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Curr Pharm Des. 2018;24(32):3842-3858. doi: 10.2174/1381612824666181102125638.

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

Tang J1,2, Zhang Y1,2, Fu J2, Wang Y2, Li Y2, Yang Q2, Yao L3, Xue W1, Zhu F1,2.

Author information

1
School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China.
2
College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 401331, China.
3
Department of Health Sciences Research, Mayo Clinic, Rochester MN 55905, United States.

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; anticancer drug; computation; label-free quantification; mass spectrometry; target discovery.

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