Single Analyzer Precursor Ion Scans in a Linear Quadrupole Ion Trap Using Orthogonal Double Resonance Excitation

Machine-Learning Classification of Bacteria Using Two-Dimensional Tandem Mass Spectrometry

Biothreat detection has continued to gain attention. Samples suspected to fall into any of the CDC's biothreat categories require identification by processes that require specialized expertise and facilities. Recent developments in analytical instrumentation and machine learning algorithms offer rapid and accurate classification of Gram-positive and Gram-negative bacterial species. This is achieved by analyzing the negative ions generated from bacterial cell extracts with a modified linear quadrupole ion-trap mass spectrometer fitted with two-dimensional tandem mass spectrometry capabilities (2D MS/MS). The 2D MS/MS data domain of a bacterial cell extract is recorded within five s using a five-scan average after sample preparation by a simple extraction. Bacteria were classified at the species level by their lipid profiles using the random forest, k-nearest neighbor, and multilayer perceptron machine learning models. 2D MS/MS data can also be treated as image data for use with image recognition algorithms such as convolutional neural networks. The classification accuracy of all models tested was greater than 99%. Adding to previously published work on the 2D MS/MS analysis of bacterial growth and the profiling of sporulating bacteria, this study demonstrates the utility and information-rich nature of 2D MS/MS in the identification of bacterial pathogens at the species level when coupled with machine learning.

Development of a linear ion trap mass spectrometer capable of analyzing megadalton MALDI ions

Detecting megadalton matrix-assisted laser desorption/ionization (MALDI) ions in an ion trap mass spectrometer is a technical challenge. In this study, megadalton protein and polymer ions were successfully measured by MALDI linear ion trap mass spectrometer (LIT-MS) for the first time. The LIT-MS is comprised of a Thermo linear ion trap mass analyzer and a highly sensitive charge-sensing particle detector (CSPD). A newly designed radio frequency (rf) scan mode with dipolar resonance ejection techniques is proposed to extend the mass range of LIT-MS up to one million Thomson (Th). We analyze high mass ions with mass-to charge (m/z) ratios ranging from 100 kTh to 1 MTh, including thyroglobulin, alpha-2-macroglobulin, immunoglobulins (e.g., IgG and IgM), and polymer (∼ 940 kTh) ions. Besides, it is also very challenging for ion trap mass spectrometry to detect megadalton ions at low concentrations. By adopting high affinity carboxylated/oxidized detonation nanodiamonds (oxDNDs) to enrich IgM molecules and form antibody-nanodiamond conjugates, we have successfully reached ∼ 5 nM (5 μg/mL) concentration which is better than that by the other techniques.

Synchronized Reverse Scan Collision Induced Dissociation in Digital Ion Trap Mass Spectrometer for Improving Fragment Ion Detection

Development of fragment ion detection methods is of great importance for mass spectrometer advancement or substance identification. To date, collision induced dissociation (CID) remains the most commonly used ion activation method in MS/MS experiments, and the effectiveness of CID in an ion trap mass spectrometer is limited by low mass cutoff and weak fragmentation yields. Theoretically, controlling the q value is the key to maintain the fragment efficiency and trapping efficiency of MS/MS, thus improving the detection of fragment ion, while currently reported techniques usually require complex circuitry and often produce different CID patterns. In this paper, with the developed synchronized reversed scanning-collision induced dissociation (SRS-CID) technique, we demonstrate its effective improvement in fragment ion detection. The SRS-CID is implemented on a digital ion trap mass spectrometer (DITMS) by reverse scanning the q values during CID process, or specifically, the frequency is increased during the CID process. With the SRS-CID technique, the fragmentation efficiency of precursor ions can be slightly improved. For reserpine analyte, the trapping efficiency for low-mass fragment ions is improved at least 3 times, and for YGGFL, the trapping efficiency for low-mass fragment ions is improved at least 9 times. These experimental results can also be validated by simulations, and the kinetic energy variation plot suggests consecutive fragmentation occurs. In any case, the SRS-CID provides a solution to the low efficiency of fragment ion detection during tandem MS analysis, which will certainly be useful in the future.

Bacterial growth monitored by two-dimensional tandem mass spectrometry

The growth of the bacterium E. coli was monitored by targeting the phospholipid constituents through desorption electrospray ionization and characterizing individual sets of isomers by recording the full 2D MS/MS data domain in a single scan of a modified quadrupole ion trap mass spectrometer. The experiments tested the applicability of the new instrumental capabilities which include sample interrogation at the molecular level for multiple components at speeds of <10 seconds/sample. The major lipids observed were phosphatidylethanolamines and phosphatidylglycerols and the growth experiment showed fatty acid chain modification from alkene to cyclopropyl groups over time. Notably, these novel MS scans were also performed using desorption electrospray ionization (DESI) to quickly sample complex mixtures without pre-separation. This demonstration experiment has implications for the value of ambient ionization mass spectrometry for monitoring biological systems on physiologically relevant timescales.

Novel Ion Trap Scan Modes to Develop Criteria for On-Site Detection of Sulfonamide Antibiotics

Advances in ambient ionization techniques have facilitated the direct analysis of complex mixtures without sample preparation. Significant attention has been given to innovating ionization methods so that multiple options are now available, allowing for ready selection of the best methods for particular analyte classes. These ambient techniques are commonly implemented on benchtop systems, but their potential application with miniature mass spectrometers for in situ measurements is even more powerful. These applications require that attention be paid to tailoring the mass spectrometric methodology for the on-site operation. In this study, combinations of scan modes are employed to efficiently determine what tandem mass spectrometry (MS/MS) operations are most useful for detecting sulfonamides using a miniature ion trap after ionization. First, mixtures of representative sulfonamide antibiotics were interrogated using a 2D MS/MS scan on a benchtop ion trap in order to determine which class-specific fragments (ionic or neutral) are shared between the sulfonamides and thus have diagnostic value. Then, three less-used combination scans were recorded: (i) a simultaneous precursor ion scan was used to detect both analytes and an internal standard in a single ion injection event to optimize quantitative performance; (ii) a simultaneous precursor/neutral loss scan was used to improve detection limits; and finally, (iii) the simultaneous precursor/neutral loss scan was implemented in a miniature mass spectrometer and representative sulfonamides were detected at concentrations as low as 100 ng/mL by nano-electrospray and 0.5 ng absolute by paper spray ionization, although improvements in the stability of the home-built instrumentation are needed to further optimize performance.

Applications of Mass Spectrometry for Clinical Diagnostics: The Influence of Turnaround Time

This critical review discusses how the need for reduced clinical turnaround times has influenced chemical instrumentation. We focus on the development of modern mass spectrometry (MS) and its application in clinical diagnosis. With increased functionality that takes advantage of novel front-end modifications and computational capabilities, MS can now be used for non-traditional clinical analyses, including applications in clinical microbiology for bacteria differentiation and in surgical operation rooms. We summarize here recent developments in the field that have enabled such capabilities, which include miniaturization for point-of-care testing, direct complex mixture analysis via ambient ionization, chemical imaging and profiling, and systems integration.

Two-Dimensional Tandem Mass Spectrometry in a Single Scan on a Linear Quadrupole Ion Trap

A two-dimensional tandem mass spectrometry (2D MS/MS) scan has been developed for the linear quadrupole ion trap. Precursor ions are mass-selectively excited using a nonlinear ac frequency sweep at constant rf voltage, while simultaneously, all product ions of the excited precursor ions are ejected from the ion trap using a broad-band waveform. The fragmentation time of the precursor ions correlates with the precursor m/z value (the first mass dimension) and also with the ejection time of the product ions, allowing the correlation between precursor and product ions. Additionally, the second mass dimension (product ions' m/z values) is recovered through fast Fourier transform of each mass spectral peak, revealing either intentionally introduced "frequency tags" or the product ion micropacket frequencies, both of which can be converted to product ion m/z through the classical Mathieu parameters, thereby revealing a product ion mass spectrum for every precursor ion without prior isolation. We demonstrate the utility of this method for analyzing a broad range of structurally related precursor ions, including chemical warfare agent simulants, fentanyls and other opioids, amphetamines, cathinones, antihistamines, and tetracyclic antidepressants.

Selective Gas-Phase Mass Tagging via Ion/Molecule Reactions Combined with Single Analyzer Neutral Loss Scans to Probe Pharmaceutical Mixtures

We have demonstrated the use of a simple single ion trap mass spectrometer to identify classes of compounds as well as individual components in complex mixtures. First, a neutral reagent was used to mass tag oxygen-containing analytes using a gas-phase ion/molecule reaction. Then, a neutral loss scan was used to indicate the carboxylic acids. The lack of unit mass selectivity in the neutral loss scan required subsequent product ion scans to confirm the presence and identity of the individual carboxylic acids. The neutral loss scan technique reduced the number of data-dependent MS/MS scans required to confirm identification of signals as protonated carboxylic acids. The method was demonstrated on neat mixtures of standard carboxylic acids as well as on solutions of relevant pharmaceutical tablets and may be generalizable to other ion/molecule reactions.

Logical MS/MS scans: a new set of operations for tandem mass spectrometry

A new set of operations for tandem mass spectrometry in a linear ion trap is described. Logical MS/MS operations categorize compounds in mixtures based on characteristic structural features as revealed by MS/MS behavior recorded in multiple fragmentation pathways. This approach is a conceptual extension of tandem mass spectrometry in which interrogation of the full data domain is performed by simultaneous implementation of precursor and neutral loss scans. This process can be thought of as moving through the 2D MS/MS data domain along multiple scan lines simultaneously, which allows experiments that explore the 2D data domain of MS/MS to be couched in terms of logical operations, AND, NAND (not and), OR (inclusive or), XOR (exclusive or), NOT, etc. Examples of particular logical conditions include all precursor ions that fragment to both of two selected product ions (logical AND), or all precursor ions that do not produce a specified fragment ion (logical NOT). These and other operational modes (TRUE/FALSE, XOR, OR, etc.) complement and extend the existing set of conventional MS/MS scans, namely product scans, precursor scans, and neutral loss scans. We describe the implementation of logical MS/MS scans on a commercial linear ion trap mass spectrometer using simple mixtures of amphetamines and fentanyl analogues and argue their utility for complex mixture analysis.

Simulation of the simultaneous dual-frequency resonance excitation of ions in a linear ion trap

The process of ion resonance dipolar excitation in a linear ion trap by 2 ejection waveforms with close frequencies is studied. The physical mechanism of increasing the resolving power using the ion excitation is a nonlinearity of the electric radio frequency fields caused by space charge. Using 2 resonance forces with 2 close frequencies leads to the completion of 2 excitation processes. In the case of the perfect quadrupole electric field, the ion motion equations are linear, and as a result, the respondent ion ensemble is also a linear and valid superposition principle. Nevertheless, the resolution increases (20%) in the case of lack of a space charge in an operating mode with a dual-frequency. The numerical simulations show that the mass shift is removed, and the mass resolution is increased via dual-frequency resonance excitation when the frequency difference (approximately 2.5 kHz) is relatively small and the phase difference of 2 harmonic signals is 0-π3 even at a high linear ion density of up to 50 000 ions per radius field r₀ .

Simultaneous and Sequential MS/MS Scan Combinations and Permutations in a Linear Quadrupole Ion Trap

Methods of performing precursor ion scans as well as neutral loss scans in a single linear quadrupole ion trap have recently been described. In this paper we report methodology for performing permutations of MS/MS scan modes, that is, ordered combinations of precursor, product, and neutral loss scans following a single ion injection event. Only particular permutations are allowed; the sequences demonstrated here are (1) multiple precursor ion scans, (2) precursor ion scans followed by a single neutral loss scan, (3) precursor ion scans followed by product ion scans, and (4) segmented neutral loss scans. (5) The common product ion scan can be performed earlier in these sequences, under certain conditions. Simultaneous scans can also be performed. These include multiple precursor ion scans, precursor ion scans with an accompanying neutral loss scan, and multiple neutral loss scans. We argue that the new capability to perform complex simultaneous and sequential MSⁿ operations on single ion populations represents a significant step in increasing the selectivity of mass spectrometry.

Single Analyzer Neutral Loss Scans in a Linear Quadrupole Ion Trap Using Orthogonal Double Resonance Excitation

In this follow-up paper to our previous work on single analyzer precursor ion scans in a linear quadrupole ion trap (Snyder, D. T.; Cooks, R. G. Single analyzer precursor ion scans in a linear quadrupole ion trap using orthogonal double resonance excitation. J. Am. Soc. Mass Spectrom. 2017, DOI: 10.1007/s13361-017-1707-y), we now report the development of single analyzer neutral loss scans in a linear quadrupole ion trap using orthogonal double resonance excitation. Methodologically, there are three key differences between single analyzer precursor ion scans and neutral loss scans under constant radiofrequency (rf) conditions: (1) in the latter experiment, both excitation and ejection frequencies must be scanned, whereas in the former the ejection frequency is fixed, (2) the need to maintain a constant neutral loss while incrementing both precursor and product ion masses, complicated by the complex relationship between secular frequency and mass, requires use of two simultaneous frequency scans, both linear in mass, and (3) because the ejection frequency is scanned, a third ac signal occurring between the ac excitation and ac ejection frequency scans must also be applied and scanned in order to reject artifact peaks caused by ejection of unfragmented precursor ions. Using this methodology, we demonstrate neutral loss scans on a commercial linear ion trap using mixtures of illicit drugs and acylcarnitines. We also demonstrate neutral loss scanning on a Populus deltoides leaf and on a lignin sample, both significantly more complex mixtures.