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International audience; Ultrahigh resolution mass spectrometry (UHR-MS) coupled with direct infusion (DI) electrospray ionization offers a fast solution for accurate untargeted profiling. Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometers have been shown to produce a wealth of insights into complex chemical systems because they enable unambiguous molecular formula assignment even if the vast majority of signals is of unknown identity. Interlaboratory comparisons are required to apply this type of instrumentation in quality control (for food industry or pharmaceuticals), large-scale environmental studies, or clinical diagnostics. Extended comparisons employing different FT-ICR MS instruments with qualitative direct infusion analysis are scarce since the majority of detected compounds cannot be quantified. The extent to which observations can be reproduced by different laboratories remains unknown. We set up a preliminary study which encompassed a set of 17 laboratories around the globe, diverse in instrumental characteristics and applications, to analyze the same sets of extracts from commercially available standard human blood plasma and Standard Reference Material (SRM) for blood plasma (SRM1950), which were delivered at different dilutions or spiked with different concentrations of pesticides. The aim of this study was to assess the extent to which the outputs of differently tuned FT-ICR mass spectrometers, with different technical specifications, are comparable for setting the frames of a future DI-FT-ICR MS ring trial. We concluded that a cluster of five laboratories, with diverse instrumental characteristics, showed comparable and representative performance across all experiments, setting a reference to be used in a future ring trial on blood plasma.

Devices for a range of uses from chemical purification to analytical instrumentation have exploited the constant relationship between a confining magnetic field and its captured charged particle. The path to mass spectrometry from particle physics was clearly evolutionary containing key and bit players along the development pathway. Modern Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometers retain notable characteristics of many stepwise advancements dating back to the simple copper cyclotron of Lawrence. Common themes among these milestones were flexibility and performance that seemingly transcended the sum of parts of a simple device that relied on a simple physical relationship. Recent advances to this simplistic concept have enabled dramatic increases in analytical figures-of-merit beyond what could be imagined even a decade ago. The emerging instrumentation has a core competence for separation of complex mixtures to include isotopologue masses of individual isotopic peaks in those very mixtures. With this routine capability comes new ideas for analysis of biomolecules and effectively supplements the advantage of selectivity for complex mixtures with specificity of their composition or heteroatom content.

Distinguishing tumor from normal glandular breast tissue is an important step in breast-conserving surgery. Because this distinction can be challenging in the operative setting, up to 40% of patients require an additional operation when traditional approaches are used. Here, we present a proof-of-concept study to determine the feasibility of using desorption electrospray ionization mass spectrometry imaging (DESI-MSI) for identifying and differentiating tumor from normal breast tissue. We show that tumor margins can be identified using the spatial distributions and varying intensities of different lipids. Several fatty acids, including oleic acid, were more abundant in the cancerous tissue than in normal tissues. The cancer margins delineated by the molecular images from DESI-MSI were consistent with those margins obtained from histological staining. Our findings prove the feasibility of classifying cancerous and normal breast tissues using ambient ionization MSI. The results suggest that an MS-based method could be developed for the rapid intraoperative detection of residual cancer tissue during breast-conserving surgery.

Pilot Project #1--the identification and characterization of human histone H4 proteoforms by top-down MS--is the first project launched by the Consortium for Top-Down Proteomics (CTDP) to refine and validate top-down MS. Within the initial results from seven participating laboratories, all reported the probability-based identification of human histone H4 (UniProt accession P62805) with expectation values ranging from 10(-13) to 10(-105). Regarding characterization, a total of 74 proteoforms were reported, with 21 done so unambiguously; one new PTM, K79ac, was identified. Inter-laboratory comparison reveals aspects of the results that are consistent, such as the localization of individual PTMs and binary combinations, while other aspects are more variable, such as the accurate characterization of low-abundance proteoforms harboring2 PTMs. An open-access tool and discussion of proteoform scoring are included, along with a description of general challenges that lie ahead including improved proteoform separations prior to mass spectrometric analysis, better instrumentation performance, and software development.

Hydrogen/deuterium exchange (HDX) mass spectrometry (MS) is used for analyzing protein dynamics, protein folding/unfolding, and molecular interactions. Until this study, HDX MS experiments employed mass spectral resolving powers that afforded only one peak per nominal mass in a given peptide's isotope distribution, and HDX MS data analysis methods were developed accordingly. A level of complexity that is inherent to HDX MS remained unaddressed, namely, various combinations of natural abundance heavy isotopes and exchanged deuterium shared the same nominal mass and overlapped at previous resolving powers. For example, an A + 2 peak is comprised of (among other isotopomers) a two-(2)H-exchanged/zero-(13)C isotopomer, a one-(2)H-exchanged/one-(13)C isotopomer, and a zero-(2)H-exchanged/two-(13)C isotopomer. Notably, such isotopomers differ slightly in mass as a result of the ∼3 mDa mass defect between (2)H and (13)C atoms. Previous HDX MS methods did not resolve these isotopomers, requiring a natural-abundance-only (before HDX or "time zero") spectrum and data processing to remove its contribution. It is demonstrated here that high-resolution mass spectrometry can be used to detect isotopic fine structure, such as in the A + 2 profile example above, deconvolving the isotopomer species resulting from deuterium incorporation. Resolving isotopic fine structure during HDX MS therefore permits direct monitoring of HDX, which can be calculated as the sum of the fractional peak magnitudes of the deuterium-exchanged isotopomers. This obviates both the need for a time zero spectrum as well as data processing to account for natural abundance heavy isotopes, saving instrument and analysis time.

Mass spectrometry continues to develop as a valuable tool in the analysis of proteins and protein complexes. In protein complex mass spectrometry studies, surface-induced dissociation (SID) has been successfully applied in quadrupole time-of-flight (Q-TOF) instruments. SID provides structural information on noncovalent protein complexes that is complementary to other techniques. However, the mass resolution of Q-TOF instruments can limit the information that can be obtained for protein complexes by SID. Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) provides ultrahigh resolution and ultrahigh mass accuracy measurements. In this study, an SID device was designed and successfully installed in a hybrid FT-ICR instrument in place of the standard gas collision cell. The SID-FT-ICR platform has been tested with several protein complex systems (homooligomers, a heterooligomer, and a protein-ligand complex, ranging from 53 to 85 kDa), and the results are consistent with data previously acquired on Q-TOF platforms, matching predictions from known protein interface information. SID fragments with the same m/z but different charge states are well-resolved based on distinct spacing between adjacent isotope peaks, and the addition of metal cations and ligands can also be isotopically resolved with the ultrahigh mass resolution available in FT-ICR.

The new endohedral fullerene, Sc2(μ2-O)@Cs(6)-C82, has been isolated from the carbon soot obtained by electric arc generation of fullerenes utilizing graphite rods doped with 90% Sc2O3 and 10% Cu (w/w). Sc2(μ2-O)@Cs(6)-C82 has been characterized by single crystal X-ray diffraction, mass spectrometry, and UV/vis spectroscopy. Computational studies have shown that, among the nine isomers that follow the isolated pentagon rule (IPR) for C82, cage 6 with Cs symmetry is the most favorable to encapsulate the cluster at T > 1200 K. Sc2(μ2-O)@Cs(6)-C82 is the first example in which the relevance of the thermal and entropic contributions to the stability of the fullerene isomer has been clearly confirmed through the characterization of the X-ray crystal structure.

Despite significant developments in mass spectrometry technology in recent years, no routine proteomics sequencing tool is currently available for peptide anions. The use of a molecular open-shell cation is presented here as a possible reaction partner to induce electron transfer dissociation with deprotonated peptide anions. In this negative electron transfer dissociation (NETD) scheme, an electron is abstracted from the peptide anion and transferred to the radical cation. This is demonstrated for the example of the fluoranthene cation, C(16)H(10)(+*), which is reacted with deprotonated phosphorylated peptides in a 3-D ion trap mass spectrometer. Selective backbone cleavage at the C(alpha)-C bond is observed to yield a and x fragments, similarly to electron detachment dissociation (EDD) of peptide anions. Crucially, the phosphorylation site is left intact in the dissociation process, allowing an identification and localization of the post-translational modification (PTM) site. In contrast, NETD using Xe(+*) as the reagent cation results in sequential neutral losses (CO(2) and H(3)PO(4)) from a/x fragments, which complicate the interpretation of the mass spectra. This difference in dissociation behavior can be understood in the framework of the reduced recombination energy of the electron transfer process for fluoranthene, which is estimated at 2.5-4.5 eV, compared to 6.7-8.7 eV for xenon. Similarly to ETD, proton transfer is found to compete with electron transfer processes in NETD. Isotope fitting of the charge-reduced species shows that in the case of fluoranthene-mediated NETD, proton transfer only accounts for20%, whereas this process highly abundant for Xe(+*) (43 and 82%). Since proton abstraction from Xe(+*) is not possible, this suggests that Xe(+*) ionizes other transient species in the ion trap, which then engage in proton transfer reactions with the peptide anions.

For Fourier transform mass spectrometry analysis of high mass ions, the signals from closely spaced isotope peaks undergo periodic destructive interference, producing a beat pattern in the time-domain signal. The mass spectra that are obtained by sampling transient signals for less than two beat periods exhibit an error in the relative abundances that are measured. This effect is shown to cause significant errors in the measurement of the relative abundances of the components of polymer distributions, leading to errors in the derived average molecular weights for such samples. Computer simulations show that isotope beating causes this error to increase as the duration of an acquired transient becomes short compared to the beating period. This error becomes insignificant when the transient is acquired for longer than twice the beat period. Experimental data are presented for polymers in which an oligomeric distribution of monoisotopic peaks is produced by stored waveform inverse Fourier transform ejection of all 13C-containing isotope peaks. The data show that the isotope beating-induced abundance errors are eliminated when there are no isotope peaks present.

We report the application of matrix-assisted laser desorption ionization (MALDI) to monitor recombinant protein expression in whole bacteria. This technique is characterized by rapid sample preparation that provides analysis of samples extracted directly from the growth media in less than 10 min. The mass spectrometric method holds several advantages over gel electrophoresis, the conventional method for examining the protein content of cells. Comparisons between the two methods of analysis are presented in terms of increased speed, efficiency, resolution, and mass accuracy. Delayed extraction time-of-flight mass spectrometry identifies posttranslational modifications and other changes in the expected structure which are not recognized by gel electrophoresis. The utility of this method is demonstrated for proteins with molecular masses ranging from 5 to 50 kDa. Low molecular mass proteins (10 kDa) can be efficiently analyzed without any treatment of the bacterial broth prior to MALDI sample preparation. The MALDI analysis of higher molecular weight proteins shows enhanced sensitivity when the bacterial solutions are first sonicated.

Improvements in the matrix assisted laser desorption/ionization analysis of polymers are obtained with Fourier transform mass spectrometry by using an open-ended cylindrical analyzer cell. These improvements include a reduced sensitivity to experimental parameters in determining the oligomer molecular weight distribution, and better mass accuracy. Ion trajectory calculations and experimental data show that the open-ended cylindrical cell is less sensitive to changes in gated trapping time for capturing a range of masses. For poly(ethylene)glycol 1000, a shift of only 20 Da is observed for a 200 μs change in gated trapping time and shift of 100 Da for the weight average is observed for a 540 μs change. The mass accuracy for determinations of end-group and repeat unit masses are presented for internal and external calibration of polymer samples. Using a linear regression method, repeat group masses were determined to within 0.1 mmu and 0.7 mmu for internal and external calibration at 2000 Da. The mass accuracy at high molecular weight with external calibration was tested with poly(methyl) methacrylate 6000, which yielded a mean squared error of 8.1 mmu for the repeat mass and 23.6 mmu for the end-group mass. Space charge is shown to affect mass accuracy. By accounting appropriately for this effect, a root mean error of 1.4 ppm is obtained for nine peaks in an externally calibrated poly(methyl) methacrylate 6000 mass spectrum.

Background: Neuropeptides are a diverse category of signaling molecules in the nervous system regulating a variety of processes including food intake, social behavior, circadian rhythms, learning, and memory. Both the identification and functional characterization of specific neuropeptides are ongoing fields of research. Matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) analysis of nervous tissues from a variety of organisms allows direct detection and identification of neuropeptides. Here, we demonstrate an analysis workflow that allows for the detection of differences in specific neuropeptides amongst a variety of neuropeptides being simultaneously measured. For sample preparation, we describe a straight-forward and rapid (minutes) method where individual adult Drosophila melanogaster brains are analyzed. Using a MATLAB-based data analysis workflow, also compatible with MALDI-TOF mass spectra obtained from other sample preparations and instrumentation, we demonstrate how changes in neuropeptides levels can be detected with this method. Results: Over fifty isotopically resolved ion signals in the peptide mass range are reproducibly observed across experiments. MALDI-TOF MS profile spectra were used to statistically identify distinct relative differences in organ-wide endogenous levels of detected neuropeptides between biological conditions. In particular, three distinct levels of a particular neuropeptide, pigment dispersing factor, were detected by comparing groups of preprocessed spectra obtained from individual brains across three different D. melanogaster strains, each of which express different amounts of this neuropeptide. Using the same sample preparation, MALDI-TOF/TOF tandem mass spectrometry confirmed that at least 14 ion signals observed across experiments are indeed neuropeptides. Among the identified neuropeptides were three products of the neuropeptide-like precursor 1 gene previously not identified in the literature. Conclusions: Using MALDI-TOF MS and preprocessing/statistical analysis, changes in relative levels of a particular neuropeptide in D. melanogaster tissue can be statistically detected amongst a variety of neuropeptides. While the data analysis methods should be compatible with other sample preparations, the presented sample preparation method was sufficient to identify previously unconfirmed D. melanogaster neuropeptides.

Drug transit through the blood-brain barrier (BBB) is essential for therapeutic responses in malignant glioma. Conventional methods for assessment of BBB penetrance require synthesis of isotopically labeled drug derivatives. Here, we report a new methodology using matrix assisted laser desorption ionization mass spectrometry imaging (MALDI MSI) to visualize drug penetration in brain tissue without molecular labeling. In studies summarized here, we first validate heme as a simple and robust MALDI MSI marker for the lumen of blood vessels in the brain. We go on to provide three examples of how MALDI MSI can provide chemical and biological insights into BBB penetrance and metabolism of small molecule signal transduction inhibitors in the brain – insights that would be difficult or impossible to extract by use of radiolabeled compounds.

A 4.7 Tesla internal source matrix-assisted laser desorption ionization (MALDI) ion cyclotron resonance (FTICR) (MALDI-FTICR) has been constructed to examine ions in the 1000–10000 Da mass range. This instrument combines several recent innovations for enhancing the trapping and detection of ions of high mass-to-charge. Ions up to m/z 11 000 have been efficiently trapped and detected with high signal-to-noise (S/N). By using quadrupolar excitation to axialize ions, resolutions of 1.5 million for gramicidin S, 65 000 for insulin, and 85 000 for the 146-mer of polyethylene glycol have been obtained. 100% remeasurement efficiency is shown for 200 remeasurement cycles at m/z 2000 at high S/N with normal detection energies. By using quadrupolar excitation for ion remeasurement, effects from detection parameters such as trapping voltage and r.f. excitation power are examined under conditions that are independent of ionization yield. A tuning method is presented that uses the ions produced by one laser shot to systematically optimize signal strength and resolution for FTICR detection.

Axial ejection is found to be the principal cause of the loss of ions during Fourier transform mass spectrometry remeasurement experiments. Ion remeasurement improves to near unit efficiency when an open-ended cylindrical analyzer cell is used with capacitive coupling of the excitation signal to the adjacent trapping plates. With capacitive coupling enabled for the entire experiment, 100% remeasurement efficiency is observed over a narrow mass range (10 Da) for 200 scans of ions of poly(ethylene glycol) formed by internal matrix-assisted laser desorption/ionization. Greater than 99.5% efficiency per remeasurement cycle has been achieved for wide mass range (1000 Da) remeasurement with capacitive coupling enabled. Further evidence for axial ejection during remeasurement comes from a comparison of remeasurement efficiencies obtained at different trapping potentials.

A study of trans-Rh(PH3)2(CO)X (X = F, Cl) using Hartree-FocWmany-body perturbation theory and density functional methods is presented. We report optimized Hartree-Fock and MBPT(2) structures employing effective core potentials with double-g plus polarization basis sets including f-type functions. Optimized structures using density functional methods, including those with gradient-corrected exchange-correlation functionals, are also reported. Both ab initio methods yield complexes which have a slightly distorted squareplanar structure with moderate bending of the phosphine ligands toward the halide. The predicted structure of the chloro complex is compared with experimental data for truns-Rh(PPh3)2(CO)Cl.

Quadrupolar excitation is achieved over a wide mass range by using repetitive chirp excitation, filtered noise excitation, and high-amplitude, single-frequency excitation for matrix-assisted laser desorption FTICR mass spectrometry. These methods efficiently axialize ions over a wide range of masses in a 4.7 T FTICR spectrometer. Remeasurement efficiencies are >99.5% for broadband repetitive chirp excitation, 99% with filtered white noise, and 99.4% with high-amplitude, single-frequency broad-band quadrupolar excitation. Results indicate that z-axis ejection of ions during detection is the primary mechanism for ion loss during remeasurement experiments. Capacitive coupling of the excitation signal to the trapping plates of the open-ended cylindrical analyzer cell is required for high remeasurement efficiency.

The new endohedral fullerene, Sc(2)(mu(2)-O)@C(s)(6)-C(82), has been isolated from the carbon soot obtained by electric arc generation of fullerenes utilizing graphite rods doped with 90% Sc(2)O(3) and 10% Cu (w/w). Sc(2)(mu(2)-O)@C(s)(6)-C(82) has been characterized by single crystal X-ray diffraction, mass spectrometry, and UV/vis spectroscopy. Computational studies have shown that, among the nine isomers that follow the isolated pentagon rule (IPR) for C(82), cage 6 with C(s) symmetry is the most favorable to encapsulate the cluster at T1200 K. Sc(2)(mu(2)-O)@C(s)(6)-C(82) is the first example in which the relevance of the thermal and entropic contributions to the stability of the fullerene isomer has been clearly confirmed through the characterization of the X-ray crystal structure.

Structural characterization of glycosaminoglycans (GAGs) has been a challenge in the field of mass spectrometry, and the application of electron detachment dissociation (EDD) Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) has shown great promise to GAG oligosaccharide characterization in a single tandem mass spectrometry experiment. In this work, we apply the technique of negative electron transfer dissociation (NETD) to GAGs on a commercial ion trap mass spectrometer. NETD of GAGs, using fluoranthene or xenon as the reagent gas, produces fragmentation very similar to previously observed EDD fragmentation. Using fluoranthene or xenon, both glycosidic and cross-ring cleavages are observed, as well as even- and odd-electron products. The loss of SO(3) can be minimized and an increase in cross-ring cleavages is observed if a negatively charged carboxylate is present during NETD, which can be controlled by the charge state or the addition of sodium. NETD effectively dissociates GAGs up to eight saccharides in length, but the low resolution of the ion trap makes assigning product ions difficult. Similar to EDD, NETD is also able to distinguish the epimers iduronic acid from glucuronic acid in heparan sulfate tetrasaccharides and suggests that a radical intermediate plays an important role in distinguishing these epimers. These results demonstrate that NETD is effective at characterizing GAG oligosaccharides in a single tandem mass spectrometry experiment on a widely available mass spectrometry platform.

Mass spectrometry is the tool of choice for sequencing peptides and determining the sites of posttranslational modifications; however, this bottom-up approach lacks in providing global information about the modification states of proteins including the number and types of isoforms and their stoichiometry. Recently, various techniques and mass spectrometers, such as high-field Fourier Transform Ion Cyclotron Resonance (FTICR) mass spectrometers, have been developed to study intact proteins (top-down proteomics). While the protein molecular mass and the qualitative and quantitative information about protein isoforms can be revealed by FTICR-MS analysis, their primary structure (including the identification of modifications and their exact locations in the amino acid sequence) can directly be determined using the MS/MS capability offered by the FTICR mass spectrometer. The distinct advantage of top-down methods are that modifications can be determined for a specific protein isoform rather than for peptides belonging to one or several isoforms. In this chapter, we describe different top-down proteomic approaches enabled by high-field (7, 9.4, and 12 T) FTICR mass spectrometers, and their applicability to answer biological and biomedical questions. We also describe the use of the free flow electrophoresis (FFE) to separate proteins prior to top-down mass spectrometric characterization.

Top-down and bottom-up mass spectrometry methods can generate gas phase fragments and use these to identify proteins. Top-down methods, in addition, can provide the mass of the protein itself and therefore additional structural information. Despite the conceptual advantage of top-down methods, the market share advantage belongs to bottom-up methods as a result of their more robust sample preparation, fragmentation, and data processing methods. Here we report improved fragmentation and data processing methods for top-down mass spectrometry. Specifically we report the use of funnel-skimmer dissociation, a variation of nozzle-skimmer dissociation, and compare its performance with electron capture dissociation. We also debut BIG Mascot, an extended version of Mascot with incorporated top-down MS(2) search ability and the first search engine that can perform both bottom-up and top-down searches. Using BIG Mascot, we demonstrated the ability to identify proteins 1) using only intact protein MS(1), 2) using only MS(2), and 3) using the combination of MS(1) and MS(2). We correctly identified proteins with a wide range of masses, including 13 amyotrophic lateral sclerosis-associated variants of the protein Cu/Zn-superoxide dismutase, and extended the upper mass limit of top-down protein identification to 669 kDa by identifying thyroglobulin.

The remarkably large cluster Sc4(mu3-O)2 has been obtained trapped inside an Ih-C80 cage by conducting the vaporization of graphite rods doped with copper(II) nitrate and scandium(III) oxide in an electric arc under a low pressure helium atmosphere with an added flow of air. The product has been isolated by chromatography and identified by high-resolution mass spectrometry. The structure of Sc4(mu3-O)2@Ih-C80 has been determined by X-ray crystallography on a crystal of Sc4(mu3-O)2@Ih-C80.NiII(OEP).2(C6H6). The Sc4(mu3-O)2 unit consists of a distorted tetrahedron of scandium atoms with oxygen atoms bridging two of its faces. The Sc-Sc distances range from 2.946(7) to 3.379(7) A.

In an effort to spectroscopically determine the structures of solvated ions composed of nucleic acid bases and amino acids, methods for their gas-phase synthesis have been studied. Ions were electrosprayed and solvated in the accumulation cell of a hybrid Q-FTICR filled with methanol or water vapor at approximately 10(-2) bar. There were subsequently transferred to the FTICR cell at 10(-10) mbar. Following their isolation in the FTICR, they can be investigated by studying their unimolecular blackbody infrared radiative dissociation (BIRD) or infrared multiple photon dissociation (IRMPD) spectroscopy. The IRMPD spectra for (Ade)(2)Li(+) and (Ade)(2)Li(H(2)O)(+) are reported and compared as well as BIRD rate constants for multiply solvated and metalated adenine ions.

Electron transfer dissociation (ETD) of proteins is demonstrated in a hybrid quadrupole-hexapole Fourier transform ion cyclotron resonance mass spectrometer (Qh-FTICRMS). Analyte ions are selected in the mass analyzing quadrupole, accumulated in the hexapole linear ion trap, reacted with fluoranthene reagent anions, and then analyzed via an FTICR mass analyzer. The hexapole trap allows for a broad fragment ion mass range and a high ion storage capacity. Using a 3 T FTICRMS, resolutions of 60 000 were achieved with mass accuracies averaging below 1.4 ppm. The high resolution, high mass accuracy ETD spectra provided by FTICR obviates the need for proton transfer reaction (PTR) charge state reduction of ETD product ions when analyzing proteins or large peptides. This is demonstrated with the ETD of ubiquitin and apomyoglobin yielding sequence coverages of 37 and 20%, respectively. We believe this represents the first reported successful combination of ETD and a FTICRMS.

The stem–loop-binding protein (SLBP) is involved in multiple aspects of histone mRNA metabolism. To characterize the modification status and sites of SLBP, we combined mass spectrometric bottom-up (analysis of peptides) and top-down (analysis of intact proteins) proteomic approaches. Drosophilia SLBP is heavily phosphorylated, containing up to seven phosphoryl groups. Accurate M r determination by Fourier transform ion cyclotron resonance (FTICR)-MS and FTICR-MS top-down experiments using a variety of dissociation techniques show there is removal of the initiator methionine and acetylation of the N terminus in the baculovirus-expressed protein, and that T230 is stoichiometrically phosphorylated. T230 is highly conserved; we have determined that this site is also completely phosphorylated in baculovirus-expressed mammalian SLBP and extensively phosphorylated in both Drosophila and mammalian cultured cells. Removal of the phosphoryl group from T230 by either dephosphorylation or mutation results in a 7-fold reduction in the affinity of SLBP for the stem–loop RNA.

The relationship of magnetic field strength and Fourier transform ion cyclotron resonance mass spectrometry performance was tested using three instruments with the same design but different fields of 4.7, 7, and 9.4 tesla. We found that the theoretically predicted "transformative" effects of magnetic field are indeed observed experimentally. The most striking effects were that mass accuracy demonstrated approximately second to third order improvement with the magnetic field, depending upon the charge state of the analyte, and that peak splitting, which prohibited automated data analysis at 4.7 T, was not observed at 9.4 T.

While collisionally activated dissociation (CAD) pathways for peptides are well characterized, those of intact proteins are not. We systematically assigned CAD product ions of ubiquitin, myoglobin, and bovine serum albumin generated using high-yield, in-source fragmentation. Assignment of >98% of hundreds of product ions implies that the fragmentation pathways described are representative of the major pathways. Protein dissociation mechanisms were found to be modulated by both source declustering potential and precursor ion charge state. Like peptides, higher charge states of proteins fragmented at lower energies next to Pro, via mobile protons, while lower charge states fragmented at higher energies after Asp and Glu, via localized protons. Unlike peptides, however, predominant fragmentation channels of proteins occurred at intermediate charge states via non-canonical mechanisms and produced extensive internal fragmentation. The non-canonical mechanisms include prominent cleavages C-terminal to Pro and Asn, and N-terminal to Ile, Leu, and Ser; these cleavages, along with internal fragments, led to a 45% increase in sequence coverage, improving the specificity of top-down protein identification. Three applications take advantage of the different mechanisms of protein fragmentation. First, modulation of declustering potential selectively fragments different charge states, allowing the source region to be used as the first stage of a low-resolution tandem mass spectrometer, facilitating pseudo-MS3 of product ions with known parent charge states. Second, development and integration of automated modulation of ion funnel declustering potential allows users access to a particular fragmentation mechanism, yielding facile cleavage on a liquid chromatography timescale. Third, augmentation of a top-down search engine improved protein characterization.

A method to combine gated trapping and capacitive coupling into a single experiment is reported. This is achieved with a circuit that allows isolation of the electronic network that gates the trapping voltage from the circuit that enables capacitive coupling of the rf excitation signal to the trapping plates. When the capacitive coupling network is not isolated from the gated trapping network, the trapping voltage changes occur on a 100 µs or longer timescale, which is incompatible with efficient capture of ions formed by matrix-assisted laser desorption ionization. Isolation of the two networks allows the trapping voltage to be gated with less than a 10 µs risetime. The effectiveness of this approach is demonstrated by a set of experiments carried out with and without the benefit of the isolation of capacitive coupling from gated trapping.

Electron transfer dissociation (ETD) is evaluated as a technique to provide local information on higher order structure and dynamics of a whole protein molecule. Isotopic labeling of highly flexible segments of a model 18 kDa protein is carried out in solution under mildly denaturing conditions by means of hydrogen/deuterium exchange (HDX), followed by transfer of intact protein ions to the gas phase by means of electrospray ionization and mass-selection of a precursor ion for subsequent reactions with fluoranthene radical anions. The ETD process gives rise to abundant fragment ions, whose deuterium content can be measured as a function of duration of the HDX reaction in solution. No backbone protection is detected for all protein segments spanning the twenty-five residue long N-terminal part of the protein, which is known to lack structure in solution. At the same time, noticeable protection is evident for segments representing the structured regions of the protein. The results of this work suggest that ETD of intact protein ions is not accompanied by detectable hydrogen scrambling and can be used in tandem with HDX to probe protein conformation in solution.