Commentary: Deep Phosphoproteomic Measurements Pinpointing Drug Induced Protective Mechanisms in Neuronal Cells

Yadav, Amit Kumar

doi:10.3389/fphys.2017.00174

Cited by 5 publications

(1 citation statement)

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“…Biological questions demand not only identification but also reliable quantitation to capture the proteome dynamics. The quantitative changes in the proteome can help us in understanding cellular mechanisms that can aid in monitoring temporal changes to stimulation, biological stress, or infection, finding new drug targets, and predicting the response to various drugs. − Numerous authors have articulated the need for better quantitative proteomics study designs to generate reproducible data across a large number of samples for systems biology analysis. , For a true systems biology approach, there is a need to generate deep profiling data with robust and reproducible quantitation, which can be used for modeling and understanding the dynamics of the system without concerns about the loss of data and quantitation fidelity . The bottom-up shotgun proteomics method has proven its value in generating a parts list of proteome catalogs, but it is suboptimal in capturing accurate quantitation with enough reliable statistical power and confidence …”

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confidence: 99%

Advances in Higher Order Multiplexing Techniques in Proteomics

2019

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Proteomics by mass spectrometry (MS) allows the large-scale identification and quantitation of the cellular proteins in a given biological context. Systems biology studies from proteomics data are largely limited by the accuracy and coverage of quantitative proteomics along with missing values. Toward this end, statistically robust biological observations are required, comprising multiple replicates, preferably with little technical variations. Multiplexed labeling techniques in proteomics allow quantitative comparisons of several biological samples or conditions. In this focused Review, we discuss an emerging technique called higher order multiplexing or enhanced multiplexing, a unique combination of traditional MS1- and MS2-based quantitative proteomics methods that allows for expanding the multiplexing capability of MS methods to save valuable instrument time, achieve statistical robustness, enhance coverage and quantitation accuracy, and reduce the run-to-run variability. We discuss the various innovative studies and experimental designs that exploit the power of this technique and its variants to provide an overview of a rapidly growing area and also to highlight the advantages and challenges that lie ahead in the widespread adoption of this technique.

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