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Computational Advances in the Label-free Quantification of Cancer Proteomics Data

[ Vol. 24 , Issue. 32 ]

Author(s):

Jing Tang, Yang Zhang, Jianbo Fu, Yunxia Wang, Yi Li, Qingxia Yang, Lixia Yao, Weiwei Xue* and Feng Zhu*   Pages 3842 - 3858 ( 17 )

Abstract:


Background: Due to its ability to provide quantitative and dynamic information on tumor genesis and development by directly profiling protein expression, the proteomics has become intensely popular for characterizing the functional proteins driving the transformation of malignancy, tracing the large-scale protein alterations induced by anticancer drug, and discovering the innovative targets and first-in-class drugs for oncologic disorders.

Objective: To quantify cancer proteomics data, the label-free quantification (LFQ) is frequently employed. However, low precision, poor reproducibility and inaccuracy of the LFQ of proteomics data have been recognized as the key “technical challenge” in the discovery of anticancer targets and drugs. In this paper, the recent advances and development in the computational perspective of LFQ in cancer proteomics were therefore systematically reviewed and analyzed.

Methods: PubMed and Web of Science database were searched for label-free quantification approaches, cancer proteomics and computational advances.

Results: First, a variety of popular acquisition techniques and state-of-the-art quantification tools are systematically discussed and critically assessed. Then, many processing approaches including transformation, normalization, filtering and imputation are subsequently discussed, and their impacts on improving LFQ performance of cancer proteomics are evaluated. Finally, the future direction for enhancing the computation-based quantification technique for cancer proteomics are also proposed.

Conclusion: There is a dramatic increase in LFQ approaches in recent year, which significantly enhance the diversity of the possible quantification strategies for studying cancer proteomics.

Keywords:

Cancer proteomics, label-free quantification, target discovery, anticancer drug, computation, mass spectrometry.

Affiliation:

College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 401331, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 401331, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 401331, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 401331, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 401331, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 401331, Department of Health Sciences Research, Mayo Clinic, Rochester MN 55905, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China; bCollege of Pharmaceutical Sciences, Zhejiang University, Hangzhou 401331, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 401331



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