EDITORIAL

Focus on in Honor of Ruedi Aebersold, 2002 Biemann Awardee

It is a pleasure to introduce this series of articles “Trypsin Catalyzed 16O-to-18O Exchange for Compara- honouring the achievements of Ruedi Aebersold, the tive Proteomics: Tandem Compari- 2002 recipient of the ASMS Biemann Medal. During the son using MALDI-TOF, ESI-QTOF and ESI-Ion Trap last decade enormous progress has been made in the Mass Spectrometers” by Manfred Heller, Hassan Mat- application of mass spectrometry to proteomics, an area tou, Christoph Menzel, and Xudong Yao illustrates the to which Ruedi has contributed both generally and use of alternative labeling strategies involving 16Oto specifically with his isotope labelling strategies. In his 18O, in conjunction with enzymatic digestion for iden- opening Account and Perspective, “A Mass Spectromet- tifying proteins in human plasma. Of additional interest ric Journey into Protein and Proteome Research,” Ruedi in this article is the comparison of the many different poses the interesting question ‘does technology drive mass spectrometry platforms emerging for analysing biology or is the converse the case, where the biological such data including LC MALDI MS/MS approaches. question drives the technological development?’ This of Chromatographic separation is at the heart of many course remains an open question but the accompanying successful proteomic strategies, and an alternative ap- series of articles exemplify the tremendous synergy proach is exemplified by Figeys and colleagues in their between biology and methodological development. article, “On-line Strong Cation Exchange ␮-HPLC-ESI- An important biological question prompts the first of MS/MS for Protein Identification and Process Optimi- the research articles; “Quantitative Proteomic Analysis zation.” Using a strong cation exchange micro LC of Chromatin-associated Factors” by Yuzuru Shiio, Eu- method for identification of proteins in mixtures, they gene C. Yi, Sam Donohoe, David R. Goodlett, Ruedi apply their approach to a tryptic digest of a protein Aebersold, and Robert N. Eisenman. A method is extract from human cells. They demonstrate that their described for determining quantitatively the changes in procedure provides complementary information to chromatin-associated factors. These factors play a cen- standard reverse phase chromatographic methods, spe- tral role in cell proliferation, differentiation and death cifically for larger molecular-weight peptides that are and yet are difficult to quantify primarily due to their often poorly represented using standard protocols. very low levels of expression. The method that is An exciting biological challenge involves definition described is based on the ICAT methodology, which of the protein composition of the editosome, a multi- Ruedi pioneered. On the same theme, the next article protein complex involved in editing mitochondrial mRNAs in trypanosomes. This subject, which is de- Published online May 21, 2003 scribed by Aswini K. Panigrahi, Thomas E. Allen, Paul

© 2003 American Society for Mass Spectrometry. Published by Elsevier Inc. 1044-0305/03/$30.00 doi:10.1016/S1044-0305(03)00328-3 (J Am Soc Mass Spectrom 2003, 14, 683–684) J Am Soc Mass Spectrom 2003, 14, 683–684 684

A. Haynes, Steven P. Gygi, and Kenneth Stuart in David R. Goodlett, Ruedi Aebersold, and Samuel I. “Mass Spectrometric Analysis of the Editosome and Miller demonstrates a quantitative approach to the Other Multiprotein Complexes in Trypanosoma brucei,” proteomic analysis of a microorganism, grown under provides an excellent example of a proteomics ap- specific conditions. Here the labeling strategy devised proach to defining functional complexes. The results by Ruedi is used to good effect illustrating its applica- reveal candidate proteins of the editosome as well as tion for large-scale quantitative proteomics. the identity of other novel mitochondrial proteins. This collection of articles exemplify how in some On a similar theme, the identity of proteins from an studies, biology is the major driving force, as is perhaps unknown plant virus illustrates a novel application of a the case for the quanfication of chromatin-associated proteomics approach. Starting with the uninfected to- factors, definition of the editosome or identification of a bacco plant and comparison of the protein components virus. In others, the methodological development is the with that of a plant infected with tobacco mosaic virus, key component, in the form of different chromato- Haynes et al in their article “Investigative Proteomics: graphic strategies, quantification of the phosphopro- Identification of an Unknown Plant Virus from Infected teome, or refinements of the isotope labelling strategies. Plants Using Mass Spectrometry” demonstrated the In either case, the impact is significant. Consequently, principle of the experiment. After separation protein whatever the stimulus, the results from these investiga- spots that were differentially expressed were identified. tions have important implications and are changing the The approach was then applied to identify an unknown ways in which biological research is conducted, now virus revealing proteins of the potato virus X. and for the foreseeable future. The final article, “Proteomic Analysis of Pseudomonas Carol V. Robinson aeruginosa Grown Under Magnesium Limitation” by Associate Editor Tina Guina, Manhong Wu, Samuel O. Purvine, Eugene Michael L. Gross C. Yi, Robert K. Ernst, Kimberly A. Lee, Jimmy Eng, Editor