Editorials

Brief Review of Proteomics at the 50^th ASMS Conference: 2-6 June 2002, Orlando, Florida by David Goodlett of the Institute for Systems Biology

The following represents a brief overview of the salient Proteomics presentations noticed by the author at ASMS 2002 and is not intended to be all encompassing. Specifically excluded in the interest of space is the use of MS in fundamental studies of the fragmentation of proteins and peptides. For a more thorough review, the reader is directed to www.asms.org where a search engine can be employed to lead the reader toward areas of specific interest. 

A total of 1618 posters and 276 oral presentations were given in four days. Of these, 33% of the orals and 34% of the posters involved proteomics, fundamentals of peptide/protein fragmentation and informatics. Attendance was ~ 4500.

Top-down proteomics (i.e., deriving sequence information from proteins or large peptides) was a popular topic with two oral sessions on the topic entitled Intact Protein Characterization and Electron Capture Dissociation. These efforts were mainly led by the FT-ICR-MS groups. Notably, a plethora of differential isotopic labeling strategies were presented based both on in vivo and in vitro labeling and for which R. Aebersold received the Biemann medal for his isotope-coded affinity tag strategy for determining protein expression between two biological states of interest. R.F. Fisher et al. from the NCI/SAIC presented an interesting approach that allowed differential isotopic labeling of intact cells such that only extracellular proteins were tagged from different cell lines and then quantified. R. Aebersold et al. presented a method for the use of differential stable isotope labeling to distinguish specific from non-specific protein-protein interactions in protein-pull down experiments. J.R. Yates et al. integrated the use of in vivo stable isotope labeling with their MUDPIT strategy to follow protein expression kinetics via measurement of two different cellular states separately but each to the same standard; i.e., (protein mixture 1 ratio)/(protein mixture 2 ratio). D.R. Goodlett et al. introduced a method for protein identification that combined the advantages of mass fingerprinting (i.e., parallel ion detection) with the fragment ion specificity of serial tandem MS by utilizing in-source CID on an ESI-TOF. S.P. Gygi et al. presented a new twist on the old method of absolute quantification called the referred to as AQUA that utilized peptides synthesized with natural heavy isotopes as internal standards. F.E. Regnier et al. presented a strategy for comparison of changes in protein expression between multiple biological states simultaneously with their GIST strategy that labels peptides in vitro. Park and Kim presented use of peptide isoelectric focusing to detect modified peptides in the presence of peptides of expected sequence. In the field of phosphorylation analysis ion metal affinity chromatography (IMAC) was definitely back in vogue probably due to the relative difficulty of phosphopeptide isolation strategies presented in the last year by the R. Aebersold and R.D. Smith groups. D.F. Hunt et al.. presented a clever modification to reduce nonspecific interactions during IMAC by prior esterification of carboxylates, but not phosphate due to relative stabilities.

While both Thermofinnigan and Sciex presented plans for linear ion traps that offered advantages over a standard cubic ion trap in terms of capacity, sensitivity, and the ability to manipulate ion populations in novel ways, Sciex officially released their instrument and showed data from it in a number of presentations. The Thermofinnigan instrument used a dual detector due to ejection of ions 180 apart and the Sciex instrument used a modified quadrupole design commonly found in quadrupole mass spectrometers. The relative merits of these instruments to the community remains to be proved, but the use of linear quadrupole traps has been popular in the field of FT-ICR-MS for a number of years as it allows manipulation of the ion packet prior to injection into the ICR cell. In fact, the group of R.D. Smith has made good use of this concept in combination with their DREAMS analysis system that increases effective dynamic range from 10⁴ to 10⁶ by ejection of the most abundant ions leaving what were previously low signal/noise peptides present, but now as the most abundant constituents.

While tandem MS analysis coupled with HPLC has enjoyed much recent success because of the availability of software such as SEQUEST and MASCOT, the proponents of mass fingerprinting will benefit from the continued development of MALDI-TOF-TOF-MS instruments from ABI and Bruker, as well as the Shimadzu MALDI-ion trap-TOF-MS instrument, all of which allow mass fingerprinting to be followed up immediately in the same instrument by tandem MS of single peptide ions. A number of presenters demonstrated that combining LC-MALDI-TOF-MS with LC-ESI-MS/MS analysis is necessary and complementary for more complete coverage of the peptides in a sample. B. Karger et al. presented improvements to their vacuum MALDI deposition strategy that allows LC to be coupled to MALDI off line and provide highly reproducible crystals across the LC elution profile. SELDI continued to be a popular method for use in detection of markers of disease, but also continued to suffer rightly or wrongly from a reputation of being difficult to reproduce. Another area that seemed on the rise in popularity was the use of mass spectrometry to phenotype whole microorganisms.

Given the large growth in the society in recent years in no small part due to the increase in popularity of mass spectrometry in proteomics, the society discussed the ramifications of splitting ASMS into two separate meetings, one on applications and one on instrumentation. As in the past when this issue has been raised the society voted not to split up due to the great benefit of mixing those doing fundamental analysis and instrument development with those who use the instruments. The next ASMS meeting will be held in Montreal Canada 8-12 June 2003. It is recommended that those wishing to attend book rooms early due to the running of the Canadian Grad Prix in Montreal the weekend after ASMS.

The articles and opinions expressed in the Editorial Corner are solely those of the author and do not necessarily reflect the opinions of the Proteome Society management and/or membership.