New and improved proteomics technologies for understanding complex biological systems: Addressing a grand challenge in the life sciences

Hood, Leroy; Omenn, Gilbert S.; Moritz, Robert L.; Aebersold, Ruedi; Yamamoto, Keith R.; Amos, Michael D.; Hunter-Cevera, Jennie; Locascio, Laurie E.

doi:10.1002/pmic.201270086

Cited by 57 publications

(46 citation statements)

References 25 publications

(24 reference statements)

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“…They then engineered five protein constructs bearing different mutations and rearrangements, and demonstrated that these constructs could be discriminated with accuracies ranging from 86 to 99%. Protein sequencing will allow studies of complex interactions among cells in different tissues [68]. …”

Section: Discussionmentioning

confidence: 99%

The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community

et al. 2016

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Section: Discussionmentioning

confidence: 99%

The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community

et al. 2016

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“…The high-throughput technical advances that have ensued through the past decade permit the global and focussed capture of dynamic changes in complex proteomes in a quantitative manner. The coming of age of quantitative proteomic methodologies, together with increasing awareness of the pre-analytical and analytical variables that confound data interpretation, have ensured that modern proteomic applications are increasingly offering a viable route to delivering robust, reproducible and standardised data sets [31,32]. The differential and quantitative profiling of the dynamic protein changes in health and disease will inevitably further our understanding of the mechanistic basis of disease.…”

Section: Proteomics In Drug Discoverymentioning

confidence: 99%

“Omics”-Informed Drug and Biomarker Discovery: Opportunities, Challenges and Future Perspectives

2016

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The pharmaceutical industry faces unsustainable program failure despite significant increases in investment. Dwindling discovery pipelines, rapidly expanding R&D budgets and increasing regulatory control, predict significant gaps in the future drug markets. The cumulative duration of discovery from concept to commercialisation is unacceptably lengthy, and adds to the deepening crisis. Existing animal models predicting clinical translations are simplistic, highly reductionist and, therefore, not fit for purpose. The catastrophic consequences of ever-increasing attrition rates are most likely to be felt in the developing world, where resistance acquisition by killer diseases like malaria, tuberculosis and HIV have paced far ahead of new drug discovery. The coming of age of Omics-based applications makes available a formidable technological resource to further expand our knowledge of the complexities of human disease. The standardisation, analysis and comprehensive collation of the “data-heavy” outputs of these sciences are indeed challenging. A renewed focus on increasing reproducibility by understanding inherent biological, methodological, technical and analytical variables is crucial if reliable and useful inferences with potential for translation are to be achieved. The individual Omics sciences—genomics, transcriptomics, proteomics and metabolomics—have the singular advantage of being complimentary for cross validation, and together could potentially enable a much-needed systems biology perspective of the perturbations underlying disease processes. If current adverse trends are to be reversed, it is imperative that a shift in the R&D focus from speed to quality is achieved. In this review, we discuss the potential implications of recent Omics-based advances for the drug development process.

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“…However, development of new diagnostic and therapeutic tools for CKD is hampered by our incomplete understanding of its underlying pathophysiology. In this direction, targeted mass spectrometry is a powerful tool, enabling simultaneous quantification of several prespecified proteins in biologic samples (Hood et al, 2012). Determining the abundance of protein components or targets of a given pathway using quantitative proteomics can generate a snapshot of the pathway status and activity within these samples.…”

Section: Introductionmentioning

confidence: 99%

An Optimized Method for Protein Extraction from OCT-Embedded Human Kidney Tissue for Protein Quantification by LC-MS/MS Proteomics

Vrana

Goodling

Afkarian

et al. 2016

Drug Metabolism and Disposition

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The existing biobanks of remnant tissue from clinically indicated kidney biopsies are attractive potential reservoirs for quantification of clinically relevant human tissue proteins by quantitative proteomics. However, a significant caveat of this strategy is that the tissues are often preserved in optimal cutting temperature (OCT) medium. Although OCT is an effective method of preserving the morphologic and immunohistological characteristics of tissues for later study, it significantly impacts efforts to quantify protein expression by liquid chromatography-tandem mass spectrometry methods. We report here a simple, reproducible, and cost-effective procedure to extract proteins from OCT-embedded tissue samples. Briefly, the excess frozen OCT medium was scraped before thawing from the tissue specimens stored at -80°C for ∼3 months. The tissue samples were homogenized and diethyl ether/methanol extraction was performed to remove the remaining OCT medium. The recovered protein was denatured, reduced, and alkylated. The second step of protein extraction and desalting was performed by chloroform/methanol/ water extraction of denatured proteins. The resultant protein pellet was trypsin-digested and the marker proteins of various kidney cellular compartments were quantified by targeted selective reaction monitoring proteomics. Upon comparison of peptide signals from OCT-embedded tissue and flash-frozen tissue from the same donors, both individual protein quantities, and their interindividual variabilities, were similar. Therefore, the approach reported here can be applied to clinical reservoirs of OCT-preserved kidney tissue to be used for quantitative proteomics studies of clinically relevant proteins expressed in different parts of the kidney (including drug transporters and metabolizing enzymes).

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New and improved proteomics technologies for understanding complex biological systems: Addressing a grand challenge in the life sciences

Cited by 57 publications

References 25 publications

The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community

The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community

“Omics”-Informed Drug and Biomarker Discovery: Opportunities, Challenges and Future Perspectives

An Optimized Method for Protein Extraction from OCT-Embedded Human Kidney Tissue for Protein Quantification by LC-MS/MS Proteomics

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