Thoughts on Writing for Review: An NSF Program Officer's Perspective.

This is an invited Account and Perspective, providing observations and advice derived from a 40 year academic career that has included over 14 years' service as a program officer at the National Science Foundation (NSF) and 27 years of service as an Associate Editor of the Journal of the American Society for Mass Spectrometry. This work describes the program officer's perspective, with observations on what reviewers look for in proposals, and what are some of the more common, best avoided mistakes. Emphasis is on NSF guidelines, but many elements are general and intended for use by both proposal authors and reviewers.

Thoughts on Writing for Review: A Former JASMS Associate Editor's Perspective.

This is an invited Account and Perspective, providing observations and advice on writing for review derived from a 40-year academic career that has included 27 years' service as an Associate Editor for the Journal of the American Society for Mass Spectrometry (JASMS) and nearly 14 years at the National Science Foundation. This work describes an Associate Editor's perspective. It offers observations on what editors and reviewers look for in manuscripts and some of the more common, best avoided mistakes. Emphasis is on JASMS guidelines, but many elements should be generally applicable and are intended for use by both authors and reviewers.

Fluorometric measurement and modeling of droplet temperature changes in an electrospray plume.

The evolution of droplet temperatures in an electrospray plume was measured via ratiometric fluorescence. Under typical operating conditions, droplet temperatures decrease ∼30 K over the first 5.0 mm along the spray axis, followed by a slight (∼2-3 K) rewarming. Experimental axial profiles (Z-axis) were fit by use of diffusion-controlled and surface-controlled evaporation models. Both models fit the experimental data well for the cooling portion of the spray (Pearson correlation coefficient R ≥ 0.994), but the surface-controlled model required unrealistic droplet radius values to obtain a good fit. In lateral profiles at a given Z near the emitter tip, temperatures are lower (by 3.0-10 K) in the periphery than on the spray axis. This behavior is consistent with the expected enrichment of the spray periphery with smaller droplets. At longer axial distances, lateral profiles were relatively flat. Droplet temperature as a function of axial displacement fell more rapidly at lower liquid flow rates, possibly attributable to changes in droplet size and/or velocity with flow rate.

Development of a multipoint quantitation method to simultaneously measure enzymatic and structural components of the Clostridium thermocellum cellulosome protein complex.

Clostridium thermocellum has emerged as a leading bioenergy-relevant microbe due to its ability to solubilize cellulose into carbohydrates, mediated by multicomponent membrane-attached complexes termed cellulosomes. To probe microbial cellulose utilization rates, it is desirable to be able to measure the concentrations of saccharolytic enzymes and estimate the total amount of cellulosome present on a mass basis. Current cellulase determination methodologies involve labor-intensive purification procedures and only allow for indirect determination of abundance. We have developed a method using multiple reaction monitoring (MRM-MS) to simultaneously quantitate both enzymatic and structural components of the cellulosome protein complex in samples ranging in complexity from purified cellulosomes to whole cell lysates, as an alternative to a previously developed enzyme-linked immunosorbent assay (ELISA) method of cellulosome quantitation. The precision of the cellulosome mass concentration in technical replicates is better than 5% relative standard deviation for all samples, indicating high precision for determination of the mass concentration of cellulosome components.

Characterizing the range of extracellular protein post-translational modifications in a cellulose-degrading bacteria using a multiple proteolyic digestion/peptide fragmentation approach.

Post-translational modifications (PTMs) are known to play a significant role in many biological functions. The focus of this study is to optimize an integrated experimental/informatics approach to more confidently characterize the range of post-translational modifications of the cellulosome protein complex used by the bacterium Clostridium thermocellum to better understand how this protein machine is tuned for enzymatic cellulose solubilization. To enhance comprehensive characterization, the extracellular cellulosome proteins were analyzed using multiple proteolytic digests (trypsin, Lys-C, Glu-C) and multiple fragmentation techniques (collisionally activated dissociation, electron transfer dissociation, decision tree). As expected, peptide and protein identifications were increased by utilizing alternate proteases and fragmentation methods, in addition to the increase in protein sequence coverage. The complementarity of these experiments also allowed for a global exploration of PTMs associated with the cellulosome based upon a set of defined PTMs that included methylation, oxidation, acetylation, phosphorylation, and signal peptide cleavage. In these experiments, 85 modified peptides corresponding to 28 cellulosome proteins were identified. Many of these modifications were located in active cellulolytic or structural domains of the cellulosome proteins, suggesting a level of possible regulatory control of protein function in various cellulotyic conditions. The use of complementary proteolytic digestion/peptide fragmentation processes allowed for independent verification of PTMs in different experiments, thus leading to increased confidence in PTM identifications.

Quantitative real-time monitoring of chemical reactions by autosampling flow injection analysis coupled with atmospheric pressure chemical ionization mass spectrometry.

Although qualitative and/or semiquantitative real-time monitoring of chemical reactions have been reported with a few mass spectrometric approaches, to our knowledge, no quantitative mass spectrometric approach has been reported so far to have a calibration valid up to molar concentrations as required by process control. This is mostly due to the absence of a practical solution that could well address the sample overloading issue. In this study, a novel autosampling flow injection analysis coupled with an atmospheric pressure chemical ionization mass spectrometry (FIA/APCI-MS) system, consisting of a 1 µL automatic internal sample injector, a postinjection splitter with 1:10 splitting ratio, and a detached APCI source connected to the mass spectrometer using a 4.5 in. long, 0.042 in. inner diameter (ID) stainless-steel capillary, was thus introduced. Using this system together with an optional FIA solvent modifier, e.g., 0.05% (v/v) isopropylamine, a linear quantitative calibration up to molar concentration has been achieved with 3.4-7.2% relative standard deviations (RSDs) for 4 replicates. As a result, quantitative real-time monitoring of a model reaction was successfully performed at the 1.63 M level. It is expected that this novel autosampling FIA/APCI-MS system can be used in quantitative real-time monitoring of a wide range of reactions under diverse reaction conditions.

Evaluation of direct analysis in real time mass spectrometry for onsite monitoring of batch slurry reactions.

Batch slurry reactions are widely used in the industrial manufacturing of chemicals, pharmaceuticals, petrochemicals and polymers. However, onsite monitoring of batch slurry reactions is still not feasible in production plants due to the challenge in analyzing heterogeneous samples without complicated sample preparation procedures. In this study, direct analysis in real time mass spectrometry (DART-MS) has been evaluated for the onsite monitoring of a model batch slurry reaction. The results suggested that automation of the sampling process of DART-MS is important to achieve quantitative results. With a sampling technique of manual sample deposition on melting point capillaries followed by automatic sample introduction across the helium beam, relative standard deviation (RSD) of the protonated molecule signals from the reaction product of the model batch slurry reaction ranged from 6 to 30%. This RSD range is improved greatly over a sampling technique of manual sample deposition followed by manual sample introduction where the RSDs are up to 110%. Furthermore, with the semi-automated sampling approach, semi-quantitative analysis of slurry samples has been achieved. Better quantification is expected with a fully automated sampling approach.

Ionization mechanism of positive-ion direct analysis in real time: a transient microenvironment concept.

A transient microenvironment mechanism (TMEM) is proposed to address matrix effects for direct analysis in real time (DART). When the DART gas stream is in contact with the sample, a transient microenvironment (TME), which can shield analytes from direct ionization, may be generated through the desorption of the matrix containing the analyte. The DART gas stream can directly ionize the matrix molecules, but the analytes will be ionized primarily through gas-phase ion/molecule reactions with the matrix ions. Experimental results showed that as little as 10 nL of liquid or 10 microg of solid was able to generate an efficient TME. Generated TMEs were able to control the ionization of an analyte below an analyte-to-matrix ratio that was dependent on the DART temperature and the boiling points of the analyte and matrix. TMEs generated by common solvents were studied in detail. The ionization of both polar and nonpolar compounds, present in a solvent or another analyte below a ratio of 1:100, were found to be mainly controlled by the generated TMEs at a DART temperature of 300 degrees C.

Complementary peptide sequence coverage using alternative enzymes for on-line digestion with a triaxial electrospray probe.

Using alternative enzymes for on-line digestion with a triaxial electrospray probe extends sequence coverage. This is the first report of utilization of our triaxial probe for on-line analysis with enzymes other than pepsin, suggesting potential for broader application. The probe allows access to processes occurring on a timescale and/or involving substrate conformations complementary to those for conventional (off-line) digestion. Some of the features observed in application to Abeta fibrils are suggestive of unique reactive intermediates during dissolution. Data obtained with enzyme mixtures suggest synergistic effects.

Oxidation artifacts in the electrospray mass spectrometry of Abeta Peptide.

Gradual corrosion of stainless steel electrospray emitters under conditions of normal use generates surface irregularities that can promote electrical discharge. The increased emission current affects the electrochemical reactions associated with the spray process. When sampling the peptide Abeta(1-40), this is manifest by oxidation of methionine at position 35 to methionine sulfoxide. The resultant mass shift and reduced sensitivity can adversely affect H/D exchange experiments. These effects can be avoided by adding a redox buffer or (preferably) by repolishing the emitter, especially to a rounded geometry.

A triaxial probe for on-line proteolysis coupled with hydrogen/deuterium exchange-electrospray mass spectrometry.

An on-line proteolysis system utilizing a triaxial electrospray probe was developed to aid localization of the hydrogen-bonding interaction sites in hydrogen/deuterium exchange-mass spectrometry (HDX-MS) studies of Abeta (1-40) fibrils. The probe allows delayed introduction of the organic solvent component needed for stable electrospray, thus enhancing hydrolysis performance relative to that of a coaxial probe. Effective on-line digestion was accomplished in approximately 12 s. The probe should be of general utility for HDX-MS studies of amyloid fibrils and other protein aggregates.

Hydrogen/deuterium exchange mass spectrometry analysis of protein aggregates.

The elucidation of the structure of amyloid fibrils and related aggregates is an important step toward understanding the pathogenesis of diseases like Alzheimer's disease, which feature protein misfolding and/or aggregation. However, the large size, heterogeneous morphology, and poor solubility of amyloid-like fibrils make them resistant to high-resolution structure determination. Using amyloid fibrils and protofibrils of the Alzheimer's plaque peptide amyloid beta as examples, we describe here the use of hydrogen/deuterium exchange methods in conjunction with electrospray ionization mass spectrometry to determine regions of the peptide involved in beta-sheet network when it is incorporated into protein aggregates. The advantages of this method are low sample utilization and high speed. The basic methodology exploits the fact that protons either involved in H-bonded secondary structures or buried in a protein's core structure exchange more slowly with deuterium than do solvent-exposed and non-H-bonded protons. Details of all aspects of this methodology, including sample preparation, data acquisition, and data analysis, are described. These data provide insights into the structures of monomers, protofibrils, and fibrils and to the structural relations among these states.

Structural differences in Abeta amyloid protofibrils and fibrils mapped by hydrogen exchange--mass spectrometry with on-line proteolytic fragmentation.

We report here structural differences between Abeta(1-40) protofibrils and mature amyloid fibrils associated with Alzheimer's disease as determined using hydrogen-deuterium exchange-mass spectrometry (HX-MS) coupled with on-line proteolysis. Specifically, we have identified regions of the Abeta(1-40) peptide containing backbone amide hydrogen atoms that are protected from HX or exposed when this peptide is incorporated into protofibrils or amyloid fibrils formed in phosphate-buffered saline without stirring at 37 degrees C. Study of protofibrils was facilitated by use of the protofibril-stabilizing agent calmidazolium chloride. Our data clearly show that both the C-terminal segment 35-40 and the N-terminal segment 1-19 are highly exposed to HX in both fibrils and protofibrils. In contrast, the internal fragment 20-34 is highly protected from exchange in fibrils but much less so in protofibrils. The data suggest that the beta-sheet elements comprising the amyloid fibril are already present in protofibrils, but that they are expanded into some adjacent residues upon the formation of mature amyloid. The N-terminal approximately ten residues appear to be unstructured in both protofibrils and fibrils. The 20-30 segment of Abeta(1-40) is more ordered in fibrils than in protofibrils, suggesting that, if protofibrils are a mechanistic precursor of fibrils, the transition from protofibril to fibril involves substantial ordering of this region of the Abeta peptide.

Profiling an electrospray plume using surface-enhanced Raman spectroscopy.

We report the use of silver nanoparticles to obtain surface-enhanced Raman spectra of Crystal Violet in an electrospray plume. Surface enhancement allowed detection at low concentrations with the high specificity afforded by vibrational spectroscopy. SERS spectra were used to obtain an axial concentration profile closely matching that obtained in previous fluorescence experiments. SERS can provide more analyte structural information than has been obtainable from fluorescence studies of the plume.

Structural properties of Abeta protofibrils stabilized by a small molecule.

Metastable oligomeric and protofibrillar forms of amyloidogenic proteins have been implicated as on-pathway assembly intermediates in amyloid formation and as the major toxic species in a number of amyloid diseases including Alzheimer's disease. We describe here a chemical biology approach to structural analysis of Abeta protofibrils. Library screening yielded several molecules that stimulate Abeta aggregation. One of these compounds, calmidazolium chloride (CLC), rapidly and efficiently converts Abeta(1-40) monomers into clusters of protofibrils. As monitored by electron microscopy, these protofibrils persist for days when incubated in PBS at 37 degrees C, with a slow transition to fibrillar structures apparent only after several weeks. Like normal protofibrils, the CLC-Abeta aggregates exhibit a low thioflavin T response. Like Abeta fibrils, the clustered protofibrils bind the anti-amyloid Ab WO1. The CLC-Abeta aggregates exhibit the same protection from hydrogen-deuterium exchange as do protofibrils isolated from a spontaneous Abeta fibril formation reaction: approximately 12 of the 39 Abeta(1-40) backbone amide protons are protected from exchange in the protofibril, compared with approximately twice that number in amyloid fibrils. Scanning proline mutagenesis analysis shows that the Abeta molecule in these protofibrillar assemblies exhibits the same flexible N and C termini as do mature amyloid fibrils. The major difference in Abeta conformation between fibrils and protofibrils is added structural definition in the 22-29 segment in the fibril. Besides aiding structural analysis, compounds capable of facilitating oligomer and protofibril formation might have therapeutic potential, if they act to sequester Abeta in a form and/or location that cannot engage the toxic pathway.

Mapping abeta amyloid fibril secondary structure using scanning proline mutagenesis.

Although the amyloid fibrils formed from the Alzheimer's disease amyloid peptide Abeta are rich in cross-beta sheet, the peptide likely also exhibits turn and unstructured regions when it becomes incorporated into amyloid. We generated a series of single-proline replacement mutants of Abeta(1-40) and determined the thermodynamic stabilities of amyloid fibrils formed from these mutants to characterize the susceptibility of different residue positions of the Abeta sequence to proline substitution. The results suggest that the Abeta peptide, when engaged in the amyloid fibril, folds into a conformation containing three highly structured segments, consisting of contiguous sequence elements 15-21, 24-28, and 31-36, that are sensitive to proline replacement and likely to include the beta-sheet portions of the fibrils. Residues relatively insensitive to proline replacement fall into two groups: (a) residues 1-14 and 37-40 are likely to exist in relatively unstructured, flexible elements extruded from the beta-sheet-rich amyloid core; (b) residues 22, 23, 29 and 30 are likely to occupy turn positions between these three structured elements. Although destabilized, fibrils formed from Abeta(1-40) proline mutants are very similar in structure to wild-type fibrils, as indicated by hydrogen-deuterium exchange and other analysis. Interestingly, however, some proline mutations destabilize fibrils while at the same time increasing the number of amide protons protected from hydrogen exchange. This suggests that the stability of amyloid fibrils, rather than being driven exclusively by the formation of H-bonded beta-sheet, is achieved, as in globular proteins, through a balance of stabilizing and destabilizing forces. The proline scanning data are most compatible with a model for amyloid protofilament structure loosely resembling the parallel beta-helix folding motif, such that each Abeta(15-36) core region occupies a single layer of a prismatic, H-bonded stack of peptides.

Enhanced correction methods for hydrogen exchange-mass spectrometric studies of amyloid fibrils.

We describe methods for minimization of and correction for artifactual forward and backward exchange occurring during hydrogen exchange-mass spectrometric (HX-MS) studies of amyloid fibrils of the Abeta(1-40) peptide. The quality of the corrected data obtained using published and new correction algorithms is evaluated quantitatively. Using the new correction methods, we have determined that 20.1 +/- 1.4 of the 39 backbone amide hydrogens in Abeta(1-40) exchange with deuteriums in 100 h when amyloid fibrils of this peptide are suspended in D(2)O. These data reinforce our previous conclusions based on uncorrected data that amyloid fibrils contain a rigid protective core structure that involves only about half of the Abeta backbone amides. The methods developed here should be of general value for HX-MS studies of amyloid fibrils and other protein aggregates.

Profiling pH changes in the electrospray plume.

Laser-induced fluorescence spectrometry is used to profile pH changes as droplets evaporate in an electrospray plume by measuring emission spectra of 2(or 4)-[10-(dimethylamino)-3-oxo-3H-benzo[c]xanthene-7-yl]-benzenedicarboxylic acid (carboxy SNARF-1), a pH-sensitive fluorescent dye. The observed pH changes depend on initial droplet pH and polarity. In some instances, small or negligible changes of pH are observed, consistent with expected buffering. The pH of initially acidic droplets decreases along the spray axis in both positive and negative ion modes, to an extent larger than expected from solvent evaporation. This phenomenon may be a manifestation of droplet cooling, droplet subdivision, or heterogeneous charge distribution within the spray plume or within individual ES droplets.

Qualitative assessment of monomer ratios in putative ionic terpolymer samples by electrospray ionization mass spectrometry with collision-induced dissociation.

Collision-induced dissociation in the source of an electrospray (ES) mass spectrometer was employed to characterize putative samples of the ionic terpolymer poly(styrene sulfonate-co-acrylic acid-co-2-acrylamido-2-methyl-1-propanesulfonic acid). Qualitative and semi-quantitative information about the monomer content was quickly obtainable from ES spectra, and indicated that some samples contained little or none of one or two expected comonomers. For two representative samples, confirmatory nuclear magnetic resonance (NMR) data were acquired. The NMR experiments required sample clean-up (to remove additives) and long acquisition times (up to 720 min) for 13C NMR. Cleanup also improved the ES results, providing better agreement with the NMR data. However, qualitative and semi-quantitative information was obtainable by ES (but not by NMR) without the cleanup step. Full quantitation of monomer ratios would require suitable standards, but even without such standards the ES measurements provide a rapid (<1 min) means for differentiating these samples (e.g., for process or quality control).