Proteomics Is Analytical Chemistry: Fitness-for-Purpose in the Application of Top-Down and Bottom-Up Analyses
Molecular mechanisms underlying health and disease function at least in part based on the flexibility and fine-tuning afforded by protein isoforms and post-translational modifications. The ability to effectively and consistently resolve these protein species or proteoforms, as well as assess quantit...
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doaj-da081b5a487945ad8b597a6eef234e012020-11-24T22:16:58ZengMDPI AGProteomes2227-73822015-12-013444045310.3390/proteomes3040440proteomes3040440Proteomics Is Analytical Chemistry: Fitness-for-Purpose in the Application of Top-Down and Bottom-Up AnalysesJens R. Coorssen0Alfred L. Yergey1Molecular Physiology and the Molecular Medicine Research Group, School of Medicine, Western Sydney University, Office 30.2.15, Campbelltown Campus, Locked Bag 1797, Penrith 2570, NSW, AustraliaNational Institute of Child Health and Human Development, NIH, Building 10, Room 9D 52, Bethesda, MD 20892, USAMolecular mechanisms underlying health and disease function at least in part based on the flexibility and fine-tuning afforded by protein isoforms and post-translational modifications. The ability to effectively and consistently resolve these protein species or proteoforms, as well as assess quantitative changes is therefore central to proteomic analyses. Here we discuss the pros and cons of currently available and developing analytical techniques from the perspective of the full spectrum of available tools and their current applications, emphasizing the concept of fitness-for-purpose in experimental design based on consideration of sample size and complexity; this necessarily also addresses analytical reproducibility and its variance. Data quality is considered the primary criterion, and we thus emphasize that the standards of Analytical Chemistry must apply throughout any proteomic analysis.http://www.mdpi.com/2227-7382/3/4/4402DEBottom-upDiscovery proteomicsLC/MS/MSprotein speciesproteoformsshotgunTop-downtwo-dimensional gel electrophoresis |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Jens R. Coorssen Alfred L. Yergey |
spellingShingle |
Jens R. Coorssen Alfred L. Yergey Proteomics Is Analytical Chemistry: Fitness-for-Purpose in the Application of Top-Down and Bottom-Up Analyses Proteomes 2DE Bottom-up Discovery proteomics LC/MS/MS protein species proteoforms shotgun Top-down two-dimensional gel electrophoresis |
author_facet |
Jens R. Coorssen Alfred L. Yergey |
author_sort |
Jens R. Coorssen |
title |
Proteomics Is Analytical Chemistry: Fitness-for-Purpose in the Application of Top-Down and Bottom-Up Analyses |
title_short |
Proteomics Is Analytical Chemistry: Fitness-for-Purpose in the Application of Top-Down and Bottom-Up Analyses |
title_full |
Proteomics Is Analytical Chemistry: Fitness-for-Purpose in the Application of Top-Down and Bottom-Up Analyses |
title_fullStr |
Proteomics Is Analytical Chemistry: Fitness-for-Purpose in the Application of Top-Down and Bottom-Up Analyses |
title_full_unstemmed |
Proteomics Is Analytical Chemistry: Fitness-for-Purpose in the Application of Top-Down and Bottom-Up Analyses |
title_sort |
proteomics is analytical chemistry: fitness-for-purpose in the application of top-down and bottom-up analyses |
publisher |
MDPI AG |
series |
Proteomes |
issn |
2227-7382 |
publishDate |
2015-12-01 |
description |
Molecular mechanisms underlying health and disease function at least in part based on the flexibility and fine-tuning afforded by protein isoforms and post-translational modifications. The ability to effectively and consistently resolve these protein species or proteoforms, as well as assess quantitative changes is therefore central to proteomic analyses. Here we discuss the pros and cons of currently available and developing analytical techniques from the perspective of the full spectrum of available tools and their current applications, emphasizing the concept of fitness-for-purpose in experimental design based on consideration of sample size and complexity; this necessarily also addresses analytical reproducibility and its variance. Data quality is considered the primary criterion, and we thus emphasize that the standards of Analytical Chemistry must apply throughout any proteomic analysis. |
topic |
2DE Bottom-up Discovery proteomics LC/MS/MS protein species proteoforms shotgun Top-down two-dimensional gel electrophoresis |
url |
http://www.mdpi.com/2227-7382/3/4/440 |
work_keys_str_mv |
AT jensrcoorssen proteomicsisanalyticalchemistryfitnessforpurposeintheapplicationoftopdownandbottomupanalyses AT alfredlyergey proteomicsisanalyticalchemistryfitnessforpurposeintheapplicationoftopdownandbottomupanalyses |
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