Strongly reduced fragmentation and soft emission processes in sputtered ion formation from amino acid films under large Ar(n)+ (n ≤ 2200) cluster ion bombardment

Matrix-Enhanced SIMS: The Influence of Primary Ion Species and Cluster Size on Ion Yield and Ion Yield Enhancement of Lipids

Time-of-flight secondary ion mass spectrometry is one of the most promising techniques for label-free analysis of biomolecules with nanoscale spatial resolution. However, high-resolution imaging of larger biomolecules such as phospholipids and peptides is often hampered by low yields of molecular ions. Matrix-enhanced SIMS (ME-SIMS), in which an organic matrix is added to the sample, is one promising approach to enhancing the ion yield for biomolecules. Optimizing this approach has, however, been challenging because the processes involved in increasing the ion yield in ME-SIMS are not yet fully understood. In this work, the matrix α-cyano-4-hydroxycinnamic acid (HCCA) has been combined with cluster primary ion analysis to better understand the roles of proton donation and reduced fragmentation on lipid molecule ion yield. A model system consisting of 1:100 mol ratio dipalmitoylphosphatidylcholine (DPPC) in HCCA as well as an HCCA-coated mouse brain cryosection have been studied using a range of Bi and Ar cluster ions. Although the molecular ion yield increased with an increase in cluster ion size, the enhancement of the signals from intact lipid molecules decreased with an increase in cluster ion size for both the model system and the mouse brain. Additionally, in both systems, protonated molecular ions were significantly more enhanced than sodium and potassium cationized molecules for all of the primary ions utilized. For the model system, the DPPC molecular ion yield was increased by more than an order of magnitude for all of the primary ions studied, and fragmentation of DPPC was dramatically reduced. However, on the brain sample, even though the HCCA matrix reduced DPPC fragmentation for all of the primary ions studied, the matrix coating suppressed the ion yield for some lipids when the larger cluster primary ions were employed. This indicated insufficient migration of the lipids into the matrix coating, so that dilution by the matrix overpowered the enhancement effect. This study provides strong evidence that the HCCA matrix both enhances protonation and reduces fragmentation. For imaging applications, the ability of the analytes to migrate to the surface of the matrix coating is also a critical factor for useful signal enhancement. This work demonstrates that the HCCA matrix provides a softer desorption environment when using Bi cluster ions than that obtained using the large gas cluster ions studied alone, indicating the potential for improved high spatial resolution imaging with ME-SIMS.

(CO2)n+, (H2O)n+, and (H2O)n+ (CO2) gas cluster ion beam secondary ion mass spectrometry: analysis of lipid extracts, cells, and Alzheimer's model mouse brain tissue

This work assesses the potential of new water cluster-based ion beams for improving the capabilities of secondary ion mass spectrometry (SIMS) for in situ lipidomics. The effect of water clusters was compared to carbon dioxide clusters, along with the effect of using pure water clusters compared to mixed water and carbon dioxide clusters. A signal increase was found when using pure water clusters. However, when analyzing cells, a more substantial signal increase was found in positive ion mode when the water clusters also contained carbon dioxide, suggesting that additional reactions are in play. The effects of using a water primary ion beam on a more complex sample were investigated by analyzing brain tissue from an Alzheimer’s disease transgenic mouse model. The results indicate that the ToF-SIMS results are approaching those from MALDI as ToF-SIMS was able to image lyso-phosphocholine (LPC) lipids, a lipid class that for a long time has eluded detection during SIMS analyses. Gangliosides, sulfatides, and cholesterol were also imaged.

Large cluster ions: soft local probes and tools for organic and bio surfaces

Ionised cluster beams have been produced and employed for thin film deposition and surface processing for half a century. In the last two decades, kiloelectronvolt cluster ions have also proved to be outstanding for surface characterisation by secondary ion mass spectrometry (SIMS), because their sputter and ion yields are enhanced in a non-linear fashion with respect to monoatomic projectiles, with a resulting step change of sensitivity for analysis and imaging. In particular, large gas cluster ion beams, or GCIB, have now become a reference in organic surface and thin film analysis using SIMS and X-ray photoelectron spectroscopy (XPS). The reason is that they induce soft molecular desorption and offer the opportunity to conduct damageless depth-profiling and 3D molecular imaging of the most sensitive organic electronics and biological samples, with a nanoscale depth resolution. In line with these recent developments, the present review focuses on rather weakly-bound, light-element cluster ions, such as noble or other gas clusters, and water or alcohol nanodroplets (excluding clusters made of metals, inorganic salts or ionic liquids) and their interaction with surfaces (essentially, but not exclusively, organic). The scope of this article encompasses three aspects. The first one is the fundamentals of large cluster impacts with surfaces, using the wealth of information provided by molecular dynamics simulations and experimental observations. The second focus is on recent applications of large cluster ion beams in surface characterisation, including mass spectrometric analysis and 2D localisation of large molecules, molecular depth-profiling and 3D molecular imaging. Finally, the perspective explores cutting edge developments, involving (i) new types of clusters with a chemistry designed to enhance performance for mass spectrometry imaging, (ii) the use of cluster fragment ion backscattering to locally retrieve physical surface properties and (iii) the fabrication of new biosurface and thin film architectures, where large cluster ion beams are used as tools to transfer biomolecules in vacuo from a target reservoir to any collector substrate.

Optimized Alkali-Metal Cationization in Secondary Ion Mass Spectrometry of Polyethylene Glycol Oligomers with up to m/z 10000: Dependence on Cation Species and Concentration

In secondary ion mass spectrometry (SIMS), the detection of large organic molecules is accomplished using cluster ion bombardment. Ion formation often proceeds via cationization, through the attachment of (alkali) metal ions to the molecule. To study this process, the emission of secondary ions sputtered from polyethylene glycol (PEG) samples with molecular weights (MW) of 1000-10000 was examined. They were mixed with alkali-metal trifluoroacetic acid (X-TFA, where X = Li, Na, K, or Cs) in a wide range of concentrations to investigate the efficiency of cationization for 10 keV Ar₂₀₀₀⁺ cluster irradiation. Typically, cationized molecular ions [M + X]⁺ (with repeat units n of up to ∼250, corresponding roughly to m/z 11000) and some characteristic fragment species were observed in the mass spectra. For all alkali cations, the oligomer intensities increase strongly with the molecular composition ratios X-TFA/PEG in the samples, and values of 5-10 seem to be optimal. With increasing molecular weight, the intensity of oligomer ions relative to the total number of ions decreases; as the latter remains rather constant, this implies that more fragment species are formed. The ion yields (detected ions per primary ions) of cationized [M + Na]⁺ oligomers sputtered from a PEG decrease very strongly with their size n: from 5.2 × 10^-6 at n = 21 (MW ∼ 1000) to 4.5 × 10^-10 at n ∼ 245 (MW ∼ 11000). By contrast, the total yields Y_tot⁺ show only a small variation for these different specimens, from 1.3 × 10^-5 to 3.7 × 10^-5.

The origins and implications of glycerol ether lipids in China coastal wetland sediments

Coastal wetlands are terrestrial-marine transition zones harboring diverse active microbial communities. The origins of diverse glycerol ether lipids preserved in coastal wetlands are rarely investigated. 16 surface sediments were collected from the coastal wetland at Guangrao (GR), Changyi (CY) and Xiamen (XM), where both climate and sedimentary environment show significant differences. Ten groups of glycerol ether lipids, including isoprenoidal and branched glycerol dialkyl glycerol tetraethers (iGDGTs and bGDGTs), isoprenoidal and branched glycerol dialkanol diethers (iGDDs and bGDDs), hydroxylated isoprenoidal GDGTs and GDDs (OH-GDGTs and OH-GDDs), overly branched GDGTs (OB-GDGTs), sparsely branched GDGTs (SB-GDGTs), hybrid isoprenoid/branched GDGTs (IB-GDGTs) and a tentatively assigned H-shaped branched GDGTs (H-B-GDGTs) were detected and quantified. Sediments collected in the north (Guangrao and Changyi) contain, in general, a lower abundance of GDGT (3.7-55.9 ng/g sed) than samples from south (Xiamen; 251-1020 ng/g sed). iGDGTs and bGDGTs are the predominant components at all sites and account for 17.2-74.3% and 16.1-75.1% of total ether lipids, respectively. The relative abundance of iGDGTs decreases but that of bGDGTs increases with the distance from sea, suggesting a marine vs. terrestrial origin of iGDGT and bGDGTs, respectively. In addition, the methylation index (MI_OB/B/SB) of branched GDGTs shows a significant inverse correlation with water content, suggesting that marine waters have a major influence on the microbial communities inhabiting wetland sediment. Such an assumption was confirmed by the distinct lipid pattern of three low water content (<5%) samples collected in an area isolated from tidal flushing. The other isoprenoidal ether lipids, such as iGDDs, OH-GDGTs and OH-GDGTs, have a similar distribution as iGDGTs, indicating a common biological source, so do the corresponding non-isoprenoidal ether lipid series with bGDGTs. The BIT value increases with increasing distance from the sea, which implies that the BIT index can be probably applied to trace past sea level change in costal wetland settings. The reconstructed temperature from TEX₈₆ shows significant offset from observed data, but only little deviation for the MBT/CBT calculated temperature. This suggests that the MBT/CBT has the potential to reconstruct past temperatures in coastal wetland settings.

Internal Energy Distribution of Secondary Ions Under Argon and Bismuth Cluster Bombardments: "Soft" Versus "Hard" Desorption-Ionization Process

The emission/ionization process under massive argon cluster bombardment was investigated by measuring the internal energy distributions of a series of benzylpyridinium ions. Argon clusters with kinetic energies between 10 and 20 keV and cluster sizes ranging from 500 to 10,000 were used to establish the influence of their size, energy, and velocity on the internal energy distribution of the secondary ions. It is shown that the internal energy distribution of secondary ions principally depends on the energy per atom or the velocity of the cluster ion beam (E/n ∝ v²). Under low energy per atom (E/n ˂ 10 eV), the mean internal energy and fragmentation yield increase rapidly with the incident energy of individual constituents. Beyond 10 eV/atom impact (up to 40 eV/atom), the internal energy reaches a plateau and remains constant. Results were compared with those generated from bismuth cluster impacts for which the mean internal energies correspond well to the plateau values for argon clusters. However, a significant difference was found between argon and bismuth clusters concerning the damage or disappearance cross section. A 20 times smaller disappearance cross section was measured under 20 keV Ar₂₀₀₀⁺ impact compared to 25 keV Bi₅⁺ bombardment, thus quantitatively showing the low damage effect of large argon clusters for almost the same molecular ion yield. Graphical Abstract ᅟ.

High resolution imaging and 3D analysis of Ag nanoparticles in cells with ToF-SIMS and delayed extraction

Within this study, the authors use human mesenchymal stem cells incubated with silver nanoparticles (AgNPs) as a model system to systematically investigate the advantages and drawbacks of the fast imaging delayed extraction mode for two-dimensional and three-dimensional (3D) analyses at the cellular level. The authors compare the delayed extraction mode with commonly employed measurement modes in terms of mass and lateral resolution, intensity, and dose density. Using the delayed extraction mode for single cell analysis, a high mass resolution up to 4000 at m/z = 184.08 combined with a lateral resolution up to 360 nm is achieved. Furthermore, the authors perform 3D analyses with Ar-clusters (10 keV) and O₂⁺ (500 eV) as sputter species, combined with Bi₃⁺ and delayed extraction for analysis. Cell compartments like the nucleus are visualized in 3D, whereas no realistic 3D reconstruction of intracellular AgNP is possible due to the different sputter rates of inorganic and organic cell materials. Furthermore, the authors show that the sputter yield of Ag increases with the decreasing Ar-cluster size, which might be an approach to converge the different sputter rates.

Development of a Knudsen-type matrix coater for sample preparation for mass spectrometry imaging

The use of time-of-flight secondary ion mass spectrometry (SIMS) is of increasing interest for biological and medical applications due to its ability to provide chemical information on a submicrometer scale. However, the detection of larger biomolecules such as phospholipids and peptides is often inhibited by high fragmentation rates and low ionization efficiencies. One way to increase the secondary ion molecular yield is to chemically modify the surface using the matrix-enhanced SIMS approach, where an organic matrix is placed upon the surface. In this study, a Knudsen cell type matrix coater was developed in order to produce well-defined thicknesses of a matrix on a sample in order to study the effect of these matrix layers on the secondary ions. Using this technique, an order of magnitude enhancement of the useful ion yield for lipids was observed and clear enhancement of image contrast for lipids in brain tissue was demonstrated. The study shows that the layer thickness has a great influence on the emission of secondary ions, and therefore, its precise control is important for optimal yield enhancement.

Changes in the molecular ion yield and fragmentation of peptides under various primary ions in ToF-SIMS and matrix-enhanced ToF-SIMS

Time of flight secondary ion mass spectrometry (ToF-SIMS) is a powerful technique for the nanoanalysis of biological samples, but improvements in sensitivity are needed in order to detect large biomolecules, such as peptides, on the individual cell level at physiological concentrations. Two promising options to improve the sensitivity of SIMS to large peptides are the use of cluster primary ions to increase desorption of intact molecules or the use of matrix-assisted laser desorption/ionization (MALDI) matrices to increase the ionization probability. In this paper, the authors have combined these two approaches in order to improve understanding of the interaction between ionization and fragmentation processes. The peptides bradykinin and melittin were prepared as neat monolayers on silicon, in a Dextran-40 matrix and in two common MALDI matrices, 2,5-dihydroxybenzoic acid (DHB) and α-cyano-4-hydroxy cinnamic acid (HCCA). ToF-SIMS spectra of these samples were collected using a range of small Bi cluster primary ions and large Ar cluster primary ions. The trends observed in the molecular ion yield and the [M+H](+)/C4H8N(+) ratio with primary ion cluster size were sample system dependent. The molecular ion yield of the bradykinin was maximized by using 30 keV Bi3 (+) primary ions in a DHB matrix but in the HCCA matrix, the maximum molecular ion yield was obtained by using 30 keV Bi7 (+) primary ions. In contrast, the molecular ion yield for melittin in both matrices was greatest using 20 keV Ar2000 (+) primary ions. Improvements in the molecular ion yield were only loosely correlated with a decrease in small fragment ions. The data indicate a complex interplay between desorption processes and ion formation processes which mean that the optimal analytical conditions depend on both the target analyte and the matrix.

Cluster TOF-SIMS imaging as a tool for micrometric histology of lipids in tissue

Recent developments in instrumentation, ion beams or analyzers, for cluster time-of-flight secondary ion mass spectrometry (TOF-SIMS) imaging are described here. The methods which are employed to increase the sensitivity or to perform three-dimensional analyses in the organic materials are also illustrated. This review shows the improvements made for lipid imaging by cluster TOF-SIMS in various types of material and applications, and gives reasons for the expansion of its utilization.

A mixed cluster ion beam to enhance the ionization efficiency in molecular secondary ion mass spectrometry

RATIONALE

Chemical modification of a rare gas cluster ion beam (GCIB) to increase the intensity of desorbed molecular ions in secondary ion mass spectrometry experiments relative to the pure Ar cluster.

METHODS

Doping of the GCIB by mixing small concentration levels (1-3% relative partial pressure) of CH4 into the Ar gas driving the cluster ion source.

RESULTS

Mass spectra measured on a trehalose film using the doped GCIB exhibit enhanced molecular ion signals. From depth profiling experiments, the results are shown to arise from an increase in the ionization efficiency of the sputtered molecules rather than a change in the sputtering yield of neutral species.

CONCLUSIONS

Tuning of the chemistry of mixed clusters is suggested as a general approach to enhancing the ionization probability of sputtered molecules.

Peptide dissociation patterns in secondary ion mass spectrometry under large argon cluster ion bombardment

RATIONALE

The analysis of organic and biological substances by secondary ion mass spectrometry (SIMS) has greatly benefited from the use of cluster ions as primary bombarding species. Thereby, depth profiling and three-dimensional (3D) imaging of such systems became feasible. Large Ar(n)(+) cluster ions may constitute a further improvement in this direction.

METHODS

To explore this option, large Ar(n)(+) cluster ions (with n ~1500 Ar atoms per cluster) were used to investigate the emission of positive secondary ions from two peptide specimens (angiotensin I and bradykinin) by orthogonal time-of-flight SIMS using bombarding energies 6, 10 and 14 keV.

RESULTS

For both peptides, the protonated molecular ion is observed in the mass spectra. In addition, distinct fragmentation patterns were observed; these indicate that fragment ions under Ar cluster irradiation form primarily via cleavage of bonds along the peptide backbone whereas the rapture of side chains occurs much less frequently. These features appear to be similar to low-energy collision-induced dissociation pathways.

CONCLUSIONS

Tentatively, these findings can then be ascribed to the concerted action of the large number of Ar atoms in the impact zone of cluster at the surface: these low-energy Ar species (with an average energy of few eV) may effect the cleavage of the peptide bonds and lead, eventually, to the emission of the fragment ions.