The proposed model is based on the measurement of the retention times of 346 tryptic peptides in the 560-to 4,000-Da mass range, derived from a mixture of 17 protein digests. These peptides were measured in HPLC-MALDI MS runs, with peptide identities confirmed by MS/MS. The model relies on summation of the retention coefficients of the individual amino acids, as in previous approaches, but additional terms are introduced that depend on the retention coefficients for amino acids at the N-terminal of the peptide. In the 17-protein mixture, optimization of two sets of coefficients, along with additional compensation for peptide length and hydrophobicity, yielded a linear dependence of retention time on hydrophobicity, with an R 2 value about 0.94. The predictive capability of the model was used to distinguish peptides with close m/z values and for detailed peptide mapping of selected proteins. Its applicability was tested on columns of different sizes, from nano-to narrow-bore, and for direct sample injection, or injection via a pre-column. It can be used for accurate prediction of retention times for tryptic peptides on reversed-phase (300-Å pore size) columns of different sizes with a linear water-ACN gradient and with TFA as the ion-pairing modifier. Molecular & Cellular Proteomics 3:908 -919, 2004.The application of MS to biomolecular analysis has revolutionized protein research within the past decade (1). This can be mostly attributed to the development of ionization techniques that are compatible with biomolecules, i.e. MALDI (2, 3) and ESI (4), as well as improved instrumentation. However, although modern mass spectrometers provide high mass accuracy and sensitivity, the protein complexity and concentration range usually found in biological samples still present a challenge. The problem has been traditionally attacked by separation of complex protein mixtures by two-dimensional gel electrophoresis, with subsequent protein in-gel digestion, followed by ESI or MALDI MS. This remains one of the most popular sample preparation procedures, especially suitable for protein identification and quantitation. However, the method is best suited for higher abundance proteins with masses greater than 12-14 kDa, and some categories of molecules, such as membrane proteins (1) or species with extremes in isoelectric points, are handled poorly. There are also difficulties in adapting the method to high-throughput applications.Alternative analytical approaches are based on pre-fractionation of protein mixtures or cell lysates before the final MS steps of analysis (5-9). This often involves proteolytic digestion, followed by one-or multi-dimensional chromatographic separation of the resulting peptides, with subsequent detection by MS/MS. Such a method may yield considerable simplification of the problem, because the fractions from on-or off-line HPLC separations have reduced complexity compared with the original sample. Indeed, the combination of HPLC-ESI (MS or MS/MS) has proved to be a "work horse" for large-scale high-throug...

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Molecular characterization of asphaltenes by conventional analytical techniques is a challenge because of their compositional complexity, high heteroatom content, and asphaltene aggregate formation at low concentrations. Thus, most common characterization techniques rely on bulk properties or solution-phase behavior (solubility). Proposed over 20 years ago, the Boduszynski model proposes a continuous progression in petroleum composition (molecular weight, structure, and heteroatom content) as a function of the atmospheric equivalent boiling point. Although exhaustive detailed compositional analysis of petroleum distillates validates the continuum model, the available compositional data from asphaltene fractions supports the extension of the continuum model into the nondistillables only indirectly. Asphaltenes, defined by their insolubility in alkane solvents, accumulate in high-boiling fractions and form stable aggregate structures at low parts per billion (ppb) concentrations, far below the concentration required for most mass analyzers. Here, we present direct mass spectral detection of stable asphaltene aggregates at lower concentrations than previously published and observe the onset of asphaltene nanoaggregate formation by time-of-flight mass spectrometry (TOF−MS). We conclude that a fraction of asphaltenes must be present as nanoaggregates (not monomers) in all atmospheric pressure and laser-based ionization methods. Thus, those methods access a subset of the asphaltene continuum.

In 2006, a mechanically-transmissible and previously uncharacterized virus was isolated in Kansas from wheat plants with mosaic symptoms. The physiochemical properties of the virus were examined by purification on cesium chloride density gradients, electron microscopy, sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), sequencing of the nucleotides and amino acids of the coat protein, and immunological reactivity. Purified preparations contained flexuous, rod-shaped particles that resembled potyviruses. The coat protein was estimated from SDS-PAGE to have a mass of approximately 35 kDa. Its amino acid sequence, as deduced from DNA sequencing of cloned, reverse-transcribed viral RNA and separately determined by time-of-flight mass spectrometry, was most closely related (49% similarity) to Sugarcane streak mosaic virus, a member of the Tritimovirus genus of the family Potyviridae. The virus gave strong positive reactions during enzyme-linked immunosorbent assays using polyclonal antibodies raised against purified preparations of the cognate virus but gave consistent negative reactions against antibodies to Wheat streak mosaic virus (WSMV), other wheat potyviruses, and the High Plains virus. When the virus was inoculated on the WSMV-resistant wheat cv. RonL, systemic symptoms appeared and plant growth was diminished significantly in contrast with WSMV-inoculated RonL. Taken together, the data support consideration of this virus as a new potyvirus, and the name Triticum mosaic virus (TriMV) is proposed.

A new algorithm, sequence-specific retention calculator, was developed to predict retention time of tryptic peptides during RP HPLC fractionation on C18, 300-A pore size columns. Correlations of up to approximately 0.98 R2 value were obtained for a test library of approximately 2000 peptides and approximately 0.95-0.97 for a variety of real samples. The algorithm was applied in conjunction with an exclusion protocol based on mass (15 ppm tolerance) and retention time (2-min tolerance for 0.66% acetonitrile/min gradient), MART criteria to significantly reduce the instrument time required for complete MS/MS analysis of a digest separated by RP HPLC. This was confirmed by reanalyzing the set of HPLC-MALDI MS/MS data with no loss in protein identifications, despite the number of virtually executed MS/MS analyses being decreased by 57%.

Tandem instruments, such as triple-quadrupole or quadrupole-time-of-flight mass spectrometers, often use collisional damping ion guides for the purpose of cooling and focusing the primary ion beam, or as a collision cell for tandem mass spectrometry experiments. A small axial field to reduce the ion residence time in such devices can give considerable improvements in performance. Reduction of the residence time reduces adduct formation caused by unwanted gas-phase reactions and allows multiple reaction monitoring (MRM) and some other types of scan to be carried out more rapidly without the risk of reaction cross-talk. Here we propose a novel electrode arrangement for creation of a suitable axial field in a multipole ion guide without significantly reducing the m/z window. As an example, a second set of four electrodes is added to an existing quadrupole collision cell. The same DC potential is applied to all four extra electrodes, which are shaped in the longitudinal direction to create a suitable axial field inside the device. The potential of these electrodes and the DC bias of the main rods determine the axial field strength. The idea was tested on a modified quadrupole collision cell of a MALDI-QqTOF instrument and experimental results are presented here, as well as a simplified theory of operation.

The influence of incident laser parameters on sensitivity in matrix-assisted laser desorption/ionization (MALDI) has been investigated using orthogonal-injection time-of-flight (TOF) instruments. A qualitative comparison was first made between the beam profiles obtained with a N(2) laser and a Nd:YAG laser using 2-m long optical fibers. The N(2) laser gives better sensitivity, consistent with a more uniform fluence distribution and therefore better coverage of the N(2) laser profile. Most of the difference disappears when a 30-m long fiber is used or when the fibers are twisted during irradiation to smooth out the fluence distribution. In more systematic measurements, the total integrated ion yield from a single spot (a measure of sensitivity) was found to increase rapidly with fluence to a maximum, and then saturate or decrease slightly. Thus, the optimum sensitivity is achieved at high fluence. For a fluence near threshold, the integrated yield has a steep (cubic) dependence on the spot size, but the yield saturates at higher fluence for smaller spots. The area dependence is much weaker (close to linear) for fluence values above saturation, with the result that the highest integrated yields per unit area are obtained with the smallest spot sizes. The results have particular relevance for imaging MALDI, where sensitivity and spatial resolution are important figures of merit.

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