Mass spectrometry is a scientific technique for measuring the mass-to-charge ratio of ions. It is often coupled to chromatographic techniques such as gas- or liquid chromatography and has found widespread adoption in the fields of analytical chemistry and biochemistry where it can be used to identify and characterize small molecules and proteins (proteomics). The large volume of data produced in a typical mass spectrometry experiment requires that computers be used for data storage and processing. Over the years, different manufacturers of mass spectrometers have developed various proprietary data formats for handling such data which makes it difficult for academic scientists to directly manipulate their data. To address this limitation, several open, XML-based data formats have recently been developed by the Trans-Proteomic Pipeline at the Institute for Systems Biology to facilitate data manipulation and innovation in the public sector. These data formats are described here.
Stable Isotope Labeling by/with Amino acids in Cell culture (SILAC) is a technique based on mass spectrometry that detects differences in protein abundance among samples using non-radioactive isotopic labeling. It is a popular method for quantitative proteomics.
Rudolf Aebersold is a Swiss biologist, regarded as a pioneer in the fields of proteomics and systems biology. He has primarily researched techniques for measuring proteins in complex samples, in many cases via mass spectrometry. Ruedi Aebersold is a professor of Systems biology at the Institute of Molecular Systems Biology (IMSB) in ETH Zurich. He was one of the founders of the Institute for Systems Biology in Seattle, Washington, where he previously had a research group.
Mascot is a software search engine that uses mass spectrometry data to identify proteins from peptide sequence databases. Mascot is widely used by research facilities around the world. Mascot uses a probabilistic scoring algorithm for protein identification that was adapted from the MOWSE algorithm. Mascot is freely available to use on the website of Matrix Science. A license is required for in-house use where more features can be incorporated.
Quantitative proteomics is an analytical chemistry technique for determining the amount of proteins in a sample. The methods for protein identification are identical to those used in general proteomics, but include quantification as an additional dimension. Rather than just providing lists of proteins identified in a certain sample, quantitative proteomics yields information about the physiological differences between two biological samples. For example, this approach can be used to compare samples from healthy and diseased patients. Quantitative proteomics is mainly performed by two-dimensional gel electrophoresis (2-DE), preparative one-dimensional gel electrophoresis, or mass spectrometry (MS). However, a recent developed method of quantitative dot blot (QDB) analysis is able to measure both the absolute and relative quantity of an individual proteins in the sample in high throughput format, thus open a new direction for proteomic research. In contrast to 2-DE, which requires MS for the downstream protein identification, MS technology can identify and quantify the changes.
The American Society for Biochemistry and Molecular Biology (ASBMB) is a learned society that was founded on December 26, 1906, at a meeting organized by John Jacob Abel. The roots of the society were in the American Physiological Society, which had been formed some 20 years earlier. ASBMB is the US member of the International Union of Biochemistry and Molecular Biology.
The Proteomics Standards Initiative (PSI) is a working group of the Human Proteome Organization. It aims to define data standards for proteomics to facilitate data comparison, exchange and verification.
The PRIDE is a public data repository of mass spectrometry (MS) based proteomics data, and is maintained by the European Bioinformatics Institute as part of the Proteomics Team.
The Human Proteome Project (HPP) is a collaborative effort coordinated by the Human Proteome Organization. Its stated goal is to experimentally observe all of the proteins produced by the sequences translated from the human genome.
Albert J.R. Heck is a Dutch scientist and professor at Utrecht University, the Netherlands in the field of mass spectrometry and proteomics. He is known for his work on technologies to study proteins in their natural environment, with the aim to understand their biological function. Albert Heck was awarded the Spinoza Prize in 2017, the highest scientific award in the Netherlands.
Catherine Clarke Fenselau is an American scientist who was the first trained mass spectrometrist on the faculty of an American medical school; she joined Johns Hopkins School of Medicine in 1968. She specializes in biomedical applications of mass spectrometry. She has been recognized as an outstanding scientist in the field of bioanalytical chemistry because of her work using mass spectrometry to study biomolecules.
Metal-coded affinity tag is a method used for quantitative proteomics by mass spectrometry that uses a metal chelate complex 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetate (DOTA) coupled to different lanthanide ions. The metal complexes attach to the cysteine residues of proteins in a sample.
Zeng Rong is a Chinese biochemist researching and developing technology for proteomics research. She is currently a professor at the Institute of Biochemistry and Cell Biology at the Shanghai Institutes for Biological Sciences.
Claire Eyers is a British biological mass spectrometrist who is professor of biological mass spectrometry at the University of Liverpool, where she heads up the Centre for Proteome Research. Her research publications list her either as Claire E Haydon or Claire E Eyers.
Ying Ge is a Chinese-American biologist who is a Professor of Cell and Regenerative Biology at the University of Wisconsin–Madison. Her research considers the molecular mechanisms that underpin cardiac disease. She has previously served on the board of directors of the American Society for Mass Spectrometry. In 2020 Ge was named on the Analytical Scientist Power List.
Olga Vitek is a biostatistician and computer scientist specializing in bioinformatics, proteomics, mass spectrometry, causal inference of biological function, and the development of open-source software for statistical analysis in these areas. She is a professor in the College of Science and Khoury College of Computer Sciences of Northeastern University.
Catherine E. Costello is the William Fairfield Warren distinguished professor in the Department of Biochemistry, Cell Biology and Genomics, and the director of the Center for Biomedical Mass Spectrometry at the Boston University School of Medicine.
Yu-Ju Chen (陳玉如) is a Taiwanese proteomics research scientist, who leads international projects in proteogenomics.
Peipei Ping is an academic specializing in cardiac physiology, system biology and data science.
