Quantitative proteomics: challenges and opportunities in basic and applied research

Schubert, Olga T.; Röst, Hannes L.; Collins, Ben C.; Rosenberger, George; Aebersold, Ruedi

doi:10.1038/nprot.2017.040

Cited by 213 publications

(180 citation statements)

References 78 publications

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“…Overall, the targeted proteomics approach is gaining momentum to be an integral part of basic research and clinics. For this to happen in an acceptable timeline, the method needs to be more accessible and easier to use . Automation at various steps, such as sample processing, instrument handling, and data analysis, is crucial for achieving this task.…”

Section: Discussionmentioning

confidence: 99%

Targeted Proteomics Comes to the Benchside and the Bedside: Is it Ready for Us?

Arora

Somasundaram

2019

BioEssays

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While mass spectrometry (MS)‐based quantification of small molecules has been successfully used for decades, targeted MS has only recently been used by the proteomics community to investigate clinical questions such as biomarker verification and validation. Targeted MS holds the promise of a paradigm shift in the quantitative determination of proteins. Nevertheless, targeted quantitative proteomics requires improvisation in making sample processing, instruments, and data analysis more accessible. In the backdrop of the genomic era reaching its zenith, certain questions arise: is the proteomic era about to come? If we are at the beginning of a new future for protein quantification, are we prepared to incorporate targeted proteomics at the benchside for basic research and at the bedside for the good of patients? Here, an overview of the knowledge required to perform targeted proteomics as well as its applications is provided. A special emphasis is placed on upcoming areas such as peptidomics, proteoform research, and mass spectrometry imaging, where the utilization of targeted proteomics is expected to bring forth new avenues. The limitations associated with the acceptance of this technique for mainstream usage are also highlighted. Also see the video abstract here https://youtu.be/mieB47B8gZw.

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Section: Discussionmentioning

confidence: 99%

Targeted Proteomics Comes to the Benchside and the Bedside: Is it Ready for Us?

Arora

Somasundaram

2019

BioEssays

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“…The success of some quantitative proteomic experiments requires chemical derivatization for better MS ionization and sensitivity, 53,54 whereas stable-isotope labeling can address experimental variability. 55,56 Because several published reviews and tutorials have covered quantitative proteomics in detail, [57][58][59][60] we focus here on a critical summary of the advantages, limitations, and utility of technique in ADME and PD applications ( Table 2C).…”

Section: Quantitative Proteomic Methodsmentioning

confidence: 99%

Toward a Consensus on Applying Quantitative Liquid Chromatography‐Tandem Mass Spectrometry Proteomics in Translational Pharmacology Research: A White Paper

Prasad

Achour

Artursson

et al. 2019

Clin Pharma and Therapeutics

122

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Quantitative translation of information on drug absorption, disposition, receptor engagement, and drug–drug interactions from bench to bedside requires models informed by physiological parameters that link in vitro studies to in vivo outcomes. To predict in vivo outcomes, biochemical data from experimental systems are routinely scaled using protein quantity in these systems and relevant tissues. Although several laboratories have generated useful quantitative proteomic data using state‐of‐the‐art mass spectrometry, no harmonized guidelines exit for sample analysis and data integration to in vivo translation practices. To address this gap, a workshop was held on September 27 and 28, 2018, in Cambridge, MA, with 100 experts attending from academia, the pharmaceutical industry, and regulators. Various aspects of quantitative proteomics and its applications in translational pharmacology were debated. A summary of discussions and best practices identified by this expert panel are presented in this “White Paper” alongside unresolved issues that were outlined for future debates.

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“…Another example of the power of transcriptome analysis has recently been the identification of allelic expression imbalance causing the dominant expression of a heterozygous pathogenic allele ( PEX6 ) in an otherwise autosomal recessive disease (Zellweger Spectrum Disorder) . Although proteomics has lagged behind genomics and transcriptomics, especially with respect to high‐throughput analysis it is clear that proteomics will also be an essential tool with great potential in the future if the current limitations have been resolved (for recent reviews see References ).…”

Section: Multi‐omics and Inborn Errors Of Metabolismmentioning

confidence: 99%

Translational Metabolism: A multidisciplinary approach towards precision diagnosis of inborn errors of metabolism in the omics era

Wanders

Vaz

Ferdinandusse

et al. 2019

J of Inher Metab Disea

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The laboratory diagnosis of inborn errors of metabolism has been revolutionized in recent years, thanks to the amazing developments in the field of DNA sequencing including whole exome and whole genome sequencing (WES and WGS). Interpretation of the results coming from WES and/or WGS analysis is definitely not trivial especially since the biological relevance of many of the variants identified by WES and/or WGS, have not been tested experimentally and prediction programs like POLYPHEN‐2 and SIFT are far from perfect. Correct interpretation of WES and/or WGS results can only be achieved by performing functional studies at multiple levels (different metabolomics platforms, enzymology, in vitro and in vivo flux analysis), often requires studies in model organisms like zebra fish, Caenorhabditis elegans, Saccharomyces cerevisiae, mutant mice and others, and also requires the input of many different disciplines to make this Translational Metabolism approach effective.

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Quantitative proteomics: challenges and opportunities in basic and applied research

Cited by 213 publications

References 78 publications

Targeted Proteomics Comes to the Benchside and the Bedside: Is it Ready for Us?

Targeted Proteomics Comes to the Benchside and the Bedside: Is it Ready for Us?

Toward a Consensus on Applying Quantitative Liquid Chromatography‐Tandem Mass Spectrometry Proteomics in Translational Pharmacology Research: A White Paper

Translational Metabolism: A multidisciplinary approach towards precision diagnosis of inborn errors of metabolism in the omics era

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