ABSTRACT
Proteomics is a rapidly maturing field aimed at the high-throughput identification and quantification of all proteins in a biological system. The cornerstone of proteomic technology is tandem mass spectrometry of peptides resulting from the digestion of protein mixtures. The fragmentation pattern of each peptide ion is captured in its tandem mass spectrum, which enables its identification and acts as a fingerprint for the peptide. Spectral libraries are simply searchable collections of these fingerprints, which have taken on an increasingly prominent role in proteomic data analysis. This review describes the historical development of spectral libraries in proteomics, details the computational procedures behind library building and searching, surveys the current applications of spectral libraries, and discusses the outstanding challenges. © 2016 Wiley Periodicals, Inc. Mass Spec Rev 36:634-648, 2017.
Subject(s)
Databases, Protein , Proteomics/methods , Tandem Mass Spectrometry/methods , Algorithms , Animals , Data Mining , History, 20th Century , History, 21st Century , Peptides/analysis , Peptides/chemistry , Peptides/metabolism , Phylogeny , Protein Processing, Post-Translational , Software , Tandem Mass Spectrometry/history , Tandem Mass Spectrometry/statistics & numerical data , User-Computer InterfaceABSTRACT
Newborn screening has evolved fast following recent advances in diagnosis and treatment of disease, particularly the development of multiplex testing and applications of molecular testing. Formal evidence of benefit from newborn screening has been largely lacking, due to the rarity of individual disorders. There are wide international differences in the choice of disorders screened, and ethical issues in both screening and not screening are apparent. More evidence is needed about benefit and harm of screening for specific disorders and renewed discussion about the basic aims of newborn screening must be undertaken.
Subject(s)
Genetic Diseases, Inborn/history , Neonatal Screening/history , Australia , Cystic Fibrosis/diagnosis , Cystic Fibrosis/history , Europe , Genetic Diseases, Inborn/diagnosis , History, 20th Century , History, 21st Century , Humans , Infant, Newborn , Metabolism, Inborn Errors/diagnosis , Metabolism, Inborn Errors/history , Neonatal Screening/ethics , Neonatal Screening/methods , New Zealand , Tandem Mass Spectrometry/history , United StatesABSTRACT
Eicosanoids are a large family that derives from arachidonic acid, i.e., eicosatetraenoic acid. Prominent members include prostaglandins, thromboxane and leukotrienes. They are biologically highly active lipid mediators and play multiple physiological roles. GC-MS/MS has played a pivotal role in the identification and quantification of eicosanoids in biological samples. This technology generated a solid knowledge of their analytical chemistry, biochemistry, physiology and pharmacology. Since about a decade, GC-MS and GC-MS/MS are increasingly displaced by the seemingly more simple, rapid and powerful LC-MS/MS in the area of instrumental analysis of physiological substances, drugs and their metabolites. In this article, we review and discuss LC-MS/MS methods published over the last decade from the perspective of the GC-MS/MS user. Our analysis revealed that the shift from the adult GC-MS/MS to the youthful emerging LC-MS/MS technology in eicosanoid analysis is associated with several important challenges. Known pitfalls and problematic issues discovered by eicosanoid pioneers by using GC-MS/MS are often ignored by LC-MS/MS users. Established reference values and intervals provided by GC-MS-based methods are not considered properly in developing and validating LC-MS/MS methods. Virtually, there is a belief in the unlimited capability of the LC-MS/MS technique in eicosanoid analysis, a thought that simulates analytical certainty. LC-MS/MS users should profit from the plethora of solid knowledge acquired from the use of GC-MS/MS in eicosanoid analysis in basic and clinical research.
Subject(s)
Chromatography, Liquid/methods , Eicosanoids/analysis , Gas Chromatography-Mass Spectrometry/methods , Tandem Mass Spectrometry/methods , Animals , Chromatography, Liquid/history , Eicosanoids/blood , Eicosanoids/urine , Gas Chromatography-Mass Spectrometry/history , History, 20th Century , History, 21st Century , Humans , Tandem Mass Spectrometry/history , Validation Studies as TopicABSTRACT
Huge changes have occurred in the measurement of hormones over the last 50 years or so. Methods have become simplified, sensitivity has increased manyfold, and automation has allowed the analysis of large number of specimens in a single day. The most significant steps in the history of hormone measurement were the development of radioimmunoassay and later the production of monoclonal antibodies. There has also been increased commercialization, the technique has been applied to an ever-increasing range of substances, and radioactive measurement has been replaced with colorimetric, fluorescent, and chemiluminescent end-points. However, all these changes have not been without their problems. Collaboration between laboratories has seen standardization of reagents and methods, the development of reference methods, and the setting up of external quality assurance schemes. All these have led to improved sensitivity, precision, and reliability. More recently tandem mass spectrometry has brought further improvements in the measurement of certain hormones. Although many hormones are now measured by automated systems there is still a place for manual assays whether developed in-house or by using a commercial kit.