The formation of oligomeric molecules, an important step in secondary organic aerosol production, is reported. Aerosols were produced by the reaction of alpha-pinene and ozone in the presence of acid seed aerosol and characterized by exact mass measurements and tandem mass spectrometry. Oligomeric products between 200 and 900 u were detected with both electrospray ionization and matrix-assisted laser desorption ionization. The exact masses and dissociation products of these ions were consistent with various combinations of the known primary products of this reaction ("monomers") with and/or without the expected acid-catalyzed decomposition products of the monomers. Oligomers as large as tetramers were detected. Both aldol condensations and gem-diol reactions are suggested as possible pathways for oligomer formation. Exact mass measurements also revealed reaction products that cannot be explained by simple oligomerization of monomers and monomer decomposition products, suggesting the existence of complex reaction channels. Chemical reactions leading to oligomer formation provide a reasonable answer to a difficult problem associated with secondary organic aerosol production in the atmosphere. It is unlikely that monomers alone play an important role in the formation and growth of nuclei in the atmosphere as their Kelvin vapor pressures are too high for them to significantly partition into the particle phase. Polymerization provides a mechanism by which partitioning to the particle phase becomes favored.

The pseuoduridine synthases (psi synthases) isomerize uridine (U) to pseudouridine (psi) in RNA, and they fall into five families that share very limited sequence similarity but have the same overall fold and active-site architecture, including an essential Asp. The mechanism by which the psi synthases operate remains unknown, and mechanistic work has largely made use of RNA containing 5-fluorouridine (f5U) in place of U. The psi synthase TruA forms a covalent adduct with such RNA, and heat disruption of the adduct generates a hydrated product of f5U, which was reasonably concluded to result from the hydrolysis of an ester linkage between the essential Asp and f5U. In contrast, the psi synthase TruB, which is a member of a different family, does not form an adduct with f5U in RNA but catalyzes the rearrangement and hydration of the f5U, which labeling studies with [18O]water showed does not result from ester hydrolysis. To extend the line of mechanistic investigation to another family of psi synthases and an enzyme that makes an adduct with f5U in RNA, the behavior of RluA toward RNA containing f5U was examined. Stem-loop RNAs are shown to be good substrates for RluA. Heat denaturation of the adduct between RluA and RNA containing f5U produces a hydrated nucleoside product, and labeling studies show that hydration does not occur by ester hydrolysis. These results are interpreted in light of a consistent mechanistic scheme for the handling of f5U by psi synthases.

RNA containing 5-fluorouridine, [f 5U]RNA, has been used as a mechanistic probe for the pseudouridine synthases, which convert uridine in RNA to its C-glycoside isomer, pseudouridine. Hydrated products of f 5U were attributed to ester hydrolysis of a covalent complex between an essential aspartic acid residue and f 5U, and the results were construed as strong support for a mechanism involving Michael addition by the aspartic acid residue. Labeling studies with [18O]water are now reported that rule out such ester hydrolysis in one pseudouridine synthase, TruB. The aspartic acid residue does not become labeled, and the hydroxyl group in the hydrated product of f 5U derives directly from solvent. The hydrated product, therefore, cannot be construed to support Michael addition during the conversion of uridine to pseudouridine, but the results do not rule out such a mechanism. A hypothesis is offered for the seemingly disparate behavior of different pseudouridine synthases toward [f 5U]RNA.

The goal of proteomics research is to be able to identify and quantify the vast numbers of proteins within an organism or tissue. "Top-down" methods address this goal without the need for proteolytic digestion prior to mass analysis. We report here an approach for top-down protein identification that has been implemented on a commercially available, unmodified Qq-TOF mass spectrometer. Intact protein molecular ions first undergo cone fragmentation in the electrospray inlet. Conventional MS/MS is then performed on a mass selected cone fragment using CID in the Qq interface of the Qq-TOF mass spectrometer to generate a sequence tag through a pseudo-MS 3 experiment. Seven proteins varying in molecular weight between 11 and 66 kDa were chosen to demonstrate applicability of method. After the molecular weight of the intact protein was determined, the cone voltage was varied to induce fragmentation. Cone fragment ions were then further dissociated using conventional CID, and the resulting MS/MS spectra were processed and analyzed for sequence tags. Sequence tags were easily identified from a MS/MS spectrum of a cone induced fragment ion both manually and through a de novo sequencing program included in the software associated with the mass spectrometer. Sequence tags were subjected to database searching using the PeptideSearch program of EMBL, and all protein sequence tags gave unambiguous search results. In all cases, sequence tags were found to originate from the n-and/or c-termini of the proteins. he field of proteomics is as dynamic as the proteome itself, constantly changing and evolving to meet the needs of researchers. The demands placed on the field increase with the yearly advancements, but the ultimate goal remains the same-global identification and quantitation of proteins in an organism or tissue. The most widely used methods for identifying whole proteomes are twodimensional gel electrophoresis (2D-GE) and the more recently developed, "shot gun" approach [1, 2]. The 2D-GE approach involves separating proteins first by their isoelectric point and subsequently by their molecular weight in a SDS gel. Individual protein spots are enzymatically digested within the gel to yield peptides that are easily extracted from the gel matrix. The peptide solution is then mass analyzed using either MALDI-MS or ESI-MS to yield a peptide mass fingerprint, sometimes after further chromatographic separation. Protein identifications are then determined from database searching on the resulting peptide mass fingerprints and/or using sequence tags obtained from MS/MS experiments on individual peptides [3,4]. In the shot gun approach, hundreds of proteins are simultaneously identified after global digestion of a protein mixture. The resultant peptide solution is then separated through multidimensional chromatography (2D-LC); strong cation exchange coupled with reverse phase is most common. The time limitations in these and most methods for proteomic analysis are found in sample preparation and separation procedures. The mass spec...

Our results represent the first metaproteomic study of aquatic microbial assemblages and demonstrate the potential of metaproteomic approaches to link metagenomic data, taxonomic diversity, functional diversity and biological processes in natural environments.