloid beta, and the mechanism by which a bacterial toxin kills host cells.

Finnish scientists analyzed the proteome of T helper 17 cells
T helper 17 (Th17) cells belong to a group of T cells with essential functions in autoimmune diseases and inflammation.

Researchers can count on improved proteomics method
Princeton's Martin Wühr has improved upon his method to accurately count the proteins present in a cell under different circumstances.

Painless real-time proteomics may one day speed up cancer surgery
Researchers at the University of Lille developed a matrix-assisted ion source for mass spectrometry that can liberate lipids and metabolites from the skin without causing pain.

Using proteomics to understand pathogens
Recent studies in the journal Molecular & Cellular Proteomics have shed light on pathogenic mechanisms of the sexually-transmitted parasite Trichomonas vaginalis and the HIV-associated opportunistic lung fungus Aspergillus.

Novel proteomics strategies aid cancer research
This month's issue of the journal Molecular & Cellular Proteomics features several studies using novel proteomics methods to address unanswered questions in cancer research, including protein variation within tumors; the failure of some candidate cancer drugs; and how chemotherapeutic combinations act synergistically.

Read More: Proteomics News and Proteomics Current Events
Brightsurf.com is a participant in the Amazon Services LLC Associates Program, an affiliate advertising program designed to provide a means for sites to earn advertising fees by advertising and linking to Amazon.com.