Structural annotation of unknown molecules in a miniaturized mass spectrometer based on a transformer enabled fragment tree method.

Structural annotation of small molecules in tandem mass spectrometry has always been a central challenge in mass spectrometry analysis, especially using a miniaturized mass spectrometer for on-site testing. Here, we propose the Transformer enabled Fragment Tree (TeFT) method, which combines various types of fragmentation tree models and a deep learning Transformer module. It is aimed to generate the specific structure of molecules de novo solely from mass spectrometry spectra. The evaluation results on different open-source databases indicated that the proposed model achieved remarkable results in that the majority of molecular structures of compounds in the test can be successfully recognized. Also, the TeFT has been validated on a miniaturized mass spectrometer with low-resolution spectra for 16 flavonoid alcohols, achieving complete structure prediction for 8 substances. Finally, TeFT confirmed the structure of the compound contained in a Chinese medicine substance called the Anweiyang capsule. These results indicate that the TeFT method is suitable for annotating fragmentation peaks with clear fragmentation rules, particularly when applied to on-site mass spectrometry with lower mass resolution.

SR-Unet: A Super-Resolution Algorithm for Ion Trap Mass Spectrometers Based on the Deep Neural Network.

The mass spectrometer is an important tool for modern chemical analysis and detection. Especially, the emergence of miniature mass spectrometers has provided new tools for field analysis and detection. The resolution of a mass spectrometer reflects the ability of the instrument to discriminate between adjacent mass-to-charge ratio ions, and the higher the resolution, the better the discrimination of complex mixtures. Quadrupole ion traps are generally considered as a low-resolution mass spectrometry method, but they have gained wide attention and development in recent years because of their suitability for miniaturization and high qualitative capability. For an ion trap mass spectrometer, the mass sensitivity and resolution can be mutually constrained and need to be balanced by setting an appropriate scanning speed. In this study, a super-resolution U-net algorithm (SR-Unet) is proposed for ion trap mass spectrometry, which can estimate the possible ions from the overlapping ion peaks of low-resolution spectra and improve the equivalent resolution while ensuring sufficient sensitivity and analysis speed of the instrument. By determining the mass spectra of a linear ion trap mass spectrometer (LTQ XL) in Turbo and Normal scan modes, the same unit mass resolution as that at a scan speed of 16,667 Da/s was successfully obtained at 125,000 Da/s. Also, the experiments demonstrated that the algorithm is capable of the mass-to-charge ratio and instrument migration. SR-Unet can be migrated and applied to a miniature mass spectrometer for cruise detection of volatile organic compounds (VOCs), and the identification of VOC species in Photochemical Assessment Monitoring Stations (PAMS) was improved from 31 to 50 species with the same monitoring and analysis speed requirement. Further, super-unit mass resolution peptide detection was achieved on a miniature mass spectrometer with the help of the SR-Unet algorithm, which reduced the full width at half-maxima (FWHM) of bradykinin divalent ions (m/z 531) from 0.35 to 0.15 Da at a scan speed of 375 Da/s and improved the equivalent resolution to 3540. The proposed method provides a new idea to enhance the field mixture detection capability of miniature ion trap mass spectrometers.

Deep learning enabled miniature mass spectrometer for rapid qualitative and quantitative analysis of pesticides on vegetable surfaces.

Excessive pesticide use poses a significant threat to food safety. Rapid on-site detection of multi-target pesticide residues in vegetables is crucial due to their widespread distribution and limited shelf life. In this study, a rapid on-site screening method for pesticide residues on vegetable surfaces was developed by employing a miniature mass spectrometer. A direct pretreatment method involves placing vegetables and elution solution into a customized flexible ziplock bag, allowing thorough mixing, washing, and filtration. This process effectively removes pesticide residues from vegetable surfaces with minimal organic solvent usage and can be completed within 2 min. Moreover, this study introduced a deep learning algorithm based on a one-dimensional convolutional neural network, coupled with a feature database, to autonomously discriminate detection outcomes. By combining full scan MS and tandem MS analysis methods, the proposed method achieved a qualitative recognition accuracy of 99.62%. Following the qualitative discrimination stage, the target pesticide residue and internal standard can be simultaneously isolated and fragmented in the ion trap, thus enabling on-site quantitative analysis and warning. This method achieved a quantitative detection limit of 10 µg/kg for carbendazim in cowpea. These results demonstrate the feasibility of the proposed analytical system and strategy in food safety applications.

SWIFTSIN: A High-Resolution Ion Isolation Waveform for the Miniaturized Linear Ion Trap Mass Spectrometer by Coarse to Fine Excitation.

To figure out the reason for the drawback of the stored waveform inverse Fourier transform (SWIFT) waveform and realize the high-resolution ion isolation on the miniaturized linear ion trap mass spectrometer, we studied the efficiency that ions can be excited under different excitation durations and amplitudes at different frequencies and compared the overlap ratios of the effective excitation frequency bandwidths of the adjacent ions. According to this, we proposed a new coarse-to-fine isolation waveform named SWIFTSIN. By superposing one or more sinusoidal waveforms on the SWIFT waveform and modulating the phases of the superposed sinusoidal waveforms, the generated SWIFTSIN waveform can achieve unit mass isolation on the miniaturized linear ion trap mass spectrometer without reducing the intensity of the target ion. The isolation ability of the SWIFTSIN waveform was verified by isolating a single isotope peak in the mixed samples.

Rapid screening of illegally added drugs in functional food using a miniature ion trap mass spectrometer.

With the expansion of the functional food market, the qualification assessment of these products has become a major challenge, and efficient analytical tools are urgently needed. Here, a miniature mass spectrometer (MS) with self-aspiration capillary electrospray ionization (SACESI) source and ion trap analyzer was developed for rapid screening of various illegally added drugs in functional foods. No chromatographic separation was required, but a simplified two-step pretreatment method was developed to reduce the operational procedures and time consumption of the entire analysis. SACESI source uses capillary action to drive solution injection, which utilizes a simple structure and convenient operation to constitute a kind of disposable MS detection solution. To achieve accurate and automatic identification, an intelligent recognition algorithm with steps of spectrum preprocessing, characteristic peak matching, and support vector machine learning was constructed. The relative accuracy of rapid screening of 31 suspicious drugs in various samples is up to 99.78%. It achieves 100% correct identification for the 55 batches of actual samples captured by on-site inspection, which demonstrates the feasibility of the proposed analytical system and strategy in food safety applications.

Fabricating an Electrospray Ionization Chip Based on Induced Polarization and Liquid Splitting.

The coupling of the microfluidic chip to mass spectrometry (MS) has attracted considerable attention in the area of chemical and biological analysis. The most commonly used ionization technique in the chip-MS system is electrospray ionization (ESI). Traditional chip-based ESI devices mainly employ direct electrical contact between the electrode and the spray solvent. In this study, a microchip ESI source based on a novel polarization-splitting approach was developed. Specifically, the droplet in the microchannel is first polarized by the electric field and then split into two sub-droplets. In this process, the charge generated by polarization is retained in the liquid, resulting in the generation of two charged droplets with opposite polarities. Finally, when these charged droplets reach the emitter, the electrospray process is initiated and both positive and negative ions are formed from the same solution. Preliminary experimental results indicate that the coupling of this polarization-splitting ESI (PS-ESI) chip with a mass spectrometer enables conventional ESI-MS analysis of various analytes.

Unsaturated lipid isomeric imaging based on the Paternò-Büchi reaction in the solid phase in ambient conditions.

In recent years, the development of unsaturated lipid isomeric imaging based on the Paternò-Büchi (PB) reaction has improved significantly. However, research on this imaging method in ambient conditions needs to expand. In this paper, a method of PB reaction in the solid phase in ambient conditions is developed, which is combined with air-flow-assisted desorption electrospray ionisation mass spectrometry (AFADESI-MS) to achieve in situ imaging of lipids at an isomeric level. Experiments showed that the efficiency of the PB reaction was much higher when spraying the reagent solution than when sprinkling the reactant powder directly, and it was not lower than that in the liquid phase. This method can simplify the reaction conditions in the imaging process and can be applied to tissue section samples with only 10 min of pre-processing. The study successfully demonstrated the spatial distribution of unsaturated lipid isomers, and the isomeric ratio corresponded to the lesion areas in mouse brain cancer tissues. Due to its simple operation and performance in ambient conditions, this method may be useful for future studies on lipid isomers in tissues.

Development of membrane inlet photoionization ion trap mass spectrometer for trace VOCs analysis.

With the development of instrumental miniaturization, the portable mass spectrometer is becoming a new tool for on-site rapid analysis of environmental samples. Membrane inlet (MI) and photoionization (PI) are two commonly used sampling and ionization techniques, respectively, as they both exhibit detection selectivity for volatile organic compounds (VOCs). In this paper, a membrane inlet photoionization ion trap mass spectrometer was developed for the direct analysis of VOCs in gaseous samples. With the new structure and timing design, various operation modes were proposed and tested. In particular, the use of pulse carrier gas can integrate the appropriate pressure conditions required by each module, thus improving the efficiency of analyte transport, ionization, and mass analysis. The detection limit of sub-ppb was obtained, and the response time can be greatly reduced by increasing the sample flow rate. Furthermore, the capability of selective enrichment for organic analytes was also realized by using a special accumulation mode with a modified sequence, which is easy to operate because no additional devices are needed.

Data-driven and coarse-to-fine baseline correction for signals of analytical instruments.

Baseline correction is an indispensable step in the signal processing of chemical analysis instruments. With the increasing demand for on-site applications, a variety of analytical instruments require a more friendly, rapid and adaptive baseline correction method. In this paper, a data-driven and coarse-to-fine (DD-CF) baseline correction scheme mainly based on the empirical mode decomposition (EMD) algorithm is proposed. For eliminating the mode-mixing effect of the original EMD, the proposed method firstly obtains a coarse baseline estimation using automatic peak detection, elimination and interpolation; and the EMD is applied on the coarse baseline to get a fine baseline finally. We have compared this method with the adaptive iteratively reweighted Penalized Least Squares algorithm (airPLS) and the sparse representation baseline correction methods using simulated signals and experimental signals from different analytical instruments. Results indicate that the proposed DD-CF scheme can effectively estimate the baseline more accurate than the comparing methods for varies of analytical signals such as mass spectrometer, ion mobility spectrometer, gas chromatograph, etc. Furthermore, with signals of different length, different peak distributions and even from totally different instruments, the proposed method requires minimal user intervention, in which the parameters of the comparing methods should be adjusted for a wide range.

Rapid Imaging of Unsaturated Lipids at an Isomeric Level Achieved by Controllable Oxidation.

Lipid imaging plays an important role in the research of some diseases, such as cancers. Unsaturated lipids are often present as isomers that can have different functions; however, traditional tandem mass spectrometry imaging (MSI) cannot differentiate between different isomers, which presents difficulties for the pathological study of lipids. Herein, we propose a method for the MSI of the C═C double-bond isomers of unsaturated lipids based on oxidative reactions coupled with air flow-assisted desorption electrospray ionization, which can conveniently achieve rapid MSI of unsaturated lipids at an isomeric level. Using this method, tissue sections can be scanned directly with MSI after only 10 min of accelerated oxidation. This method was used for the imaging of mouse lung cancer tissues, revealing a distributional difference in the unsaturated lipid isomers of normal and pathological regions. Through the MSI of unsaturated lipids at an isomeric level in tissues infected with cancer cells, the regions where the isomers were enriched were exhibited, indicating that these regions were the most concentrated regions of cancer cells. This method provides a convenient platform for studying the functional effects of the isomers of unsaturated lipids in pathological tissues.

Asymmetric rectilinear ion trap with unidirectional ion ejection capability.

In this paper, the shapes of the electrodes are modified based on a rectilinear ion trap to achieve unidirectional ejection of ions. The designed asymmetric rectilinear ion trap (ARIT) analyzer adds convex and concave circular structures with a height of 0.5 mm on the two X-electrodes, so that the electric field center of the ion trap is inclined to the concave side. The electric field lines of the convex side are compressed to the concave side. Both simulations and experimental results show that ions are more likely to emit from the slit on the concave side plate when performing ion resonance ejection. The mass spectrum signal intensity can reach more than twice that of the original rectilinear trap when using only one detector. Calculations of the electric field components in the trap show that the even-order higher field proportion in the ion trap has not been significantly affected. Combined with the experimental test results, the study further confirmed that the developed ARIT has no significant loss in mass resolution, tandem mass spectrometry capability, and quantitative analysis capability. The proposed asymmetric structure modification scheme can achieve single-side ejection without significantly affecting other performances of the analyzer, which provides a new idea for the structural optimization of the subsequent ion trap analyzers.

Discontinuous Subatmospheric Pressure Interface Reduces the Gas Flow Effects on Miniature CAPI Mass Spectrometer.

In the range of miniature mass spectrometers, the miniature ion trap mass spectrometer with continuous atmospheric pressure interface (CAPI) shows good performance potential and advantages due to its excellent sensitivity and analysis speed. However, in previous cases, placing the ion trap directly near the skimmer aperture means it will suffer high gas shock, which may affect performance. In this study, an improved miniature CAPI ion trap mass spectrometer was developed by gas flow optimization. According to the experimental results, excessive gas flow affects stability and resolution. The impact of the gas flow can be effectively reduced by reducing the inner diameter of the skimmer and adding an additional lens element to move the ion trap away from the skimmer aperture. However, this method will affect the sensitivity of the instrument to some extent, so a discontinuous subatmospheric pressure interface (DSPI) was developed to reduce the gas flow effects and improve the comprehensive performance. When using the DSPI system with a 0.4 mm skimmer and entrance lens, the resolution for roxithromycin was up to 2800 at a scanning speed of 1015 Th/s, which was 3.4-fold higher that without DSPI. The dynamic range of concentration reached 4 orders of magnitude and the detection limit for repaglinide was as low as 1 ng/mL. This study offers a new approach to develop better miniature ion trap mass spectrometers and to extend their practical application.

Native State Single-Cell Printing System and Analysis for Matrix Effects.

Mass spectrometry is subject to matrix effects, which causes severe limitations on the analysis of live single cells in their native state. Here, we propose a three-phase droplet-based single-cell printing analysis system (TP-SCP), which can package, extract, separate, print, and analyze live single cells in saline matrixes (such as phosphate buffered saline) with matrix-assisted laser desorption/ionization mass spectrometry. This method can eliminate matrix effects to obtain information on a single cell in their native state. We report that a cell packaging percentage of 44% and single-cell packaging percentage of 88% can be achieved by TP-SCP. The system was capable of processing three to four single cells per second, which was 30 to 40 times higher than the traditional droplet-based microextraction (about 10 s/cell). Additionally, the MCF-7, A2780, 293, and 4T1 cells were screened in our system. The effect of cell viability and heterogeneity analysis was investigated, suggesting that the concentration of monounsaturated phosphatidylinositol and phosphatidylethanolamine both increase in cancer cells. Compared with conventional mass spectrometry, TP-SCP can ensure the accuracy of heterogeneity analysis of live single cells in their native state. Both a principal component analysis and a linear discriminant analysis were used to perform classification and identification of cells with an accuracy of 100%. This method provides an innovative framework for research on cell quality control, cell biology, cancer diagnosis, and prevention.

Solution identification and quantitative analysis of fiber-capacitive drop analyzer based on multivariate statistical methods.

A fiber-capacitive drop analyzer is an instrument which monitors a growing droplet to produce a capacitive opto-tensiotrace (COT). Each COT is an integration of fiber light intensity signals and capacitance signals and can reflect the unique physicochemical property of a liquid. In this study, we propose a solution analytical and concentration quantitative method based on multivariate statistical methods. Eight characteristic values are extracted from each COT. A series of COT characteristic values of training solutions at different concentrations compose a data library of this kind of solution. A two-stage linear discriminant analysis is applied to analyze different solution libraries and establish discriminant functions. Test solutions can be discriminated by these functions. After determining the variety of test solutions, Spearman correlation test and principal components analysis are used to filter and reduce dimensions of eight characteristic values, producing a new representative parameter. A cubic spline interpolation function is built between the parameters and concentrations, based on which we can calculate the concentration of the test solution. Methanol, ethanol, n-propanol, and saline solutions are taken as experimental subjects in this paper. For each solution, nine or ten different concentrations are chosen to be the standard library, and the other two concentrations compose the test group. By using the methods mentioned above, all eight test solutions are correctly identified and the average relative error of quantitative analysis is 1.11%. The method proposed is feasible which enlarges the applicable scope of recognizing liquids based on the COT and improves the concentration quantitative precision, as well.

Rapid mass spectrometry analysis of a rectilinear ion trap by continuous secular frequency scanning.

RATIONALE: Secular frequency scanning is a mass spectrometry (MS) analysis method in which the frequency of the auxiliary alternating current (AC) signal is scanned. It has low requirements for radio-frequency (RF) power, which is beneficial for the miniaturization of the mass spectrometer. In this study, the MS performance in the reverse secular frequency scanning (RSFS) mode is optimized for a rectilinear ion trap (RIT), and a method for rapid MS analysis using continuous secular frequency scanning (CSFS) is proposed. METHODS: A RIT mass spectrometer with an auxiliary AC frequency scanning function was built. The resolution, tandem mass spectrometry (MS/MS) and quantitation capability in the RSFS mode were characterized and optimized. Operation in the CSFS mode was then performed by scanning the frequency of the auxiliary AC signal continuously and periodically while maintaining the RF signal and the front Z electrode in the ion injection state, so that the ion injection and cooling were performed at the same time as the mass analysis. RESULTS: With this system, the RSFS mode achieved unit mass resolution at 332 Th, and the MS/MS analysis was completed without changing the RF amplitude at q = 0.4583 for reserpine. The limit of quantitation for imatinib was about 250 ng/mL with the determination coefficient R2  = 0.9981. In the CSFS mode, a single analysis cycle of less than 20 ms could be achieved, which is 14 times faster than the traditional sweep modes. In addition, 100% ion utilization can theoretically be achieved in the CSFS mode. CONCLUSIONS: The CSFS mode is different from the traditional phased sequential operation mode of an ion trap mass spectrometer. By periodic scanning of the auxiliary AC frequency while maintaining ion injection, it is possible to improve the analysis efficiency of the mass spectrometer, which has the prospect of useful application in the field of rapid MS monitoring. Copyright © 2017 John Wiley & Sons, Ltd.

Novel control modes to improve the performance of rectilinear ion trap mass spectrometer with dual pressure chambers.

The rectilinear ion trap (RIT) has gradually become one of the preferred mass analyzers for portable mass spectrometers because of its simple configuration. In order to enhance the performance, including sensitivity, quantitation capability, throughput, and resolution, a novel RIT mass spectrometer with dual pressure chambers was designed and characterized. The studied system constituted a quadrupole linear ion trap (QLIT) in the first chamber and a RIT in the second chamber. Two control modes are hereby proposed: Storage Quadrupole Linear Ion Trap-Rectilinear Ion Trap (SQLIT-RIT) mode, in which the QLIT was used at high pressure for ion storage and isolation, and the RIT was used for analysis; and Analysis Quadrupole Linear Ion Trap-Rectilinear Ion Trap (AQLIT-RIT) mode, in which the QLIT was used for ion storage and cooling. Subsequently, synchronous scanning and analysis were carried out by QLIT and RIT. In SQLIT-RIT mode, signal intensity was improved by a factor of 30; the limit of quantitation was reduced more than tenfold to 50 ng mL-1, and an optimal duty cycle of 96.4% was achieved. In AQLIT-RIT mode, the number of ions coexisting in the RIT was reduced, which weakened the space-charge effect and reduced the mass shift. Furthermore, the mass resolution was enhanced by a factor of 3. The results indicate that the novel control modes achieve satisfactory performance without adding any system complexity, which provides a viable pathway to guarantee good analytical performance in miniaturization of the mass spectrometer.

Interlayer spray ionization mass spectrometry for the simple direct analysis of low amounts of sample.

Interlayer spray is proposed as a convenient ionization source for direct analysis by mass spectrometry. Two slices of non-absorbent substrate hold the liquid sample to form a sandwich structure. By applying a high voltage to the sample, spray is generated at the tip of the substrate. The sampling procedure can be operated easily in an open condition and the spray is processed in a semi-enclosed condition, which leads to a relatively stable process. An ultralow amount (<2 µL) of the liquid sample can be analyzed without dilution, which ensures that the natural concentration and properties of the target are maintained. Less influence from the substrate is achieved compared with the spray methods based on porous absorbent materials, which results in a sensitivity enhancement of large molecule samples. It is demonstrated that the interlayer spray is applicable for the analysis of various compounds, including therapeutic drugs, peptides, and proteins. Good linearity can be obtained at a concentration as low as 50 ng/mL in the quantitative analysis for imatinib. We also show the ability to identify the chemical residuals on surfaces with high sensitivity by the "wipe-spray" method, which is useful for the fast screening of illicit substances. Interlayer spray working with mass spectrometry provides a promising method for direct analysis in an ambient environment. Graphical Abstract The schematic of the interlayer spray ionization source.