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Lanthipeptides belong to the family of ribosomally synthesized and post-translationally modified peptides (RiPPs). The (methyl)lanthionine cross-links characteristic to lanthipeptides are essential for their stability and bioactivities. In most bacteria, lanthipeptides are maturated from single precursor peptides encoded in the corresponding biosynthetic gene clusters. However, cyanobacteria engage in combinatorial biosynthesis and encode as many as 80 substrate peptides with highly diverse sequences that are modified by a single lanthionine synthetase into lanthipeptides of different lengths and ring patterns. It is puzzling how a single enzyme could exert control over the cyclization processes of such a wide range of substrates. Here, we used a library of ProcA3.3 precursor peptide variants and show that it is not the enzyme ProcM but rather its substrate sequences that determine the regioselectivity of lanthionine formation. We also demonstrate the utility of trapped ion mobility spectrometry-tandem mass spectrometry (TIMS-MS/MS) as a fast and convenient method to efficiently separate lanthipeptide constitutional isomers, particularly in cases where the isomers cannot be resolved by conventional liquid chromatography. Our data allowed identification of factors that are important for the cyclization outcome, but also showed that there are no easily identifiable predictive rules for all sequences. Our findings provide a platform for future deep learning approaches to allow such prediction of ring patterns of products of combinatorial biosynthesis.

Liquid extraction surface analysis (LESA) is an ambient surface sampling technique that allows the analysis of intact proteins directly from tissue samples via mass spectrometry. Integration of ion mobility separation to LESA mass spectrometry workflows has shown significant improvements in the signal-to-noise ratios of the resulting protein mass spectra and hence the number of proteins detected. Here, we report the use of a quadrupole-cyclic ion mobility-time-of-flight mass spectrometer (Q-cIM-ToF) for the analysis of proteins from mouse brain and rat kidney tissues sampled via LESA. Among other features, the instrument allows multiple pass cyclic ion mobility separation, with concomitant increase in resolving power. Single-pass experiments enabled the detection of 30 proteins from mouse brain tissue, rising to 44 when quadrupole isolation was employed. In the absence of ion mobility separation, 21 proteins were detected in rat kidney tissue including the abundant α- and β-globin chains from hemoglobin. Single-pass cyclic ion mobility mass spectrometry enabled the detection of 60 additional proteins. Multipass experiments of a narrow m / z range ( m / z 870-920) resulted in the detection of 24 proteins (one pass), 37 proteins (two passes) and 54 proteins (three passes), thus demonstrating the benefits of improved mobility resolving power.

Carbon cluster emission from thin carbon foils (5-40 nm) impacted by individual Au(n) (+q) cluster projectiles (95-125 qkeV, n/q = 3-200) reveals features regarding the energy deposition, projectile range, and projectile fate in matter as a function of the projectile characteristics. For the first time, the secondary ion emission from thin foils has been monitored simultaneously in both forward and backward emission directions. The projectile range and depth of emission were examined as a function of projectile size, energy, and target thickness. A key finding is that the massive cluster impact develops very differently from that of a small polyatomic projectile. The range of the 125 qkeV Au(100q) (+q) (q ≈ 4) projectile is estimated to be 20 nm (well beyond the range of an equal velocity Au(+)) and projectile disintegration occurs at the exit of even a 5 nm thick foil.

Accurate density functional theory (DFT) and coupled-cluster (CCSD) calculations on a series of (LiF) n =2,36 neutral clusters suggest that nanotube structures with hexagonal and octagonal transversal cross sections show stability equal to or greater than that of the typical cubic form of large LiF crystals. The nanotube stability was further corroborated by quantum dynamic calculations at room temperature. The fact that stable nanotube structures were also found for other alkali halides (e.g., NaCl and KBr) suggests that this geometry may be widely implemented in material sciences.

This letter presents the first application of high energy, single nanoparticle probes (e.g., 520 keV Au(400) 2nm NP) in the characterization of surfaces containing fluorescent proteins (e.g., GFP variants) by their co-emitted photon, electron and secondary ion signals. NP induced protein luminescence increases with the NP incident energy, is originated by the NP impact and is transferred to the protein fluorophor via electronic energy transfer. Multi-electron emission is observed per single NP impacts and their distributions are specific to the target morphology and composition. Fragment ions of protein sub-units consisting of 2-7 amino acid peptides are observed under individual NP impacts that can be correlated to the random protein orientation relative to the impact site (e.g., outer layer or "skin" of the protein).

In the present work, the advantages of a new, 100 kV platform equipped with a massive gold cluster source for the analysis of native biological surfaces are shown. Inspection of the molecular ion emission as a function of projectile size demonstrates a secondary ion yield increase of ~100× for 520 keV Au(400)(4+) as compared to 130 keV Au(3)(1+) and 43 keV C(60). In particular, yields of tens of percent of molecular ions per projectile impact for the most abundant components can be observed with the 520 keV Au(400)(4+) probe. A comparison between 520 keV Au(400)(4+) time-of-flight-secondary ion mass spectrometry (TOF-SIMS) and matrix assisted laser desorption ionization-mass spectrometry (MALDI-MS) data showed a similar pattern and similar relative intensities of lipid components across a rat brain sagittal section. The abundant secondary ion yield of analyte-specific ions makes 520 keV Au(400)(4+) projectiles an attractive probe for submicrometer molecular mapping of native surfaces.

This paper presents the first observation of coincidental emission of photons, electrons and secondary ions from individual C(60) keV impacts. An increase in photon, electron and secondary ion yields is observed as a function of C(60) projectile energy. The effect of target structure/composition on photon and electron emissions at the nanometer level is shown for a CsI target. The time-resolved photon emission may be characterized by a fast component emission in the UV-Vis range with a short decay time, while the electron and secondary ion emission follow a Poisson distribution.

The emission of negative cluster ions produced by the impact of approximately 60 MeV (252)Cf fission fragments on a (7)LiF polycrystalline target is analyzed. The negative ion mass spectrum is dominated by the ((7)LiF)(n)F(-) series, n = 1 to approximately 30. The desorption yield distribution of the ((7)LiF)(n)F(-) members has a maximum at n = 2 and then decreases as the sum of two exponentials whose decay parameters are k(Fast) = 0.9 and k(Slow) = 0.08. These k values are the same as those observed for the positive series and close to others obtained for condensed gas targets. Relative cluster ion stabilities, deduced from the experimental ion abundances for the (LiF)(n)F(-) series, are proposed to be correlated with theoretical structures according to their internal energy by using the deviation plot (D-plot) methodology. A pool of candidate cluster structures was generated using a genetic algorithm and further analyzed and optimized using density functional theory (DFT) with the hybrid functional B3LYP (DFT/B3LYP) and Moller-Plesset perturbation theory (MP2). For the small clusters (n = 1 to 2), the most stable structures are found to be linear, whereas the larger clusters (n = 4 to 6) present cubic or polyhedral structures. Fragmentation energies, ionization potentials, and relative stabilities are reported for the most abundant families of the (LiF)(n)F(-) and (LiF)(n)(-) series.

Here, complementary ion mobility/mass spectrometry (IM/MS) and ultrahigh-resolution Fourier transform ion cyclotron resonance (FTICR) MS analyses of light, medium, and heavy petroleum crude oils yielded distributions of the heteroatom-containing hydrocarbons, as well as multiple conformational classes. The IM/MS technique provides unique fingerprints for fast identification of signature conformational/compositional patterns, whereas FTICR MS analysis provides comprehensive heteroatom class distributions. IM/MS and FTICR MS results reveal an increase in compositional complexity in proceeding from light to medium to heavy crude oils. Inspection of the mobility results shows a high structural diversity for the C(n)H(h)XY (XY = N(1), S(1), N(1), O(1), NS, SO(1-2), NO(1-2), etc.) series, as well as a shift from planar to more compact three-dimensional structures with increasing mass.

A new approach is described for the elucidation of gas-phase peptide ion structures combining ion mobility spectrometry (IMS) data and molecular dynamics (MD)-cluster analysis (CA) prediction. The new approach is based on the determination of the gas-phase ion structure identity vectors (e.g., structure and population vectors) that generate the total conformational space of the gas-phase ion as a function of the IMS experimental conditions (e.g., field strength, pressure, bath gas temperature, and IM cell geometry). Two methods to efficiently sample the gas-phase conformational space of molecular ions as a function of the effective ion temperature characteristic of the IMS experiments are described: (i) a simulated annealing MD-CA-constant temperature MD-CA, and (ii) a generalized non-Boltzmann sampling MD-free energy analysis-CA. The new theoretical method has been successfully applied to two model peptide ions (Bradykinin fragments 1-5 and 1-8, RPPGF and RPPGFSPF, respectively) for which multiple conformations sensitive to the effective ion temperature have been suggested in previous studies.

The positive and neutral clusters produced by the impact of approximately 60 MeV (252)Cf fission fragments on a LiF polycrystalline target are analyzed. The positive ion spectrum is dominated by the (LiF)(n)Li(+) series, n = 0-7, exhibiting a total yield 2 orders of magnitude higher than that of the (LiF)(n)(+) series. The yield for the dominant (LiF)(n)Li(+) series decreases roughly as exp(-kn), where k approximately 0.9 for n = 0-3 and k approximately 0.6 for the heavier clusters (n = 4-9), while the yield of the (LiF)(n)(+) series also decreases exponentially as n increases with k approximately 0.6. Theoretical calculations were performed for the (LiF)(n)Li(0), (LiF)(n)Li(+), and (LiF)(n)(0) series for n up to 9. For the smaller clusters the structures first obtained with a genetic algorithm generator were further optimized at the DFT/B3LYP/6-311+G(3df), DFT/B3LYP/LACV3P*, and MP2/LACV3P* levels of theory. An energy criterion is used for a proper taxonomic description of the optimized cluster isomers. Cluster properties such as fragmentation energy and stability are discussed for the proposed configurations. The results show that for all three series the most stable isomers present a linear structure for small cluster size (n = 1-3), while cubic cells or polyhedral structures are preferred for larger cluster sizes (n = 4-9). Fragmentation energy results suggest that a desorbed excited (LiF)(n)Li(+) ion preferentially dissociates via a cascade of (LiF)(n)(0) units, in agreement with the slope modification in the exponential decay of the (LiF)(n)Li(+) ion abundances for n > or = 3.

An ion mobility-mass spectrometer (IM-MS) interface is described that can be employed to perform collisional activation and/or collision-induced dissociation (CID) with good transmission of mobility separated ions to the MS analyzer. The IM-MS interface consists of a stacked-ring ion guide design, where the field strength and pressure ratio can be operated such that structural rearrangement reactions and/or CID are achieved as a function of the effective ion temperature. The ion dynamics and collisional activation processes in the IM-MS interface are described as a function of the ion-neutral collisions, ion kinetic energies, and effective ion temperature. The applicability of the IM-CID-MS methodology to studies of peptide ion fragmentation is illustrated using a series of model peptides.

Collision cross-sections of gas-phase (CsI)n = (1-7)Cs(+) cluster ions formed by pulsed-UV laser (355 nm) desorption ionization are measured by ion mobility-mass spectrometry. Experimental collision cross-sections are compared with calculated cross sections of candidate structures generated from a search for the lowest energy structures at the DFT/B3LYP/LACV3P** and MP2/LACVP3P** levels. The relative stabilities of these candidate structures are examined by IM-CID-MS, and the experimental results are compared to theoretical predictions. Analysis of (CsI)n = (1-7)Cs(+) cluster ion dissociation energies shows that the lower fragmentation thresholds are observed for cluster ions with the lower predicted stability.

This paper reports the first characterization of the (NH(3))(n)NH+ cluster series produced by a 252Cf fission fragments (FF) impact onto a NH(3) ice target. The (NH(3))(n=1-6)NH+ members of this series have been analyzed theoretically and experimentally. Their ion desorption yields show an exponential dependence of the cluster population on its mass, presenting a relative higher abundance at n = 5. The results of DFT/B3LYP calculations show that two main series of ammonium clusters may be formed. Both series follow a clear pattern: each additional NH(3) group makes a new hydrogen bond with one of the hydrogen atoms of the respective {NH(3)NH}+ and {NH(2)NH(2)}+ cores. The energy analysis (i.e., D-plot and stability analysis) shows that the calculated members of the (NH(3))(n-1){NH(2)NH(2)}+ series are more stable than those of the (NH(3))(n-1){NH(3)NH}+ series. The trend on the relative stability of the members of more stable series, (NH(3))(n-1){NH(2)NH(2)}+, shows excellent agreement with the experimental distribution of cluster abundances. In particular, the (NH(3))4{NH(2)NH(2)}+ structure is the most stable one, in agreement with the experiments.

Positive and negatively charged ammonia clusters produced by the impact of (252)Cf fission fragments (FF) on an NH(3) ice target have been examined theoretical and experimentally. The ammonia clusters generated by (252)Cf FF show an exponential dependence of the cluster population on its mass, and the desorption yields for the positive (NH(3))(n)NH(4)(+) clusters are 1 order of magnitude higher than those for the negative (NH(3))(n)NH(2)(-) clusters. The experimental population analysis of (NH(3))(n)NH(4)(+) (n = 0-18) and (NH(3))(n)NH(2)(-) (n = 0-8) cluster series show a special stability at n = 4 and 16 and n = 2, 4, and 6, respectively. DFT/B3LYP calculations of the (NH(3))(0)(-)(8)NH(4)(+) clusters show that the structures of the more stable conformers follow a clear pattern: each additional NH(3) group makes a new hydrogen bond with one of the hydrogen atoms of an NH(3) unit already bound to the NH(4)(+) core. For the (NH(3))(0)(-)(8)NH(2)(-) clusters, the DFT/B3LYP calculations show that, within the calculation error, the more stable conformers follow a clear pattern for n = 1-6: each additional NH(3) group makes a new hydrogen bond to the NH(2)(-) core. For n = 7 and 8, the additional NH(3) groups bind to other NH(3) groups, probably because of the saturation of the NH(2)(-) core. Similar results were obtained at the MP2 level of calculation. A stability analysis was performed using the commonly defined stability function E(n)(-)(1) + E(n)(+1) - 2E(n), where E is the total energy of the cluster, including the zero point correction energy (E = E(t) + ZPE). The trend on the relative stability of the clusters presents an excellent agreement with the distribution of experimental cluster abundances. Moreover, the stability analysis predicts that the (NH(3))(4)NH(4)(+) and the even negative clusters [(NH(3))(n)NH(2)(-), n = 2, 4, and 6] should be the most stable ones, in perfect agreement with the experimental results.

Cyclohexano-15-crown-5, cyclohexano-18-crown-6, dicyclohexano-15-crown-5, and dicyclohexano-18-crown-6, but not dicylohexano-16-crown-5, in THF dissolve potassium metal to form dark blue potassium alkalide solutions at ambient temperature. On standing, the potassium alkalide complexes decompose and the solutions turn colorless at differing rates. Identification of the products provides insight into the decomposition mechanism.