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Crowgey EL, Matlock A, Fort-Bober J, Van Eky JE, Van Eyk JE. Mapping Biological Networks from Quantitative Data-Independent Acquisition Mass Spectrometry: Data to Knowledge Pipelines. Methods Mol Biol 2017; 1558:395-413. [PMID: 28150249 PMCID: PMC6844627 DOI: 10.1007/978-1-4939-6783-4_19] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Data-independent acquisition mass spectrometry (DIA-MS) strategies and applications provide unique advantages for qualitative and quantitative proteome probing of a biological sample allowing constant sensitivity and reproducibility across large sample sets. These advantages in LC-MS/MS are being realized in fundamental research laboratories and for clinical research applications. However, the ability to translate high-throughput raw LC-MS/MS proteomic data into biological knowledge is a complex and difficult task requiring the use of many algorithms and tools for which there is no widely accepted standard and best practices are slowly being implemented. Today a single tool or approach inherently fails to capture the full interpretation that proteomics uniquely supplies, including the dynamics of quickly reversible chemically modified states of proteins, irreversible amino acid modifications, signaling truncation events, and, finally, determining the presence of protein from allele-specific transcripts. This chapter highlights key steps and publicly available algorithms required to translate DIA-MS data into knowledge.
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Affiliation(s)
| | - Andrea Matlock
- Advanced Clinical BioSystems Research Institute, Cedars Sinai Medical Center, Heart Institute, 127 S. San Vicente Blvd, Los Angeles, CA 90048
| | | | - Jennifer E Van Eky
- Cedar Sinai, Advanced Clinical BioSystems Research Institute, Cedars Sinai Medical Center, Heart Institute, 127 S. San Vicente Blvd, Los Angeles, CA 90048
| | - Jennifer E Van Eyk
- Advanced Clinical BioSystems Research Institute, Cedars Sinai Medical Center, Heart Institute, Los Angeles, CA, 90048, USA
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Abu-Elmagd M, Assidi M, Schulten HJ, Dallol A, Pushparaj PN, Ahmed F, Scherer SW, Al-Qahtani M. Individualized medicine enabled by genomics in Saudi Arabia. BMC Med Genomics 2015; 8 Suppl 1:S3. [PMID: 25951871 PMCID: PMC4315314 DOI: 10.1186/1755-8794-8-s1-s3] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The biomedical research sector in Saudi Arabia has recently received special attention from the government, which is currently supporting research aimed at improving the understanding and treatment of common diseases afflicting Saudi Arabian society. To build capacity for research and training, a number of centres of excellence were established in different areas of the country. Among these, is the Centre of Excellence in Genomic Medicine Research (CEGMR) at King Abdulaziz University, Jeddah, with its internationally ranked and highly productive team performing translational research in the area of individualized medicine. Here, we present a panorama of the recent trends in different areas of biomedical research in Saudi Arabia drawing from our vision of where genomics will have maximal impact in the Kingdom of Saudi Arabia. We describe advances in a number of research areas including; congenital malformations, infertility, consanguinity and pre-implantation genetic diagnosis, cancer and genomic classifications in Saudi Arabia, epigenetic explanations of idiopathic disease, and pharmacogenomics and personalized medicine. We conclude that CEGMR will continue to play a pivotal role in advances in the field of genomics and research in this area is facing a number of challenges including generating high quality control data from Saudi population and policies for using these data need to comply with the international set up.
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Affiliation(s)
- Muhammad Abu-Elmagd
- Centre of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, P.O. Box: 80216 Jeddah 21589, KSA
- KACST Technology Innovation Centre in Personalized Medicine at King Abdulaziz University (CIPM), P.O. Box: 80216 Jeddah 21589, KSA
- School of Biological Sciences, University of East Anglia, Norwich, Norfolk, NR4 7TJ, UK
- Zoology Department, Faculty of Science, Minia University, Minia, P.O. Box 61519, Egypt
| | - Mourad Assidi
- Centre of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, P.O. Box: 80216 Jeddah 21589, KSA
- KACST Technology Innovation Centre in Personalized Medicine at King Abdulaziz University (CIPM), P.O. Box: 80216 Jeddah 21589, KSA
| | - Hans-Juergen Schulten
- Centre of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, P.O. Box: 80216 Jeddah 21589, KSA
| | - Ashraf Dallol
- Centre of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, P.O. Box: 80216 Jeddah 21589, KSA
- KACST Technology Innovation Centre in Personalized Medicine at King Abdulaziz University (CIPM), P.O. Box: 80216 Jeddah 21589, KSA
| | - Peter Natesan Pushparaj
- Centre of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, P.O. Box: 80216 Jeddah 21589, KSA
| | - Farid Ahmed
- Centre of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, P.O. Box: 80216 Jeddah 21589, KSA
| | - Stephen W Scherer
- Centre of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, P.O. Box: 80216 Jeddah 21589, KSA
- The Centre for Applied Genomics and Program in Genetics and Genome Biology, the Hospital for Sick Children, Toronto, Ontario, Canada
- McLaughlin Centre and Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Mohammed Al-Qahtani
- Centre of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, P.O. Box: 80216 Jeddah 21589, KSA
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