Proteomics and phosphoproteomics in precision medicine: applications and challenges

Briefings in Bioinformatics
Girolamo Giudice, Evangelia Petsalaki

Abstract

Recent advances in proteomics allow the accurate measurement of abundances for thousands of proteins and phosphoproteins from multiple samples in parallel. Therefore, for the first time, we have the opportunity to measure the proteomic profiles of thousands of patient samples or disease model cell lines in a systematic way, to identify the precise underlying molecular mechanism and discover personalized biomarkers, networks and treatments. Here, we review examples of successful use of proteomics and phosphoproteomics data sets in as well as their integration other omics data sets with the aim of precision medicine. We will discuss the bioinformatics challenges posed by the generation, analysis and integration of such large data sets and present potential reasons why proteomics profiling and biomarkers are not currently widely used in the clinical setting. We will finally discuss ways to contribute to the better use of proteomics data in precision medicine and the clinical setting.

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Citations

Jun 26, 2018·Expert Review of Molecular Diagnostics·Emily C LydonEphraim L Tsalik
Nov 16, 2019·NPJ Systems Biology and Applications·Anika LiuJulio Saez-Rodriguez
Aug 13, 2020·Current Heart Failure Reports·Jan D LanzerJulio Saez-Rodriguez
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Jan 15, 2022·Cancer Control : Journal of the Moffitt Cancer Center·Alfredo AguilarClaudio J Flores

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Methods Mentioned

BETA
PCA

Software Mentioned

KinasePA ( Perturbation analysis
SVM
TieDie
PAM ( Prediction Analysis for Microarrays )
SAM ( Significance Analysis of Microarrays )
ProHits
HotNet2
OpenMS
IKAP
CLUE ( CLUster Evaluation

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