DCT-net: Dual-domain cross-fusion transformer network for MRI reconstruction.

Current challenges in Magnetic Resonance Imaging (MRI) include long acquisition times and motion artifacts. To address these issues, under-sampled k-space acquisition has gained popularity as a fast imaging method. However, recovering fine details from under-sampled data remains challenging. In this study, we introduce a pioneering deep learning approach, namely DCT-Net, designed for dual-domain MRI reconstruction. DCT-Net seamlessly integrates information from the image domain (IRM) and frequency domain (FRM), utilizing a novel Cross Attention Block (CAB) and Fusion Attention Block (FAB). These innovative blocks enable precise feature extraction and adaptive fusion across both domains, resulting in a significant enhancement of the reconstructed image quality. The adaptive interaction and fusion mechanisms of CAB and FAB contribute to the method's effectiveness in capturing distinctive features and optimizing image reconstruction. Comprehensive ablation studies have been conducted to assess the contributions of these modules to reconstruction quality and accuracy. Experimental results on the FastMRI (2023) and Calgary-Campinas datasets (2021) demonstrate the superiority of our MRI reconstruction framework over other typical methods (most are illustrated in 2023 or 2022) in both qualitative and quantitative evaluations. This holds for knee and brain datasets under 4× and 8× accelerated imaging scenarios.

[Determination of seven indicative ingredients in oral liquids of Chinese medicine by liquid chromatography-electrospray ionization-ion mobility spectrometry].

A two-dimensional separation and analysis method, based on liquid chromatography-electrospray ionization-ion mobility spectrometry (LC-ESI-IMS), is developed for the determination of seven indicative ingredients (danshensu, glycyrrhizic acid, gastrodin, chlorogenic acid, puerarin, baicalin, and rutin) in oral liquids of Chinese medicine. The sample was first separated on an ACQUITY UPLC BEH C18 column (50 mm×1 mm, 1.7 µm). The post-column effluent was directed to an adjustable flow splitter with a split ratio of 50:1. The low-flow and high-flow outlets were connected to an ion mobility spectrometer and a triple quadrupole mass spectrometer, respectively. The experimental conditions for LC, spray voltage, drift tube temperature, gas pre-heating temperature, and drift gas velocity were systematically optimized. The limits of detection (LODs) and quantitation (LOQs) for the seven analytes were 2-10 µg/mL and 5-25 µg/mL, respectively. The proposed method was applied for the analysis of real oral liquids of Chinese medicine samples. By coupling LC and IMS, two-dimensional separation could be achieved based on hydrophobicity difference and ionic mobility disparity, thus providing more comprehensive measurement information than LC or IMS used alone.

Generating Supercharged Protein Ions for Breath Analysis by Extractive Electrospray Ionization Mass Spectrometry.

Supercharged protein ions produced by electrospray ionization are extremely efficient proton donors for secondary ionization. Here, by electrospraying the protein solutions containing 5% 1,2-butylene carbonate, the supercharged protein ions with unusually high proton density were produced as the primary ions for the ionization of exhaled breath samples in the extractive electrospray ionization mass spectrometry (EESI-MS), which resulted in the enhanced ionization efficiency for the breath analytes even with relatively low gas phase basicity. Moreover, the total number of metabolites detected in breath increased by about 260% in the mass range of 200-500 Da, owing to the substantial signal enhancement for breath metabolites, providing complementary and additional information to conventional SESI.

Ion manipulation and enrichment mass spectrometer for cleavage of disulfide bond via ion/ion reaction.

A novel mass spectrometer with the capability of ion manipulation and enrichment was developed to perform gas-phase ion/ion reactions followed by product ions accumulation. The development of this apparatus opens opportunities for more complex sequences of ion manipulations, thus offers the potential on extensive application involving ion/ion reaction. Here, cleavage of disulfide bond in peptide was demonstrated based upon this ion manipulation and enrichment mass spectrometer. Two typical peptides including S-glutathionylated ARACAKA with an intermolecular disulfide bond, and oxytocin with an intramolecular disulfide bond were chosen as typical samples to demonstrate the ability of the apparatus. After ion/ion reaction between selected peptide cations and periodate ions (IO4 - ), two kinds of product ions (eg, [M + O + H]+ and [M + H + Na + IO4 ]+ ) were enriched with a number of accumulation events. Afterwards, the enriched ions were subjected to activation, and the disulfide bond cleavage was clearly observed from the tandem mass spectra. These results illustrate the potential of this apparatus for ion manipulation performing ion/ion reaction, and low abundance product ion enrichment.

Enhanced Desorption Electrospray Ionization Mass Spectrometry via Synchronizing Ion Generation and Ion Injection.

A modified version of desorption electrospray ionization mass spectrometry was developed for (i) better utilization of analyte ions and (ii) larger sampling area via synchronization the pulsed nebulizer gas with ion injection. To synchronize the sheath gas, gas flow was paused for 50 ms within each cycle, leading to solvent accumulation at the end of emitter tip. That solvent accumulation enlarged the desorption areas. As a result, the amount of analytes increased. Thus, the improved signal intensity (~ 2-5-folds for various substrates) was benefit from both better analyte ion utilization and larger desorption areas. Finally, the enhanced signal intensity was confirmed with both garlic homogenate and brain homogenate. Graphical Abstract ᅟ.

Boosting the Signal Intensity of Nanoelectrospray Ionization by Using a Polarity-Reversing High-Voltage Strategy.

Continuous efforts have been made to further improve the performance of nano-ESI. In this work, we made use of a polarity-reversing high-voltage strategy for the generation of nano-ESI (PR-nESI). Typically, a negative high voltage of -3.0 kV was first applied to the electrode and maintained for 6 s. Then the polarity was reversed, and a positive high voltage of +1.75 kV was applied for the generation of electrospray. Compared with conventional nano-ESI, PR-nESI significantly enhanced the signal intensity of protonated protein ions. The signal-to-noise ratio (S/N) of protonated protein ions was increased by 1-2 orders of magnitude. The increase of S/N was even more remarkable at lower concentrations. Furthermore, PR-nESI also had a desalting effect. Metal ion adducts of proteins were effectively removed. No metal ion adducts were identified from the spectra, even if the concentration of salt was increased to the millimolar level. The performance of PR-nESI was confirmed in the detection of different molecules including proteins, peptides, amino acids, and other small-molecule compounds. The intact folded structure of proteins was preserved during PR-nESI. No unfolding was observed in the spectra. PR-nESI was further applied to the analysis of noncovalent protein-ligand complexes and protein digest. At last, investigations into the mechanism of PR-nESI were carried out. The enhancement of signal intensity and desalting effect were related to the electromigration of the solutes in solution. With all the advantages above, PR-nESI would be a promising method in the future analytical and bioanalytical applications.

Dual-Polarity Ion Trap Mass Spectrometry: Dynamic Monitoring and Controlling Gas-phase Ion-Ion Reactions.

A dual-polarity linear ion trap (LIT) mass spectrometer was developed in this study, and the method for simultaneously controlling and detecting cations and anions was proposed and realized in the LIT. With the application of an additional dipolar DC field on the ejection electrodes of an LIT, dual-polarity mass spectra could be obtained, which include both the mass-to-charge (m/z) ratio and charge polarity information of an ion. Compared with conventional method, the ion ejection and detection efficiency could also be improved by about one-fold. Furthermore, ion-ion reactions within the LIT could be dynamically controlled and monitored by manipulating the distributions of ions with opposite charge polarities. This method was then used to control and study the reaction kinetics of ion-ion reactions, including electron transfer dissociation (ETD) and charge inversion reactions. A dual-polarity collision-induced dissociation (CID) experiment was proposed and performed to enhance the sequence coverage of a peptide ion. Ion trajectory simulations were also carried out for concept validation and system optimization. Graphical Abstract ᅟ.

Detecting Low-Abundance Molecules at Single-Cell Level by Repeated Ion Accumulation in Ion Trap Mass Spectrometer.

Low-abundance metabolites or proteins in single-cell samples are usually undetectable by mass spectrometry (MS) due to the limited amount of substances in single cells. This limitation inspired us to further enhance the sensitivity of commercial mass spectrometers. Herein, we developed a technique named repeated ion accumulation by ion trap MS, which is capable of enhancing the sensitivity by selectively and repeatedly accumulating ions in a linear ion trap for up to 25 cycles. The increase in MS sensitivity was positively correlated with the number of repeated cycles. When ions were repeatedly accumulated for 25 cycles, the sensitivity of adenosine triphosphate detection was increased by 22-fold within 1.8 s. Our technique could stably detect low-abundance ions, especially MSn ions, at the single-cell level, such as 5-methylcytosine hydrolyzed from sample equivalent to ∼0.2 MCF7 cell. The strategy presented in this study offers the possibility to aid single-cell analysis by enhancing MS detection sensitivity.

Investigating the structural transitions of proteins during dissolution by mass spectrometry.

An appropriate solvent environment is essential for the implementation of biological functions of proteins. Interactions between protein residues and solvent molecules are of great importance for proteins to maintain their active structure and catalyze biochemical reactions. In this study, we investigated such interactions and studied the structural transitions of proteins during their dissolution process. Our previously developed technique, namely solvent assisted electric field induced desorption/ionization, was used for the dissolution and immediate ionization of proteins. Different solvents and proteins were involved in the investigation. According to the results, cytochrome c underwent significant unfolding during dissolution in the most commonly used NH4Ac buffer. The unfolding got more serious when the concentration of NH4Ac was further increased. Extending the dissolution time resulted in the re-folding of cytochrome c. In comparison, no unfolding was observed if cytochrome c was pre-dissolved in NH4Ac buffer and detected by nano-ESI. Furthermore, no unfolding was observed during the dissolution process of cytochrome c in water. Interactions between the residues of cytochrome c and the solute of NH4Ac might be the reason for the unfolding phenomenon. Similar unfolding phenomenon was observed on holo-myoglobin. However, the observed dissolution feature of insulin was different. No unfolding was observed on insulin during dissolution in NH4Ac buffers. Insulin underwent observable unfolding when water was used for dissolution. This might be due to the structural difference between different proteins. The obtained results in the present study furthered our insights into the interactions between proteins and the solvents during the phase transition of dissolution.

Electro-kinetic assisted electrospray ionization for enhanced complex sample analysis.

In this work, an electro-kinetic assisted electrospray ionization (EK-ESI) source is proposed and characterized. In EK-ESI, an additional auxiliary electric field is introduced in the liquid flow of a nano-ESI. While traveling forward in the electrospray flow, charged analytes also experience a reverse electric field, which pushes them backwards. As a result, analytes could be separated preliminarily based on their electrophoretic mobility during the electrospray process. Experiments show that EK-ESI can reduce charge competition effects in the ESI source and increase biomolecule detection sensitivities. It was also found that EK-ESI effectively ionizes proteins in a relatively mild solvent condition, which does not require the addition of acids or salt buffers into the solvent. As a proof-of-concept study, a very rough separation effect was observed in this study, further experiments and theoretical study will be carried out to enhance its performances.

Atg20- and Atg24-family proteins promote organelle autophagy in fission yeast.

Autophagy cargos include not only soluble cytosolic materials but also bulky organelles, such as ER and mitochondria. In budding yeast, two proteins that contain the PX domain and the BAR domain, Atg20 and Atg24 (also known as Snx42 and Snx4, respectively) are required for organelle autophagy and contribute to general autophagy in a way that can be masked by compensatory mechanisms. It remains unclear why these proteins are important for organelle autophagy. Here, we show that in a distantly related fungal organism, the fission yeast Schizosaccharomyces pombe, autophagy of ER and mitochondria is induced by nitrogen starvation and is promoted by three Atg20- and Atg24-family proteins - Atg20, Atg24 and SPBC1711.11 (named here as Atg24b). These proteins localize at the pre-autophagosomal structure, or phagophore assembly site (PAS), during starvation. S. pombe Atg24 forms a homo-oligomer and acts redundantly with Atg20 and Atg24b, and the latter two proteins can form a hetero-oligomer. The organelle autophagy defect caused by the loss of these proteins is associated with a reduction of autophagosome size and a decrease in Atg8 accumulation at the PAS. These results provide new insights into the autophagic function of Atg20- and Atg24-family proteins.

Intramolecular Halogen Transfer via Halonium Ion Intermediates in the Gas Phase.

The fragmentation of halogen-substituted protonated amines and quaternary ammonium ions (R(1)R(2)R(3)N(+)CH2(CH2)nX, where X = F, Cl, Br, I, n = 1, 2, 3, 4) was studied by electrospray ionization tandem mass spectrometry. A characteristic fragment ion (R(1)R(2)R(3)N(+)X) resulting from halogen transfer was observed in collision-induced dissociation. A new mechanism for the intramolecular halogen transfer was proposed that involves a reactive intermediate, [amine/halonium ion]. A potential energy surface scan using DFT calculation for CH2-N bond cleavage process of protonated 2-bromo-N,N-dimethylethanamine supports the formation of this intermediate. The bromonium ion intermediate-involved halogen transfer mechanism is supported by an examination of the ion/molecule reaction between isolated ethylenebromonium ion and triethylamine, which generates the N-bromo-N,N,N-triethylammonium cation. For other halogens, Cl and I also can be involved in similar intramolecular halogen transfer, but F cannot be involved. With the elongation of the carbon chain between the halogen (bromine as a representative example) and amine, the migration ability of halogen decreases. When the carbon chain contains two or three CH2 units (n = 1, 2), formal bromine cation transfer can take place, and the transfer is easier when n = 1. When the carbon chain contains four or five CH2 units (n = 3, 4), formal bromine cation transfer does not occur, probably because the five- and six-membered cyclic bromonium ions are very stable and do not donate the bromine to the amine.

Pulsed Direct Current Electrospray: Enabling Systematic Analysis of Small Volume Sample by Boosting Sample Economy.

We had developed pulsed direct current electrospray ionization mass spectrometry (pulsed-dc-ESI-MS) for systematically profiling and determining components in small volume sample. Pulsed-dc-ESI utilized constant high voltage to induce the generation of single polarity pulsed electrospray remotely. This method had significantly boosted the sample economy, so as to obtain several minutes MS signal duration from merely picoliter volume sample. The elongated MS signal duration enable us to collect abundant MS(2) information on interested components in a small volume sample for systematical analysis. This method had been successfully applied for single cell metabolomics analysis. We had obtained 2-D profile of metabolites (including exact mass and MS(2) data) from single plant and mammalian cell, concerning 1034 components and 656 components for Allium cepa and HeLa cells, respectively. Further identification had found 162 compounds and 28 different modification groups of 141 saccharides in a single Allium cepa cell, indicating pulsed-dc-ESI a powerful tool for small volume sample systematical analysis.

Desalting by crystallization: detection of attomole biomolecules in picoliter buffers by mass spectrometry.

Sensitive detection of biomolecules in small-volume samples by mass spectrometry is, in many cases, challenging because of the use of buffers to maintain the biological activities of proteins and cells. Here, we report a highly effective desalting method for picoliter samples. It was based on the spontaneous separation of biomolecules from salts during crystallization of the salts. After desalting, the biomolecules were deposited in the tip of the quartz pipet because of the evaporation of the solvent. Subsequent detection of the separated biomolecules was achieved using solvent assisted electric field induced desorption/ionization (SAEFIDI) coupled with mass spectrometry. It allowed for direct desorption/ionization of the biomolecules in situ from the tip of the pipet. The organic component in the assistant solvent inhibited the desorption/ionization of salts, thus assured successful detection of biomolecules. Proteins and peptides down to 50 amol were successfully detected using our method even if there were 3 × 10(5) folds more amount of salts in the sample. The concentration and ion species of the salts had little influence on the detection results.

GPU Assisted Simulation Study of Ion-Ion Reactions within Quadrupole Ion Traps.

In this study, a gas-phase ion-ion reaction model was developed, and it was integrated into an ion trajectory simulation program. GPU parallel computation techniques were also applied to accelerate the simulation process. With this simulation tool, the dependence of ion-ion reaction rate within 3D quadrupole ion traps on both ion trap operation parameters and the characteristics of reaction pair were investigated. It was found that the m/z values and charge states of ions have significant influences on the reaction rate. Moreover, higher ion-ion reaction rate was achieved under higher trapping voltages and higher buffer gas pressures. Furthermore, secondary reaction and/or neutralization of ETD fragment ions were observed from simulation. The reaction and/or neutralization rate depends on the charge state and m/z of each fragment ion.

Realistic modeling of ion-neutral collisions in quadrupole ion traps.

In this study, three ion-neutral collision models have been discussed and compared, including the Langevin, the hard-sphere and the mixed collision models. With the pseudo-potential approximation, analytical expressions of ion secular motions with the hard-sphere and mixed collision models have been obtained for the first time. Through numerical simulations and theoretical calculations, it is found that the mixed collision model could be used as a general description of ion-neutral collisions under different conditions. Langevin collision model is a good description of low energy collisions between small ions and neutrals, while hard-sphere collision model could be used to describe high energy collisions and/or ions with higher masses (larger physical sizes). These analytical expressions of ion motion decay profiles enable the creation of direct relationships between time-domain image currents with ion collision cross sections.

Data processing and analysis for mass spectrometry imaging.

Mass spectrometry imaging produces large numbers of spectra that need to be efficiently stored, processed, and analyzed. In this chapter, we describe the protocol and methods for data processing, visualization, and statistical analysis, with related techniques and tools available presented. Examples are given with data collected for a 3D MS imaging of a mouse brain and 2D MS imaging of human bladder tissues.

Ion collision crosssection measurements in quadrupole ion traps using a time-frequency analysis method.

In this study, a method for measuring ion collision crosssections (CCSs) was proposed through time-frequency analysis of ion trajectories in quadrupole ion traps. A linear ion trap with added high-order electric fields was designed and simulated. With the presence of high-order electric fields and ion-neutral collisions, ion secular motion frequency within the quadrupole ion trap will be a function of ion motion amplitude, thus a function of time and ion CCS. A direct relationship was then established between ion CCS and ion motion frequency with respect to time, which could be obtained through time-frequency analysis of ion trajectories (or ion motion induced image currents). To confirm the proposed theory, realistic ion trajectory simulations were performed, where the CCSs of bradykinin, angiotensin I and II, and ubiquitin ions were calculated from simulated ion trajectories. As an example, differentiation of isomeric ubiquitin ions was also demonstrated in the simulations.

Ambient mass spectrometry imaging: plasma assisted laser desorption ionization mass spectrometry imaging and its applications.

Mass spectrometry imaging (MSI) has been widely used in many research areas for the advantages of providing informative molecular distribution with high specificity. Among the recent progress, ambient MSI has attracted increasing interests owing to its characteristics of ambient, in situ, and nonpretreatment analysis. Here, we are presenting the ambient MSI for traditional Chinese medicines (TCMs) and authentication of work of art and documents using plasma assisted laser desorption ionization mass spectrometry (PALDI-MS). Compared with current ambient MSI methods, an excellent average resolution of 60 µm × 60 µm pixel size was achieved using this system. The feasibility of PALDI-based MSI was confirmed by seal imaging, and its authentication applications were demonstrated by imaging of printed Chinese characters. Imaging of the Radix Scutellariae slice showed that the two active components, baicalein and wogonin, mainly were distributed in the epidermis of the root, which proposed an approach for distinguishing TCMs' origins and the distribution of active components of TCMs and exploring the environmental effects of plant growth. PALDI-MS imaging provides a strong complement for the MSI strategy with the enhanced spatial resolution, which is promising in many research fields, such as artwork identification, TCMs' and botanic research, pharmaceutical applications, etc.

Space charge induced nonlinear effects in quadrupole ion traps.

A theoretical method was proposed in this work to study space charge effects in quadrupole ion traps, including ion trapping, ion motion frequency shift, and nonlinear effects on ion trajectories. The spatial distributions of ion clouds within quadrupole ion traps were first modeled for both 3D and linear ion traps. It is found that the electric field generated by space charge can be expressed as a summation of even-order fields, such as quadrupole field, octopole field, etc. Ion trajectories were then solved using the harmonic balance method. Similar to high-order field effects, space charge will result in an "ocean wave" shape nonlinear resonance curve for an ion under a dipolar excitation. However, the nonlinear resonance curve will be totally shifted to lower frequencies and bend towards ion secular frequency as ion motion amplitude increases, which is just the opposite effect of any even-order field. Based on theoretical derivations, methods to reduce space charge effects were proposed.