Peptide structural analysis using continuous Ar cluster and C60 ion beams

Evaluation of Time-of-Flight Secondary Ion Mass Spectrometry Spectra of Peptides by Random Forest with Amino Acid Labels: Results from a Versailles Project on Advanced Materials and Standards Interlaboratory Study

We report the results of a VAMAS (Versailles Project on Advanced Materials and Standards) interlaboratory study on the identification of peptide sample TOF-SIMS spectra by machine learning. More than 1000 time-of-flight secondary ion mass spectrometry (TOF-SIMS) spectra of six peptide model samples (one of them was a test sample) were collected using 27 TOF-SIMS instruments from 25 institutes of six countries, the U. S., the U. K., Germany, China, South Korea, and Japan. Because peptides have systematic and simple chemical structures, they were selected as model samples. The intensity of peaks in every TOF-SIMS spectrum was extracted using the same peak list and normalized to the total ion count. The spectra of the test peptide sample were predicted by Random Forest with 20 amino acid labels. The accuracy of the prediction for the test spectra was 0.88. Although the prediction of an unknown peptide was not perfect, it was shown that all of the amino acids in an unknown peptide can be determined by Random Forest prediction and the TOF-SIMS spectra. Moreover, the prediction of peptides, which are included in the training spectra, was almost perfect. Random Forest also suggests specific fragment ions from an amino acid residue Q, whose fragment ions detected by TOF-SIMS have not been reported, in the important features. This study indicated that the analysis using Random Forest, which enables translation of the mathematical relationships to chemical relationships, and the multi labels representing monomer chemical structures, is useful to predict the TOF-SIMS spectra of an unknown peptide.

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.

Gas Cluster Ion Beam Time-of-Flight Secondary Ion Mass Spectrometry High-Resolution Imaging of Cardiolipin Speciation in the Brain: Identification of Molecular Losses after Traumatic Injury

Gas cluster ion beam-secondary ion mass spectrometry (GCIB-SIMS) has shown the full potential of mapping intact lipids in biological systems with better than 10 μm lateral resolution. This study investigated further the capability of GCIB-SIMS in imaging high-mass signals from intact cardiolipin (CL) and gangliosides in normal brain and the effect of a controlled cortical impact model (CCI) of traumatic brain injury (TBI) on their distribution. A combination of enzymatic and chemical treatments was employed to suppress the signals from the most abundant phospholipids (phosphatidylcholine (PC) and phosphatidylethanolamine (PE)) and enhance the signals from the low-abundance CLs and gangliosides to allow their GCIB-SIMS detection at 8 and 16 μm spatial resolution. Brain CLs have not been observed previously using other contemporary imaging mass spectrometry techniques at better than 50 μm spatial resolution. High-resolution images of naive and injured brain tissue facilitated the comparison of CL species across three multicell layers in the CA1, CA3, and DG regions of the hippocampus. GCIB-SIMS also reliably mapped losses of oxidizable polyunsaturated CL species (but not the oxidation-resistant saturated and monounsaturated gangliosides) to regions including the CA1 and CA3 of the hippocampus after CCI. This work extends the detection range for SIMS measurements of intact lipids to above m/z 2000, bridging the mass range gap compared with MALDI. Further advances in high-resolution SIMS of CLs, with the potential for single cell or supra-cellular imaging, will be essential for the understanding of CL's functional and structural organization in normal and injured brain.

Lipid specific molecular ion emission as a function of the primary ion characteristics in TOF-SIMS

In the present work, the emission characteristics of lipids as a function of the primary ion cluster size and energy were studied using time-of-flight secondary ion mass spectrometry (TOF-SIMS). Characteristic fragmentation patterns for common lipids are described, and changes in secondary ion (SI) yields using various primary ion beams are reported. In particular, emission characteristics were studied for pairs of small polyatomic and nanoparticle primary ion beams (e.g., Bi3+ versus Ar1000+ and Au3+ versus Au400+4) based on the secondary ion yield of characteristic fragment and intact molecular ions as a function of the lipid class. Detailed descriptions of the fragmentation patterns are shown for positive and negative mode TOF-SIMS. Results demonstrate that the lipid structure largely dictates the spectral presence of molecular and/or fragment ions in each ionization mode due to the localization of the charge carrier (head group or fatty acid chain). Our results suggest that the larger the energy per atom for small polyatomic projectiles (Bi3+ and Au3+), the larger the SI yield; in the case of nanoparticle projectiles, the SI increase with primary ion energy (200-500 keV range) for Au400+4 and with the decrease of the energy per atom (10-40 eV/atom range) for Arn=500-2000+ clusters. The secondary ion yield of the molecular ion of lipids from a single standard or from a mixture of lipids does not significantly change with the primary ion identity in the positive ion mode TOF-SIMS and slightly decreases in the negative ion mode TOF-SIMS.

Peptide Fragmentation and Surface Structural Analysis by Means of ToF-SIMS Using Large Cluster Ion Sources

Peptide or protein structural analysis is crucial for the evaluation of biochips and biodevices, therefore an analytical technique with the ability to detect and identify protein and peptide species directly from surfaces with high lateral resolution is required. In this report, the efficacy of ToF-SIMS to analyze and identify proteins directly from surfaces is evaluated. Although the physics governing the SIMS bombardment process precludes the ability for researchers to detect intact protein or larger peptides of greater than a few thousand mass unit directly, it is possible to obtain information on the partial structures of peptides or proteins using low energy per atom argon cluster ion beams. Large cluster ion beams, such as Ar clusters and C60 ion beams, produce spectra similar to those generated by tandem MS. The SIMS bombardment process also produces peptide fragment ions not detected by conventional MS/MS techniques. In order to clarify appropriate measurement conditions for peptide structural analysis, peptide fragmentation dependency on the energy of a primary ion beam and ToF-SIMS specific fragment ions are evaluated. It was found that the energy range approximately 6 ≤ E/n ≤ 10 eV/atom is most effective for peptide analysis based on peptide fragments and [M + H] ions. We also observed the cleaving of side chain moieties at extremely low-energy E/n ≤ 4 eV/atom.

Mass spectrometric imaging of brain tissue by time-of-flight secondary ion mass spectrometry--How do polyatomic primary beams C₆₀⁺, Ar₂₀₀₀⁺, water-doped Ar₂₀₀₀⁺ and (H₂O)₆₀₀₀⁺ compare?

RATIONALE

To discover the degree to which water-containing cluster beams increase secondary ion yield and reduce the matrix effect in time-of-flight secondary ion mass spectrometry (TOF-SIMS) imaging of biological tissue.

METHODS

The positive SIMS ion yields from model compounds, mouse brain lipid extract and mouse brain tissue together with mouse brain images were compared using 20 keV C60(+), Ar2000(+), water-doped Ar2000(+) and pure (H2O)6000(+) primary beams.

RESULTS

Water-containing cluster beams where the beam energy per nucleon (E/nucleon) ≈ 0.2 eV are optimum for enhancing ion yields dependent on protonation. Ion yield enhancements over those observed using Ar2000(+) lie in the range 10 to >100 using the (H2 O)6000 (+) beam, while with water-doped (H2O)Ar2000(+) they lie in the 4 to 10 range. The two water-containing beams appear to be optimum for tissue imaging and show strong evidence of increasing yields from molecules that experience matrix suppression under other primary beams.

CONCLUSIONS

The application of water-containing primary beams is suggested for biological SIMS imaging applications, particularly if the beam energy can be raised to 40 keV or higher to further increase ion yield and enhance spatial resolution to ≤1 µm.

Characterization and Application of a Hybrid Optical Microscopy/Laser Ablation Liquid Vortex Capture/Electrospray Ionization System for Mass Spectrometry Imaging with Sub-micrometer Spatial Resolution

A commercial optical microscope, laser microdissection instrument was coupled with an electrospray ionization mass spectrometer via a low profile liquid vortex capture probe to yield a hybrid optical microscopy/mass spectrometry imaging system. The instrument has bright-field and fluorescence microscopy capabilities in addition to a highly focused UV laser beam that is utilized for laser ablation of samples. With this system, material laser ablated from a sample using the microscope was caught by a liquid vortex capture probe and transported in solution for analysis by electrospray ionization mass spectrometry. Both lane scanning and spot sampling mass spectral imaging modes were used. The smallest area the system was able to ablate was ∼0.544 μm × ∼0.544 μm, achieved by oversampling of the smallest laser ablation spot size that could be obtained (∼1.9 μm). With use of a model photoresist surface, known features as small as ∼1.5 μm were resolved. The capabilities of the system with real world samples were demonstrated first with a blended polymer thin film containing poly(2-vinylpyridine) and poly(N-vinylcarbazole). Using spot sampling imaging, sub-micrometer sized features (0.62, 0.86, and 0.98 μm) visible by optical microscopy were clearly distinguished in the mass spectral images. A second real world example showed the imaging of trace amounts of cocaine in mouse brain thin tissue sections. With use of a lane scanning mode with ∼6 μm × ∼6 μm data pixels, features in the tissue as small as 15 μm in size could be distinguished in both the mass spectral and optical images.

Peptide fragmentation caused by Ar cluster ions depending on primary ion energy

RATIONALE

Time-of-flight secondary ion mass spectrometry (TOF-SIMS) with an Ar cluster ion beam as a primary ion source provides useful information in terms of peptide analysis. It is, however, difficult to interpret the spectra. The ToF-SIMS peptide spectra obtained with Ar clusters having different energies have been investigated in order to classify the secondary ions into the peptide fragment ions and those related to contaminants or the substrate.

METHODS

Three peptides having different molecular weights from 600 to 1300 u were measured with Ar cluster beams having different energies per atom from 4 to 40 eV/atom.

RESULTS

In the spectra normalized to a geometric average of all the spectra, the amino acid fragment ions are distinguished from other secondary ions. In the mass range above 600 u, the peptide fragment ions increase with mass while those not related to the peptide decrease with mass.

CONCLUSIONS

Energy-dependence fragmentation helps in understanding the peptide spectra. Specific peptide fragment ions of the larger peptides are likely to be detected under lower energy than energy higher than 10 eV/atom. Although it is difficult to interpret the TOF-SIMS spectra of a peptide obtained with an Ar cluster ion beam, the secondary ions can be classified by comparing those obtained with different energy Ar cluster ion beams.

Visualization of acetaminophen-induced liver injury by time-of-flight secondary ion mass spectrometry

Time-of-flight secondary ion mass spectrometry (MS) provides secondary ion images that reflect distributions of substances with sub-micrometer spatial resolution. To evaluate the use of time-of-flight secondary ion MS to capture subcellular chemical changes in a tissue specimen, we visualized cellular damage showing a three-zone distribution in mouse liver tissue injured by acetaminophen overdose. First, we selected two types of ion peaks related to the hepatocyte nucleus and cytoplasm using control mouse liver. Acetaminophen-overdosed mouse liver was then classified into three areas using the time-of-flight secondary ion MS image of the two types of peaks, which roughly corresponded to established histopathological features. The ion peaks related to the cytoplasm decreased as the injury became more severe, and their origin was assumed to be mostly glycogen based on comparison with periodic acid-Schiff staining images and reference compound spectra. This indicated that the time-of-flight secondary ion MS image of the acetaminophen-overdosed mouse liver represented the chemical changes mainly corresponding to glycogen depletion on a subcellular scale. In addition, this technique also provided information on lipid species related to the injury. These results suggest that time-of-flight secondary ion MS has potential utility in histopathological applications.

Molecular imaging of biological tissue using gas cluster ions

An Ar n+ (n = 1-6000) gas cluster ion source has been utilized to map the chemical distribution of lipids in a mouse brain tissue section. We also show that the signal from high mass species can be further enhanced by doping a small amount of CH4 into the Ar cluster to enhance the ionization of several biologically important molecules. Coupled with secondary ion mass spectrometry instrumentation which utilizes a continuous Ar cluster ion projectile, maximum spatial resolution and maximum mass resolution can be achieved at the same time. With this arrangement, it is possible to achieve chemically resolved molecular ion images at the 4-µm resolution level. The focused Ar n+/[Ar x (CH4) y ]+ beams (4-10 µm) have been applied to the study of untreated mouse brain tissue. A high signal level of molecular ions and salt adducts, mainly from various phosphocholine lipids, has been seen and directly used to map the chemical distribution. The signal intensity obtained using the pure Ar cluster source, the CH4-doped cluster source and C60 is also presented.

Ion sources for mass spectrometric identification and imaging of molecular species

Covering: 2013 The ability to transfer molecular species to the gas phase and ionize them is central to the study of natural products and other molecular species by mass spectrometry (MS). MS-based strategies in natural products have focused on a few established ion sources, such as electron impact and electrospray ionization. However, a variety of other ion sources are either currently in use to evaluate natural products or show significant future promise. This review discusses these various ion sources in the context of other articles in this special issue, but is also applicable to other fields of analysis, including materials science. Ion sources are grouped based on the current understanding of their predominant ion formation mechanisms. This broad overview groups ion sources into the following categories: electron ionization and single photon ionization; chemical ionization-like and plasma-based; electrospray ionization; and, laser desorption-based. Laser desorption-based methods are emphasized with specific examples given for laser desorption postionization sources and their use in the analysis of intact microbial biofilms. Brief consideration is given to the choice of ion source for various sample types and analyses, including MS imaging.