Ion mobility-mass spectrometry

This review article compares and contrasts various types of ion mobility-mass spectrometers available today and describes their advantages for application to a wide range of analytes. Ion mobility spectrometry (IMS), when coupled with mass spectrometry, offers value-added data not possible from mass spectra alone. Separation of isomers, isobars, and conformers; reduction of chemical noise; and measurement of ion size are possible with the addition of ion mobility cells to mass spectrometers. In addition, structurally similar ions and ions of the same charge state can be separated into families of ions which appear along a unique mass-mobility correlation line. This review describes the four methods of ion mobility separation currently used with mass spectrometry. They are (1) drift-time ion mobility spectrometry (DTIMS), (2) aspiration ion mobility spectrometry (AIMS), (3) differential-mobility spectrometry (DMS) which is also called field-asymmetric waveform ion mobility spectrometry (FAIMS) and (4) traveling-wave ion mobility spectrometry (TWIMS). DTIMS provides the highest IMS resolving power and is the only IMS method which can directly measure collision cross-sections. AIMS is a low resolution mobility separation method but can monitor ions in a continuous manner. DMS and FAIMS offer continuous-ion monitoring capability as well as orthogonal ion mobility separation in which high-separation selectivity can be achieved. TWIMS is a novel method of IMS with a low resolving power but has good sensitivity and is well intergrated into a commercial mass spectrometer. One hundred and sixty references on ion mobility-mass spectrometry (IMMS) are provided.     

Comprehensive theoretical analysis and experimental exploration of ultrafast microchip‐based high‐field asymmetric ion mobility spectrometry (FAIMS) technique

High‐field asymmetric ion mobility spectrometry (FAIMS) has become an efficient technique for separation and characterization of gas‐phase ions at ambient pressure, which utilizes the mobility differences of ions at high and low fields. Micro FAIMS devices made by micro‐electromechanical system technology have small gaps of the channels, high electric field and good installation precision, as thus they have received great attentions. However, the disadvantage of relatively low resolution limits their applications in some areas. In this study, theoretical analysis and experimental exploration were carried out to overcome the disadvantage. Multiple scans, characteristic decline curves of ion transmission and pattern recognitions were proposed to improve the performance of the microchip‐based FAIMS. The results showed that although micro FAIMS instruments as a standalone chemical analyzer suffer from low resolution, by using one or more of the methods proposed, they can identify chemicals precisely and provide quantitative analysis with low detection limit in some applications. Copyright © 2015 John Wiley & Sons, Ltd.     

Separation of peptides from detergents using ion mobility spectrometry

Mass spectrometry (MS) has dramatically evolved in the last two decades and has been the driving force of the spectacular expansion of proteomics during this period. However, the very poor compatibility of MS with detergents is still a technical obstacle in some studies, in particular on membrane proteins. Indeed, the high hydrophobicity of membrane proteins necessitates the use of detergents for their extraction and solubilization. Here, we address the analytical potential of high-field asymmetric waveform ion mobility spectrometry (FAIMS) for separating peptides from detergents. The study was focused on peptides from the human integral membrane protein CD9. A tryptic peptide was mixed with the non-ionic detergents Triton X-100 or beta-D-dodecyl maltoside (DDM) as well as with the ionic detergents sodium dodecyl sulfate (SDS) or sodium deoxycholate (SDC). Although electrospray ionization (ESI) alone led to a total suppression of the peptide ion signal on mass spectra with only detection of the detergents, use of FAIMS allowed separation and clear identification of the peptide with any of the detergents studied. The detection and identification of the target compound in the presence of an excess of detergents are then feasible. FAIMS should prove especially useful in the structural and proteomic analysis of membrane proteins.     

High‐field asymmetric waveform ion mobility spectrometry (FAIMS) coupled with high‐resolution electron transfer dissociation mass spectrometry for the analysis of isobaric phosphopeptides

We have applied high‐field asymmetric waveform ion mobility spectrometry (FAIMS) to the analysis of the phosphopeptides APLpSFRGSLPKSYVK, APLSFRGpSLPKSYVK, and APLSFRGSLPKpSYVK. The peptides have identical amino acid sequences and differ only in the site of phosphorylation. The results show that FAIMS is capable of at least partially separating these species. Separation was confirmed by coupling FAIMS with high‐resolution electron transfer dissociation (ETD) mass spectrometry. Phosphorylation is retained on the ETD peptide fragments thereby allowing assignment of the site of the modification. Co‐eluting phosphopeptides which differ only in the site of modification are frequently observed in liquid chromatography/tandem mass spectrometry phosphoproteomics experiments, and therefore these proof‐of‐principle results have implications for the application of FAIMS in that field. Copyright © 2009 John Wiley & Sons, Ltd.     

Tandem mass spectra of tryptic peptides at signal-to-background ratios approaching unity using electrospray ionization high-field asymmetric waveform ion mobility spectrometry/hybrid quadrupole time-of-flight mass spectrometry

High-field asymmetric waveform ion mobility spectrometry (FAIMS) has been coupled to a quadrupole time-of-flight mass spectrometer for the tandem mass spectrometric analysis of tryptic peptides of pig hemoglobin. Using FAIMS, low levels (fmol/microL) of multiply charged tryptic peptides were separated from relatively intense chemical background such that their tandem mass spectra (MS/MS) lacked many background-related fragment ions observed using a conventional ESI-QqTOFMS instrument. Substantial improvements in both first-order and tandem mass spectra were realized while maintaining approximately the same absolute intensities.     

Strategies for analysis of isomeric peptides

This review presents an overview and recent progress of strategies for detecting isomerism in peptides, with focus on d /l epimerization and the various isomers that the presence of an aspartic acid residue may yield in a protein or peptide. While mass spectrometry has become a majorly used method of choice within proteomics, isomerism is inherently difficult to analyze because it is a modification that does not yield any change in mass of the analyte. Here, several techniques used for analysis of peptide isomerism are discussed, including enzymatic assays, liquid chromatography, and capillary electrophoresis. Recent progress in method development using mass spectrometry is also discussed, including labeling strategies, fragmentation techniques, and ion‐mobility spectrometry.     

The influence and utility of varying field strength for the separation of tryptic peptides by ion mobility-mass spectrometry

The influence of field strength on the separation of tryptic peptides by drift tube-based ion mobility-mass spectrometry is reported. Operating the ion mobility drift tube at elevated field strengths (expressed in V cm(-1) torr(-1)) reduces separation times and increases ion transmission efficiencies. Several accounts in the literature suggest that performing ion mobility separation at elevated field strength can change the selectivity of ion separation. To evaluate the field strength dependant selectivity of ion mobility separation, we examined a data set of 65 singly charged tryptic peptide ion signals (mass range 500-2500 m/z) at six different field strengths and four different drift gas compositions (He, N2, Ar, and CH4). Our results clearly illustrate that changing the field strength from low field (15 V cm(-1) torr(-1)) to high field (66 V cm(-1) torr(-1)) does not significantly alter the selectivity or peak capacity of IM-MS. The implications of these results are discussed in the context of separation methodologies that rely on the field strength dependence of ion mobility for separation selectivity, e.g., high-field asymmetric ion mobility spectrometry (FAIMS).     

Separation and characterization of oxidized isomeric lipid–peptide adducts by ion mobility mass spectrometry

Phospholipids are major components of cell membranes and lipoprotein complexes. They are prone to oxidation by endogenous and exogenous reactive oxygen species yielding a large variety of modified lipids including small aliphatic and phospholipid bound aldehydes and ketones. These carbonyls are strong electrophiles that can modify proteins and, thereby, alter their structures and functions triggering various pathophysiological conditions. The analysis of lipid–protein adducts by liquid chromatography‐MS is challenged by their mixed chemical nature (polar peptide and hydrophobic lipid), low abundance in biological samples, and formation of multiple isomers. Thus, we investigated traveling wave ion mobility mass spectrometry (TWIMS) to analyze lipid–peptide adducts generated by incubating model peptides corresponding to the amphipathic β₁ sheet sequence of apolipoprotein B‐100 with 1‐palmitoyl‐2‐(oxo‐nonanoyl)‐sn‐glycerophosphatidylcholine (PONPC). The complex mixture of peptides, lipids, and peptide–lipid adducts was separated by TWIMS, which was especially important for the identification of two mono‐PONPC‐peptide isomers containing Schiff bases at different lysine residues. Moreover, TWIMS separated structural conformers of one peptide–lipid adduct possessing most likely different orientations of the hydrophobic sn‐1 fatty acyl residue and head group of PONPC, relative to the peptide backbone. Copyright © 2015 John Wiley & Sons, Ltd.     

High-field asymmetric waveform ion mobility spectrometry: a new tool for mass spectrometry

High-field asymmetric waveform ion mobility spectrometry (FAIMS) is a new technology for ion separation at atmospheric pressure. This review introduces the reader to FAIMS, covering topics ranging from the fundamentals and extraction of physical parameters from the raw data, to applications of FAIMS extending from homeland security to environmental analysis to proteomics. The investigation of FAIMS as an ion pre-processing tool for mass spectrometry is in its infancy, but reports in the literature illustrate that FAIMS separates isobaric ions including diastereoisomers, separates isotopes, reduces background ions by isolating ions of interest, and simplifies spectra of complex mixtures by dividing the mixture into a series of simpler subsets of ions. Applications ranging from quantitative analysis of inorganic and organometallic compounds, to studies of the conformers of intact proteins, have been reported. This review is a launching point for further exploration of FAIMS.     

Analysis of tryptic peptides using desorption electrospray ionisation combined with ion mobility spectrometry/mass spectrometry

A novel method is reported for rapid protein identification by the analysis of tryptic peptides using desorption electrospray ionisation (DESI) coupled with hyphenated ion mobility spectrometry and quadrupole time-of-flight mass spectrometry (IMS/Q-ToF-MS). Confident protein identification is demonstrated for the analysis of tryptically digested bovine serum albumin (BSA), with no sample pre-treatment or clean-up. Electrophoretic ion mobility separation of ions generated by DESI allowed examination of charge-state and mobility distributions for tryptic peptide mixtures. Selective interrogation of singly charged ions allowed isobaric peptide responses to be distinguished, along with a reduction in spectral noise. The mobility-selected singly charged peptide responses were presented as a pseudo-peptide mass fingerprint (p-PMF) for protein database searching. Comparative data are shown for electrospray ionisation (ESI) of the BSA digest, without sample clean-up, from which confident protein identification could not be made. Implications for the robustness of the DESI method, together with potential insights into mechanisms for DESI of proteolytic digests, are discussed.     

Probing the Complementarity of FAIMS and Strong Cation Exchange Chromatography in Shotgun Proteomics

High field asymmetric waveform ion mobility spectrometry (FAIMS), also known as differential ion mobility spectrometry, coupled with liquid chromatography tandem mass spectrometry (LC-MS/MS) offers benefits for the analysis of complex proteomics samples. Advantages include increased dynamic range, increased signal-to-noise, and reduced interference from ions of similar m/z. FAIMS also separates isomers and positional variants. An alternative, and more established, method of reducing sample complexity is prefractionation by use of strong cation exchange chromatography. Here, we have compared SCX-LC-MS/MS with LC-FAIMS-MS/MS for the identification of peptides and proteins from whole cell lysates from the breast carcinoma SUM52 cell line. Two FAIMS approaches are considered: (1) multiple compensation voltages within a single LC-MS/MS analysis (internal stepping) and (2) repeat LC-MS/MS analyses at different and fixed compensation voltages (external stepping). We also consider the consequence of the fragmentation method (electron transfer dissociation or collision-induced dissociation) on the workflow performance. The external stepping approach resulted in a greater number of protein and peptide identifications than the internal stepping approach for both ETD and CID MS/MS, suggesting that this should be the method of choice for FAIMS proteomics experiments. The overlap in protein identifications from the SCX method and the external FAIMS method was ~25 % for both ETD and CID, and for peptides was less than 20 %. The lack of overlap between FAIMS and SCX highlights the complementarity of the two techniques. Charge state analysis of the peptide assignments showed that the FAIMS approach identified a much greater proportion of triply-charged ions.      

Behaviour of tetraalkylammonium ions in high‐field asymmetric waveform ion mobility spectrometry

High‐field asymmetric waveform ion mobility spectrometry (FAIMS) is an ion‐filtering technique recently adapted for use with liquid chromatography/mass spectrometry (LC/MS) to remove interferences during analysis of complex matrices. This is the first systematic study of a series of singly charged tetraalkylammonium ions by FAIMS‐MS. The compensation voltage (CV) is the DC offset of the waveform which permits the ion to emerge from FAIMS and it was determined for each member of the series under various conditions. The electrospray ionization conditions explored included spray voltage, vaporizer temperature, and sheath and auxiliary gas pressure. The FAIMS conditions explored included carrier gas flow rate, electrode temperature and composition of the carrier gas. Optimum desolvation was achieved using sufficient carrier gas (flow rate ≥2 L/min) to ensure stable response. Low‐mass ions (m/z 100–200) are more susceptible to changes in electrode temperature and gas composition than high mass ions (m/z 200–700). As a result of this study, ions are reliably analyzed using standard FAIMS conditions (dispersion voltage ?5000 V, carrier gas flow rate 3 L/min, 50% helium/50%nitrogen, inner electrode temperature 70°C and outer electrode temperature 90°C). Variation of FAIMS conditions may be of great use for the separation of very low mass tetraalkylammonium (TAA) ions from other TAA ions. The FAIMS conditions do not appear to have a major effect on higher mass ions. Copyright © 2010 John Wiley & Sons, Ltd.     

Precise determination of nonlinear function of ion mobility for explosives and drugs at high electric fields for microchip FAIMS

High‐field asymmetric waveform ion mobility spectrometry (FAIMS) separates ions by utilizing the characteristics of nonlinear ion mobility at high and low electric fields. Accurate ion discrimination depends on the precise solution of nonlinear relationships and is essential for accurate identification of ion species for applications. So far, all the nonlinear relationships of ion mobility obtained are based at low electric fields (E/N <65 Td). Microchip FAIMS (μ‐FAIMS) with small dimensions has high electric field up to E/N = 250 Td, making the approximation methods and conclusions for nonlinear relationships inappropriate for these systems. In this paper, we deduced nonlinear functions based on the first principle and a general model. Furthermore we considered the hydrodynamics of gas flow through microchannels. We then calculated the specific alpha coefficients for cocaine, morphine, HMX, TNT and RDX, respectively, based on their FAIMS spectra measured by μ‐FAIMS system at ultra‐high fields up to 250 Td. The results show that there is no difference in nonlinear alpha functions obtained by the approximation and new method at low field (<120 Td), but the error induced by using approximation method increases monotonically with the increase in field, and could be as much as 30% at a field of 250 Td. Copyright © 2015 John Wiley & Sons, Ltd.     

Adding a new separation dimension to MS and LC–MS: What is the utility of ion mobility spectrometry?

Ion mobility spectrometry is an analytical technique known for more than 100 years, which entails separating ions in the gas phase based on their size, shape, and charge. While ion mobility spectrometry alone can be useful for some applications (mostly security analysis for detecting certain classes of narcotics and explosives), it becomes even more powerful in combination with mass spectrometry and high‐performance liquid chromatography. Indeed, the limited resolving power of ion mobility spectrometry alone can be tackled when combining this analytical strategy with mass spectrometry or liquid chromatography with mass spectrometry. Over the last few years, the hyphenation of ion mobility spectrometry to mass spectrometry or liquid chromatography with mass spectrometry has attracted more and more interest, with significant progresses in both technical advances and pioneering applications. This review describes the theoretical background, available technologies, and future capabilities of these techniques. It also highlights a wide range of applications, from small molecules (natural products, metabolites, glycans, lipids) to large biomolecules (proteins, protein complexes, biopharmaceuticals, oligonucleotides).     

Evaluation and validation of an ion mobility quadrupole time‐of‐flight mass spectrometry pesticide screening approach

An ion mobility quadrupole time‐of‐flight mass spectrometry‐based pesticide suspect screening methodology was developed and validated covering 20 plant‐derived food matrices deriving from six commodity groups of different complexity according to the actual European Commission document SANTE/11813/2017 applying a QuEChERS sample preparation protocol. The method combines ultra‐performance liquid chromatography, traveling wave ion mobility, and quadrupole time‐of‐flight mass spectrometry. Besides the determination of the physicochemical property collision cross‐section and the establishment of a corresponding scientific suspect screening database comprising 280 pesticides for several pesticides, different protomers, sodium adducts, as well as dimers were identified in ion mobility spectrometry traces. Additionally, collision cross‐section values were included in the validation requirements regarding chromatography and mass spectrometry for the detection of pesticides. A collision cross‐section value window was analyzed within a tolerable error of ±2%. For this cross‐matrix validation, screening detection limits were determined at concentration levels of 0.100 mg/kg (84% of the original pesticide scope), 0.010 mg/kg (56%), and 0.001 mg/kg (21%). By application of ion mobility spectrometry, the compound identification was improved due to independence of commodity of concern and concentration levels of analyte molecules, as false assignments are reduced by application of a collision cross‐section range.     

Application of ESI-FAIMS-MS to the analysis of tryptic peptides

High-field asymmetric waveform ion mobility spectrometry (FAIMS) separates gas-phase analyte ions from chemical background, offering substantial improvements in the detection of peptides from complex protein digests. For a digest of enolase 1 (baker's yeast), the focusing and separation offered by FAIMS produced an average intensity gain of 3.5 for the tryptic ions and reductions in background intensity of 5- to 10-fold when compared with ESI-MS. The increased signal-to-background in the ESI-FAIMS-MS experiment resulted in a greater number of identifiable peptides and therefore greater sequence coverage. Compensation voltage (CV) maps for a total of 282 tryptic peptides from thirteen proteins, generated according to charge-state, mass-to-charge ratios, and chain length, show that a majority of tryptic peptides can be detected by operating FAIMS at a few discrete values of CV rather than scanning CV across a wide range. The ability to reduce scanning requirements has potential benefits for coupling FAIMS with LC-MS. In select cases, FAIMS can be used to eliminate isobaric MS overlap between tryptic peptides; however, the primary advantage of FAIMS in an LC-FAIMS-MS analysis is foreseen to be the attenuation of chemical background noise rather than the separation of individual peptides. Using FAIMS to reduce mass spectral noise will offer improved detection of peptides from low abundance proteins in complex biological samples.     

基于质谱的蛋白质组学技术在神经退行性疾病生物标志物研究中的应用

蛋白质组学是在整体水平上研究细胞、组织或生物体蛋白质组成及变化规律的科学.与传统的生物学研究相比,蛋白质组学具有快速、灵敏、高通量的优点.神经退行性疾病是一类由神经系统内特定神经细胞的进程性病变或丢失而导致神经功能障碍的疾病,严重危害人类健康.近年来,基于质谱的蛋白质组学技术在神经退行性疾病的研究中得到了广泛应用.本文简要介绍了蛋白质组学在样品分离、多肽定量、质谱检测及生物标志物临床验证等方面的技术发展,并结合实例综述了基于质谱的蛋白质组学在神经退行性疾病生物标志物发现与验证中的研究进展.     

Acid‐based approach for separation of peptide epimers using IM‐MS

Chiral molecules frequently remain undistinguishable using ion mobility mass spectrometry (IM‐MS), due to insufficient differences of their collision cross sections at the available mobility resolution of the ion mobility drift tubes. The influence of the complexation with organic acids on the ion mobility separation of peptide epimers is evaluated using traveling‐wave ion mobility (TWIMS). The examined epimeric tripeptides containing Arg residue with the sequence: Ac‐Phe‐Arg‐Trp‐NH₂ formed stable complexes in the gas phase, and under the increased pressure in ion mobility drift tube, noncovalent associates formed with carboxylic or sulfonic monoacids and diacids with chiral variation of certain acids. Overall, the complexation with an acid leads to the improvement in stereodifferentiation among epimeric peptides, in comparison to the analysis of pure epimers. Detailed characterization of peptide epimer‐acid associates obtained for dibenzoyl‐D‐tartaric acid by theoretical calculations and collisional dissociation studies revealed that the presence of multiple hydrogen bonding interactions between carboxylate anions and hydrogens from N―H of both the guanidinium group of arginine and the indole of tryptophan, as well as the amide backbone hydrogens in the peptide, is responsible for stability of acid‐peptide complexes and for their differentiation in the ion mobility drift tube. The specificity of complex formation toward Arg was determined in terms of complex stability. Based on the reported results, we present general conclusions regarding the utility of the acid‐based complexation in the separation of peptide isomers.     

Quantitative mapping of glycoprotein micro‐heterogeneity and macro‐heterogeneity: an evaluation of mass spectrometry signal strengths using synthetic peptides and glycopeptides

Mass spectrometry (MS) is used to quantify the relative distribution of glycans attached to particular protein glycosylation sites (micro‐heterogeneity) and evaluate the molar site occupancy (macro‐heterogeneity) in glycoproteomics. However, the accuracy of MS for such quantitative measurements remains to be clarified. As a key step towards this goal, a panel of related tryptic peptides with and without complex, biantennary, disialylated N‐glycans was chemically synthesised by solid‐phase peptide synthesis. Peptides mimicking those resulting from enzymatic deglycosylation using PNGase F/A and endo D/F/H were synthetically produced, carrying aspartic acid and N‐acetylglucosamine‐linked asparagine residues, respectively, at the glycosylation site. The MS ionisation/detection strengths of these pure, well‐defined and quantified compounds were investigated using various MS ionisation techniques and mass analysers (ESI‐IT, ESI‐Q‐TOF, MALDI‐TOF, ESI/MALDI‐FT‐ICR‐MS). Depending on the ion source/mass analyser, glycopeptides carrying complex‐type N‐glycans exhibited clearly lower signal strengths (10–50% of an unglycosylated peptide) when equimolar amounts were analysed. Less ionisation/detection bias was observed when the glycopeptides were analysed by nano‐ESI and medium‐pressure MALDI. The position of the glycosylation site within the tryptic peptides also influenced the signal response, in particular if detected as singly or doubly charged signals. This is the first study to systematically and quantitatively address and determine MS glycopeptide ionisation/detection strengths to evaluate glycoprotein micro‐heterogeneity and macro‐heterogeneity by label‐free approaches. These data form a much needed knowledge base for accurate quantitative glycoproteomics. Copyright © 2013 John Wiley & Sons, Ltd.