Report from the MS Terms and Definitions Workshop
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The workshop convened at 5:30 pm May 25, 2004 at the American Society for Mass Spectrometry Conference Nashville, Tennessee, USA. Four speakers gave 10 to 15 minute presentations, interspersed with questions and discussion. Phil Price of the Dow Chemical Company and incoming Member-at-large for Measurements & Standards discussed M&S Committee current and future projects. Kermit Murray of Louisiana State University discussed the IUPAC project "Standard Definitions of Terms Relating to Mass Spectrometry." David Sparkman of the University of the Pacific gave a presentation entitled "What's in a Name," an overview of MS nomenclature issues. Randall Julian of Eli Lilly discussed the Proteomics Standardization Initiative and the PSI Mass Spectrometry work-group.
Phil Price discussed the current status of MS terms and definitions and past efforts of the Measurements & Standards Committee in establishing nomenclature standards. The association of ASMS with standardization of terms and definitions began with John Beynon's work in the late 1960s through the early 1980s. Further efforts in the 1980s culminated in the "Recommendations for nomenclature and symbolism for mass spectroscopy" prepared by J. F. Todd for IUPAC and the concurrent ASMS sanctioned lists of MS terms (Price, P., "Standard Definitions of Terms Relating to Mass Spectrometry," J. Am. Soc. Mass Spectrom. 1991, 2, 336-348). Although workshops and independent efforts have taken place in the intervening years, no sanctioned recommendations for terms and definitions have been made. Price emphasized that future efforts must deal with conflicting nomenclature, trademarks, prematurely assigned names, and names with conflicting definitions. It is especially important to have both user and journal editor acceptance. The Measurements & Standards Committee will be working on an updated list of terms and will coordinate this work with the IUPAC project described below.
Kermit Murray gave an overview of the recently funded IUPAC project 2003-056-2-500 "Standard Definitions of Terms Relating to Mass Spectrometry." IUPAC is the world authority on chemical nomenclature and terminology and has in the past provided guidance on mass spectrometry nomenclature. The IUPAC Compendium of Analytical Nomenclature ("Orange Book") has a chapter on mass spectrometry nomenclature that was last updated more than a decade ago. The title of the chapter "Mass Spectroscopy" grates on the ears of most mass spectrometrists and is emblematic of the need for an update. The IUPAC Analytical Chemistry Division (V) supports the update of MS Terms and is, along with the Physical and Biophysical Chemistry Division (I), is sponsoring the project. Murray is chair of the Project Task Group and the other members of the international group are Robert Boyd (NRC, Canada), Marcos N. Eberlin (Universidade Estadual de Campinas, Brazil), John Langley (University of Southampton, UK), Liang Li (University of Alberta, Canada), Yasuhide Naito (Osaka University, Japan), and Jean-Claude Tabet (Universite Pierre et Marie Curie, France). The target completion date for the project is 2006 and the goal is to present the final document at the International Mass Spectrometry Conference in Prague, Czech Republic, in August 2006. More information on the project can be found at the project web page:
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David Sparkman emphasized that standardization of terminology is critical to good communications. No matter how significant a scientific discovery is, if the discover cannot communicate the results of studies that lead to the discovery, the work may go unrecognized. Journal publishers copy editors, editors and associate editors, peer reviewers, instrument manufacturers, and authors themselves often fail to adhere to publish and agreed to standards. One example is the use of symbol amu for the atomic mass unit. When the change was made from the separate and not equal chemical and physical definitions of the atomic mass unit based on oxygen in 1962, the use of the amu symbol was discontinued and the symbol u (unified atomic mass unit) was established. Although not as pervasive as in the past, amu is still seen in the literature. Even recent freshman chemistry books use this obsolete term. The most egregious of the misuse offenders are the instrument manufacturers, in print and oral presentations, even at meeting such as ASMS. Another, but less obtrusive misused term is empirical formal as opposed to elemental composition when referring to an ion, radical, or molecule. In many cases the elemental composition is the empirical formula (e.g., C3H6O+); however, as we all should have learned in high school or freshman college chemistry, the empirical formula represents the lowest common denominator (the relative proportion of the elements) for the elements in a substance, not the actual number of atoms of each element. The empirical formula for benzene is CH, not C6H6, which is the elemental composition. Sparkman stressed that establishment of lists of terms is meaningless unless we can get those lists used and enforced, not just agreed to and then set aside.
Randall Julian gave an overview of the Proteomics Standards Initiative and how it relates to mass spectrometry nomenclature. The PSI was founded by the Human Proteome Organization in April 2002. One of the first tasks of the PSI is developing standards for mass spectrometry and protein-protein interaction data. The PSI mass spectrometry work group is developing a format for the standard representation of spectra that will facilitate data exchange and the comparison of results from different instruments and research groups. The standard is being developed using extensible markup language (XML), a simple and flexible text format, and is being coordinated with the analytical information exchange standard that is currently being developed by the American Society for Tests and Measures (ASTM). A draft XML interchange standard has been demonstrated, along with tools for converting from MS text formats to PSI-MS XML format, viewing and browsing data stored in PSI-MS XML format, and using PSI-MS XML data as a search engine input. More information on the project can be found on the web at http://psidev.sourceforge.net/ms/.
All speakers emphasized the need for participation by members of the mass spectrometry community and welcome any and all comments by e-mail, face-to-face or Internet discussion.