We provide modeling and experimental data describing the dominant ion-loss mechanisms for differential mobility spectrometry (DMS). Ion motion is considered from the inlet region of the mobility analyzer to the DMS exit, and losses resulting from diffusion to electrode surfaces, insufficient effective gap, ion fragmentation, and fringing field effects are considered for a commercial DMS system with 1-mm gap height. It is shown that losses due to diffusion and radial oscillations can be minimized with careful consideration of residence time, electrode spacing, gas flow rate, and waveform frequency. Fragmentation effects can be minimized by limitation of the separation field. When these parameters were optimized, fringing field effects at the DMS inlet contributed the most to signal reduction. We also describe a new DMS cell configuration that improves the gas dynamics at the mobility cell inlet. The new cell provides a gas jet that decreases the residence time for ions within the fringing field region, resulting in at least twofold increase in ion signal as determined by experimental data and simulations.
With recent advances in understanding the genomic underpinnings and oncogenic drivers of pathogenesis in different subtypes, it is increasingly clear that proper pretreatment diagnostics are essential for the choice of appropriate treatment options for non-small cell lung cancer (NSCLC). Tumor tissue preservation in optimal cutting temperature (OCT) compound is commonly used in the surgical suite. However, proteins recovered from OCT-embedded specimens pose a challenge for LC-MS/MS experiments, due to the large amounts of polymers present in OCT. Here we present a simple workflow for whole proteome analysis of OCT-embedded NSCLC tissue samples, which involves a simple trichloroacetic acid precipitation step. Comparisons of protein recovery between frozen versus OCT-embedded tissue showed excellent consistency with more than 9200 proteins identified. Using an isobaric labeling strategy, we quantified more than 5400 proteins in tumor versus normal OCT-embedded core needle biopsy samples. Gene ontology analysis indicated that a number of proliferative as well as squamous cell carcinoma (SqCC) marker proteins were overexpressed in the tumor, consistent with the patient’s pathology based diagnosis of “poorly differentiated SqCC”. Among the most downregulated proteins in the tumor sample, we noted a number of proteins with potential immunomodulatory functions. Finally, interrogation of the aberrantly expressed proteins using a candidate approach and cross-referencing with publicly available databases led to the identification of potential druggable targets in DNA replication and DNA damage repair pathways. We conclude that our approach allows LC-MS/MS proteomic analyses on OCT-embedded lung cancer specimens, opening the way to bring powerful proteomics into the clinic.
The efficient formation of gaseous ions is the crucial step in all successful mass spectrometric experiments. The invention of electrospray ionization (ESI) has strongly facilitated this step by transferring preformed ions directly from solution to the gas phase – thereby circumventing the need to first convert analytes to the gas phase and then ionize them – and therefore ESI has become an extremely useful and widely applied MS technique. The invention of sonic spray ionization (SSI) has also allowed for the transfer of ions from solution into the gas phase, but without the assistance of a voltage or heating. Numerous ionization techniques, using similar principles to those applied in either ESI or SSI, have subsequently been developed. Although experimental conditions used in such techniques vary markedly, herein we argue that they are all based on either one of two basic principles by which ions can be transferred from solution to the gas phase, that is: via (1) neutralizing the counter ion, or (2) separating the ions. We have selected 35 such techniques and categorized them accordingly. This article thereby aims to establish the basic principles by which gaseous ions can be obtained from solvated ions. We further propose that any new ionization technique used to transfer solvated ions to the gas phase will similarly fall into one of these two mechanistic categories.
Radical activation methods, such as electron transfer dissociation (ETD), produce structural information complementary to collision-induced dissociation. Herein, electron transfer dissociation of 3-fold protonated DNA hexamers was studied to gain insight into the fragmentation mechanism. The fragmentation patterns of a large set of DNA hexamers confirm cytosine as the primary target of electron transfer. The reported data reveal backbone cleavage by internal electron transfer from the nucleobase to the phosphate linker leading either to a?/w or d/z? ion pairs. This reaction pathway contrasts with previous findings on the dissociation processes after electron capture by DNA cations, suggesting multiple, parallel dissociation channels. However, all these channels merely result in partial fragmentation of the precursor ion because the charge-reduced DNA radical cations are quite stable. Two hypotheses are put forward to explain the low dissociation yield of DNA radical cations: it is either attributed to non-covalent interactions between complementary fragments or to the stabilization of the unpaired electron in stacked nucleobases. MS3 experiments suggest that the charge-reduced species is the intact oligonucleotide. Moreover, introducing abasic sites significantly increases the dissociation yield of DNA cations. Consequently, the stabilization of the unpaired electron by π–π-stacking provides an appropriate rationale for the high intensity of DNA radical cations after electron transfer.
A method for relating traveling-wave ion mobility spectrometry (TWIMS) drift times with collisional cross-sections using computational simulations is presented. This method is developed using SIMION modeling of the TWIMS potential wave and equations that describe the velocity of ions in gases induced by electric fields. The accuracy of this method is assessed by comparing the collisional cross-sections of 70 different reference ions obtained using this method with those obtained from static drift tube ion mobility measurements. The cross-sections obtained here with low wave velocities are very similar to those obtained using static drift (average difference?=?0.3%) for ions formed from both denaturing and buffered aqueous solutions. In contrast, the cross-sections obtained with high wave velocities are significantly greater, especially for ions formed from buffered aqueous solutions. These higher cross-sections at high wave velocities may result from high-order factors not accounted for in the model presented here or from the protein ions unfolding during TWIMS. Results from this study demonstrate that collisional cross-sections can be obtained from single TWIMS drift time measurements, but that low wave velocities and gentle instrument conditions should be used in order to minimize any uncertainties resulting from high-order effects not accounted for in the present model and from any protein unfolding that might occur. Thus, the method presented here eliminates the need to calibrate TWIMS drift times with collisional cross-sections measured using other ion mobility devices.
Atmospheric solids analysis probe mass spectrometry (ASAP-MS) is a powerful tool for analysis of solid and liquid samples. It is an excellent alternative for crude oil analysis without any sample preparation step. Here, ASAP-MS in positive ion mode, ASAP(+)-MS, has been optimized for analysis of condensed aromatics (CA) standards, crude oil, and paraffinic fraction samples using a Synapt G2-S HDMS. Initially, two methodologies were used to access the chemical composition of samples: (1) using a temperature gradient varying from 150 to 600 °C at a heating rate of 150 °C min–1, and (2) with constant temperature of 300 and 400 °C. ASAP(+)-MS ionized many compounds with a typical petroleum profile, showing a greater signals range of m/z 250–1300 and 200–1400 for crude oil and paraffin samples, respectively. Such performance, mainly related to the detection of high molecular weight compounds (>1000 Da), is superior to that of other traditional ionization sources, such as ESI, APCI, DART, and DESI. Additionally, the CA standards were identified in both forms: radicals, [M]+?, and protonated cations, [M + H]+, with minimum fragmentation. Therefore, ASAP was more efficient in accessing the chemical composition of nonpolar and polar compounds. It is promising in its application with ultrahigh resolution MS instruments, such as FT-ICR MS and Orbitrap, since molecular formulas with greater resolution and mass accuracy (<1 ppm) would be assigned.
Sample throughput in electrospray ionization mass spectrometry (ESI-MS) is limited by the need for frequent ion path cleaning to remove accumulated debris that can lead to charging and general performance degradation. Contamination of ion optics within the vacuum system is particularly problematic as routine cleaning requires additional time for cycling the vacuum pumps. Differential mobility spectrometry (DMS) can select targeted ion species for transmission, thereby reducing the total number of charged particles entering the vacuum system. In this work, we characterize the nature of instrument contamination, describe efforts to improve mass spectrometer robustness by applying DMS prefiltering to reduce contamination of the vacuum ion optics, and demonstrate the capability of DMS to extend the interval between mass spectrometer cleaning. In addition, we introduce a new approach to effectively detect large charged particles formed during the electrospray ionization (ESI) process.
Untargeted omics analyses aim to comprehensively characterize biomolecules within a biological system. Changes in the presence or quantity of these biomolecules can indicate important biological perturbations, such as those caused by disease. With current technological advancements, the entire genome can now be sequenced; however, in the burgeoning fields of lipidomics, only a subset of lipids can be identified. The recent emergence of high resolution tandem mass spectrometry (HR-MS/MS), in combination with ultra-high performance liquid chromatography, has resulted in an increased coverage of the lipidome. Nevertheless, identifications from MS/MS are generally limited by the number of precursors that can be selected for fragmentation during chromatographic elution. Therefore, we developed the software IE-Omics to automate iterative exclusion (IE), where selected precursors using data-dependent topN analyses are excluded in sequential injections. In each sequential injection, unique precursors are fragmented until HR-MS/MS spectra of all ions above a user-defined intensity threshold are acquired. IE-Omics was applied to lipidomic analyses in Red Cross plasma and substantia nigra tissue. Coverage of the lipidome was drastically improved using IE. When applying IE-Omics to Red Cross plasma and substantia nigra lipid extracts in positive ion mode, 69% and 40% more molecular identifications were obtained, respectively. In addition, applying IE-Omics to a lipidomics workflow increased the coverage of trace species, including odd-chained and short-chained diacylglycerides and oxidized lipid species. By increasing the coverage of the lipidome, applying IE to a lipidomics workflow increases the probability of finding biomarkers and provides additional information for determining etiology of disease.
