Systems proteomics for translational network medicine.

@article{Arrell2012SystemsPF,
  title={Systems proteomics for translational network medicine.},
  author={D. Kent Arrell and Andre Terzic},
  journal={Circulation. Cardiovascular genetics},
  year={2012},
  volume={5 4},
  pages={
          478
        }
}
Proteomics encompasses diverse methods by which to study proteins, their abundance, structure, posttranslational modifications, and physical or functional interacting partners to map the proteome, the protein complement of a genome. Although such methods can be applied to individual proteins, proteomics facilitates large-scale analysis of complete proteomes or targeted subproteomes (Table 1). Moreover, proteomics enables comparisons between distinct conditions/states, from defined biological… 

Tables from this paper

Proteomic Network Systems Analysis
TLDR
Providing a framework to proteomic newcomers and experienced practitioners alike, this work outlines data analytic approaches and provides concrete examples of the pairing of network systems prognostication with informed follow-up, through application of complementary physiological experimentation to validate proteomic observations in cardiovascular health and disease.
From data gathering to systems medicine.
  • M. Mayr
  • Biology
    Cardiovascular research
  • 2013
TLDR
Four reviews summarize strategies how to advance the field of ‘-omics’, which aims to link variations in the DNA sequence directly to distinct phenotypes to understand the complex interplay of molecular changes related to cardiovascular disease.
Substrate-guided proteomics enhances degradome resolution.
TLDR
High-throughput proteomics offers a robust, adaptable technological foundation from which to systematically comprehend the underpinnings of (patho)physiological processes.
Network Biology in Medicine and Beyond
TLDR
High-throughput genomic and proteomic profiling technologies, such as DNA microarrays, next-generation sequencing and mass spectrometry–based proteomics and metabolomics, provide new opportunities to understand human diseases, identify potential biomarkers, and develop new treatments.
Transformative Impact of Proteomics on Cardiovascular Health and Disease: A Scientific Statement From the American Heart Association
TLDR
This scientific statement is to summarize advances over this period that have catalyzed the capacity to address the experimental, translational, and clinical implications of proteomics as applied to cardiovascular health and disease and to evaluate the current status of the field.
Stem cell systems informatics for advanced clinical biodiagnostics: tracing molecular signatures from bench to bedside
TLDR
Comprehensive elucidation of genomic, transcriptomic, proteomic, and metabolomic networks that define normal and pathological states, in combination with reprogrammed patient cells are thus poised to become high value resources in modern diagnosis and prognosis of patient disease.
Systems biology surveillance decrypts pathological transcriptome remodeling
TLDR
Diagnostic surveillance, through an algorithm that integrates pluripotent stem cell transcriptomes with advanced high throughput assays and computational bioinformatics, revealed collective gene expression network changes that underlie differential phenotype development.
Aha Scientific Statement Transformative Impact of Proteomics on Cardiovascular Health and Disease a Scientific Statement from the American Heart Association
TLDR
Approaches for proteomics to drive basic science research, facilitate clinical translation, and establish diagnostic and therapeutic healthcare algorithms are discussed and challenges that remain to be solved before proteomic technologies can be readily translated from scientific discoveries to meaningful advances in cardiovascular care are addressed.
KATP channel dependent heart multiome atlas
TLDR
The Kir6.2 deficit precipitates multiome reorganization, mapping a comprehensive atlas of the KATP channel dependent landscape and revealing functional convergence and an integrated signature of disease susceptibility.
An overview of the human brain myelin proteome and differences associated with schizophrenia
TLDR
The characterisation of the human myelinome was characterised in schizophrenia patients and healthy controls to visualise differences in proteomic profiles, consistent with the dysconnectivity hypothesis of schizophrenia.
...
...

References

SHOWING 1-10 OF 106 REFERENCES
Cardiovascular proteomics: evolution and potential.
TLDR
Proteomics provides researchers with cellular protein "inventories" at specific moments in time, making it ideal for documenting protein modification due to a particular disease, condition, or treatment, and should lead to functional proteomic studies, in which identification of protein modification has the ability to further the understanding of the interplay between proteome change and cardiovascular disease.
Overview: The Maturing of Proteomics in Cardiovascular Research
TLDR
4 articles provide concrete examples of how proteomics can be incorporated into cardiovascular research and address specific biological questions and illustrate how novel discoveries can be made and how proteomic technology has continued to evolve.
Overview: the maturing of proteomics in cardiovascular research.
TLDR
4 articles provide concrete examples of how proteomics can be incorporated into cardiovascular research and address specific biological questions and illustrate how novel discoveries can be made and how proteomic technology has continued to evolve.
Comprehensive Analysis of Protein Modifications by Top-Down Mass Spectrometry
TLDR
Top-down MS with ECD has been successfully applied to cardiovascular research, with the unique advantages in unraveling the molecular complexity, quantifying modified protein forms, complete mapping of modifications with full-sequence coverage, discovering unexpected modifications, identifying and quantifying positional isomers, and determining the order of multiple modifications.
Interpretation of Shotgun Proteomic Data
TLDR
The difficulties of interpreting shotgun proteomic data are illustrated and the need for common nomenclature and transparent informatic approaches are discussed and related issues such as the state of protein sequence databases and their role in shotgun proteomics analysis, interpretation of relative peptide quantification data in the presence of multiple protein isoforms, and the integration of proteomic and transcriptional data are discussed.
Proteomics of the heart: unraveling disease.
TLDR
The current status of proteomic technologies are reviewed, describing the 2-DE proteomics workflow, with an overview of protein identification by MS and how these technologies are being applied to studies of human heart disease.
Proteomic analysis of metabolic, cytoskeletal and stress response proteins in human heart failure
TLDR
The regulatory pathway to uncover the mechanism underlying heart failure is determined, and marked differences in the expression of selected proteins, including HSP27 and HSP20, were further confirmed by Western blot.
Proteins Involved in Platelet Signaling Are Differentially Regulated in Acute Coronary Syndrome: A Proteomic Study
TLDR
The present study provides novel information on platelet proteome changes associated with platelet activation in NSTE-ACS, highlighting the presence of proteins involved in platelet signaling.
...
...