Three-dimensional molecular reconstruction of rat heart with mass spectrometry imaging

Cardiovascular diseases are the world’s number one cause of death, accounting for 17.1 million deaths a year. New high-resolution molecular and structural imaging strategies are needed to understand underlying pathophysiological mechanism. The aim of our study is (1) to provide a molecular basis of the heart animal model through the local identification of biomolecules by mass spectrometry imaging (MSI) (three-dimensional (3D) molecular reconstruction), (2) to perform a cross-species validation of secondary ion mass spectrometry (SIMS)-based cardiovascular molecular imaging, and (3) to demonstrate potential clinical relevance by the application of this innovative methodology to human heart specimens. We investigated a MSI approach using SIMS on the major areas of a rat and mouse heart: the pericardium, the myocardium, the endocardium, valves, and the great vessels. While several structures of the heart can be observed in individual two-dimensional sections analyzed by metal-assisted SIMS imaging, a full view of these structures in the total heart volume can be achieved only through the construction of the 3D heart model. The images of 3D reconstruction of the rat heart show a highly complementary localization between Na⁺, K⁺, and two ions at m/z 145 and 667. Principal component analysis of the MSI data clearly identified different morphology of the heart by their distinct correlated molecular signatures. The results reported here represent the first 3D molecular reconstruction of rat heart by SIMS imaging.

Twelve Million Resolving Power on 4.7 T Fourier Transform Ion Cyclotron Resonance Instrument with Dynamically Harmonized Cell—Observation of Fine Structure in Peptide Mass Spectra

Resolving power of about 12,000 000 at m/z 675 has been achieved on low field homogeneity 4.7 T magnet using a dynamically harmonized Fourier transform ion cyclotron resonance (FT ICR) cell. Mass spectra of the fine structure of the isotopic distribution of a peptide were obtained and strong discrimination of small intensity peaks was observed in case of resonance excitation of the ions of the whole isotopic cluster to the same cyclotron radius. The absence of some peaks from the mass spectra of the fine structure was explained basing on results of computer simulations showing strong ion cloud interactions, which cause the coalescence of peaks with m/z close to that of the highest magnitude peak. The way to prevent peak discrimination is to excite ion clouds of different m/z to different cyclotron radii, which was demonstrated and investigated both experimentally and by computer simulations.

Electron Capture Dissociation of Divalent Metal-adducted Sulfated N-Glycans Released from Bovine Thyroid Stimulating Hormone

Sulfated N-glycans released from bovine thyroid stimulating hormone (bTSH) were ionized with the divalent metal cations Ca²⁺, Mg²⁺, and Co by electrospray ionization (ESI). These metal-adducted species were subjected to infrared multiphoton dissociation (IRMPD) and electron capture dissociation (ECD) and the corresponding fragmentation patterns were compared. IRMPD generated extensive glycosidic and cross-ring cleavages, but most product ions suffered from sulfonate loss. Internal fragments were also observed, which complicated the spectra. ECD provided complementary structural information compared with IRMPD, and all observed product ions retained the sulfonate group, allowing sulfonate localization. To our knowledge, this work represents the first application of ECD towards metal-adducted sulfated N-glycans released from a glycoprotein. Due to the ability of IRMPD and ECD to provide complementary structural information, the combination of the two strategies is a promising and valuable tool for glycan structural characterization. The influence of different metal ions was also examined. Calcium adducts appeared to be the most promising species because of high sensitivity and ability to provide extensive structural information.

Influence of Metal–Peptide Complexation on Fragmentation and Inter-Fragment Hydrogen Migration in Electron Transfer Dissociation

The use of metal salts in electrospray ionization (ESI) of peptides increases the charge state of peptide ions, facilitating electron transfer dissociation (ETD) in tandem mass spectrometry. In the present study, K⁺ and Ca²⁺ were used as charge carriers to form multiply-charged metal–peptide complexes. ETD of the potassium- or calcium-peptide complex was initiated by transfer of an electron to a proton remote from the metal cation, and a c'-z? fragment complex, in which the c' and z? fragments were linked together via a metal cation coordinating with several amino acid residues, was formed. The presence of a metal cation in the precursor for ETD increased the lifetime of the c'-z? fragment complex, eventually generating c? and z' fragments through inter-fragment hydrogen migration. The degree of hydrogen migration was dependent on the location of the metal cation in the metal-peptide complex, but was not reconciled with conformation of the precursor ion obtained by molecular mechanics simulation. In contrast, the location of the metal cation in the intermediate suggested by the ETD spectrum was in agreement with the conformation of “proton-removed” precursors, indicating that the charge reduction of precursor ions by ETD induces conformational rearrangement during the fragmentation process.

Electron ionization induced metastable decompositions of isomeric trimethylsilylmethanol, (CH3)3SiCH2OH, and methoxytrimethylsilane, (CH3)3SiOCH3

The metastable decompositions of trimethylsilylmethanol, (CH₃)₃SiCH₂OH (MW: 104, 1) and methoxytrimethylsilane, (CH₃)₃SiOCH₃ (MW: 104, 2) upon electron ionization have been investigated by use of mass-analyzed ion kinetic energy (MIKE) spectroscopy and D labeling. The metastable ions of 1 ^·+ decompose to give the fragment ions m/z 89 (CH ₃ ^· loss) and 73 (^·CH₂OH loss), whereas those of 2 ^·+ only yield the fragment ion m/z 89 (CH ₃ ^· loss). The latter fragment ion is generated by loss of a methyl radical from the trimethylsilyl group via a simple cleavage reaction as shown by D labeling. However, the fragment ions m/z 89 and 73 from 1 ^·+ are generated following an almost statistical exchange of the original methyl and methylene hydrogen atoms in the molecular ion as shown also by D labeling. This exchange indicates a complex rearrangement of the molecular ion of 1 ^·+ prior to metastable decomposition for which as key step a 1,2-trimethylsilyl group migration from carbon to oxygen is suggested. A different behavior is also found between the source-generated m/z 89 ions from 1 ^·+ which decompose in the metastable time region to give ions m/z 61 by loss of ethylene and those from 2 ^·+ which decompose in the metastable region to yield ions m/z 59 by elimination of formaldehyde.     

Linkage Determination of Linear Oligosaccharides by MSn (n > 2) Collision-Induced Dissociation of Z1 Ions in the Negative Ion Mode

Obtaining unambiguous linkage information between sugars in oligosaccharides is an important step in their detailed structural analysis. An approach is described that provides greater confidence in linkage determination for linear oligosaccharides based on multiple-stage tandem mass spectrometry (MSⁿ, n >2) and collision-induced dissociation (CID) of Z₁ ions in the negative ion mode. Under low energy CID conditions, disaccharides ¹⁸O-labeled on the reducing carbonyl group gave rise to Z₁ product ions (m/z 163) derived from the reducing sugar, which could be mass-discriminated from other possible structural isomers having m/z 161. MS³ CID of these m/z 163 ions showed distinct fragmentation fingerprints corresponding to the linkage types and largely unaffected by sugar unit identities or their anomeric configurations. This unique property allowed standard CID spectra of Z₁ ions to be generated from a small set of disaccharide samples that were representative of many other possible isomeric structures. With the use of MSⁿ CID (n = 3 – 5), model linear oligosaccharides were dissociated into overlapping disaccharide structures, which were subsequently fragmented to form their corresponding Z₁ ions. CID data of these Z₁ ions were collected and compared with the standard database of Z₁ ion CID using spectra similarity scores for linkage determination. As the proof-of-principle tests demonstrated, we achieved correct determination of individual linkage types along with their locations within two trisaccharides and a pentasaccharide.

Controlled Ion Ejection from an External Trap for Extended m/z Range in FT-ICR Mass Spectrometry

An auxiliary rf waveform of the same amplitude and phase applied to all the rods of an ion accumulation multipole creates an m/z-dependent axial pseudo potential. Controlled decrease of the auxiliary rf amplitude releases ions from the accumulation multipole sequentially from high to low m/z. The slope of the auxiliary rf voltage ramp is adjusted so that ions of different m/z reach the center of the ICR cell at the same time point, which mitigates the typical time dispersion observed in external source FT-ICR and extends the observable mass range for a single data acquisition by 2- to 3-fold. For complex mixture analysis, twice the number of elemental compositions are assigned when the auxiliary rf ejection is applied compared with the standard gated trapping.

Boundaries of Mass Resolution in Native Mass Spectrometry

Over the last two decades, native mass spectrometry (MS) has emerged as a valuable tool to study intact proteins and noncovalent protein complexes. Studied experimental systems range from small-molecule (drug)–protein interactions, to nanomachineries such as the proteasome and ribosome, to even virus assembly. In native MS, ions attain high m/z values, requiring special mass analyzers for their detection. Depending on the particular mass analyzer used, instrumental mass resolution does often decrease at higher m/z but can still be above a couple of thousand at m/z 5000. However, the mass resolving power obtained on charge states of protein complexes in this m/z region is experimentally found to remain well below the inherent instrument resolution of the mass analyzers employed. Here, we inquire into reasons for this discrepancy and ask how native MS would benefit from higher instrumental mass resolution. To answer this question, we discuss advantages and shortcomings of mass analyzers used to study intact biomolecules and biomolecular complexes in their native state, and we review which other factors determine mass resolving power in native MS analyses. Recent examples from the literature are given to illustrate the current status and limitations.

Enantioselective separation and simultaneous determination of fenarimol and nuarimol in fruits, vegetables, and soil by liquid chromatography–tandem mass spectrometry

A method for simultaneous enantioselective determination of fenarimol and nuarimol in apple, grape, cucumber, tomato, and soil was developed using liquid chromatography–tandem mass spectrometry. The enantioseparation results of the two fungicides through three different cellulose-based chiral columns are discussed. The influence of column temperature on the resolution of the enantiomers of the two fungicides was examined. Complete enantioseparation of the two fungicides’ enantiomers was obtained on a cellulose tris(4-methylbenzoate) column (Lux Cellulose-3) at 25?°C using methanol and 0.1?% formic acid solution (80:20, v/v) as mobile phase. The linearity, matrix effect, recovery, and precision were evaluated. Good linearity was obtained over the concentration range of 1–500?μg?L^?1 for each enantiomer in the standard solution and sample matrix calibration solution. There was no significant matrix effect in apple, grape, cucumber, or tomato samples, but signal suppression was typically observed with the soil extracts. The mean recoveries, repeatability, and reproducibility were 76.5–103?%, 2.1–9.0?%, and 4.2–11.8?%, respectively. The limit of quantification for enantiomers of the two fungicides in fruits, vegetables and soil was 5?μg?kg^?1. Moreover, the absolute configuration of the enantiomers of fenarimol and nuarimol was determined from a combination of experimentally determined and predicted electronic circular dichroism spectra.

Rapid comprehensive characterization of crude oils by thermogravimetry coupled to fast modulated gas chromatography–single photon ionization time-of-flight mass spectrometry

Comprehensive multi-dimensional hyphenation of a thermogravimetry device (i.e. a thermobalance) to gas chromatography and single photon ionization–time-of-flight mass spectrometry (TG–GC×SPI–MS) has been used to investigate two crude oil samples of different geographical origin. The source of the applied vacuum ultraviolet radiation is an electron beam pumped rare gas excimer lamp (EBEL). The soft photoionization favors the formation of molecular ions. Introduction of a fast, rapidly modulated gas chromatographic separation step in comparison with solely TG–SPI–MS enables strongly enhanced detection especially with such highly complex organic matrices as crude oil. In contrast with former TG–SPI–MS measurements, separation and identification of overlying substances is possible because of different GC retention times. The specific contribution of isobaric compounds to one mass signal is determined for alkanes, naphthalenes, alkylated benzenes, and other compounds.

Clustering and Filtering Tandem Mass Spectra Acquired in Data-Independent Mode

Data-independent mass spectrometry activates all ion species isolated within a given mass-to-charge window (m/z) regardless of their abundance. This acquisition strategy overcomes the traditional data-dependent ion selection boosting data reproducibility and sensitivity. However, several tandem mass (MS/MS) spectra of the same precursor ion are acquired during chromatographic elution resulting in large data redundancy. Also, the significant number of chimeric spectra and the absence of accurate precursor ion masses hamper peptide identification. Here, we describe an algorithm to preprocess data-independent MS/MS spectra by filtering out noise peaks and clustering the spectra according to both the chromatographic elution profiles and the spectral similarity. In addition, we developed an approach to estimate the m/z value of precursor ions from clustered MS/MS spectra in order to improve database search performance. Data acquired using a small 3 m/z units precursor mass window and multiple injections to cover a m/z range of 400–1400 was processed with our algorithm. It showed an improvement in the number of both peptide and protein identifications by 8 % while reducing the number of submitted spectra by 18 % and the number of peaks by 55 %. We conclude that our clustering method is a valid approach for data analysis of these data-independent fragmentation spectra. The software including the source code is available for the scientific community.

Traveling Wave Ion Mobility Mass Spectrometry and Ab Initio Calculations of Phosphoric Acid Clusters

Positive and negative ion electrospray mass spectra obtained from 50 mM phosphoric acid solutions presented a large number of phosphoric acid clusters: [(H₃PO₄)_n?+?zH] ^z+ or [(H₃PO₄)_n – zH] ^z– , with n up to 200 and z up to 4 for positively charged clusters, and n up to 270 and z up to 7 for negatively charged cluster ions. Ion mobility experiments allowed very explicit separation of the different charge states. Because of the increased pressures involved in ion mobility experiments, dissociation to smaller clusters was observed both in the trap and transfer areas. Voltages along the ion path could be optimized so as to minimize this effect, which can be directly associated with the cleavage of hydrogen bonds. Having excluded the ion mobility times that resulted from dissociated ions, each cluster ion appeared at a single drift time. These drift times showed a linear progression with the number of phosphoric atoms for cluster ions of the same charge state. Cross section calculations were carried out with MOBCAL on DFT optimized geometries with different hydrogen locations and with three types of atomic charges. DFT geometry optimizations yielded roughly spherical structures. Our results for nitrogen gas interaction cross sections showed that values were dependent on the atomic charges definition used in the MOBCAL calculation. This pinpointed the necessity to define a clear theoretical framework before any comparative interpretations can be attempted with uncharacterized compounds.

The Effective Temperature of Ions Stored in a Linear Quadrupole Ion Trap Mass Spectrometer

The extent of internal energy deposition into ions upon storage, radial ejection, and detection using a linear quadrupole ion trap mass spectrometer is investigated as a function of ion size (m/z 59 to 810) using seven ion-molecule thermometer reactions that have well characterized reaction entropies and enthalpies. The average effective temperatures of the reactants and products of the ion-molecule reactions, which were obtained from ion-molecule equilibrium measurements, range from 295 to 350 K and do not depend significantly on the number of trapped ions, m/z value, ion trap q _z value, reaction enthalpy/entropy, or the number of vibrational degrees of freedom for the seven reactions investigated. The average of the effective temperature values obtained for all seven thermometer reactions is 318?±?23 K, which indicates that linear quadrupole ion trap mass spectrometers can be used to study the structure(s) and reactivity of ions at near ambient temperature.

Compressive Mass Analysis on Quadrupole Ion Trap Systems

Conventionally, quadrupole ion trap mass spectrometers eject ions of different mass-to-charge ratio (m/z) in a sequential fashion by performing a scan of the rf trapping voltage amplitude. Due to the inherent sparsity of most mass spectra, the detector measures no signal for much of the scan time. By exploiting this sparsity property, we propose a new compressive and multiplexed mass analysis approach—multi Resonant Frequency Excitation (mRFE) ejection. This new approach divides the mass spectrum into several mass subranges and detects all the subrange spectra in parallel for increased mass analysis speed. Mathematical estimation of standard mass spectrum is demonstrated while statistical classification on the parallel measurements remains viable because of the sparse nature of the mass spectra. This method can reduce mass analysis time by a factor of 3–6 and increase system duty cycle by 2×. The combination of reduced analysis time and accurate compound classification is demonstrated in a commercial quadrupole ion trap (QIT) system.

Über cyclische Guanidin—Mesityloxid- und Guanidin—Phoron-Kondensate

The basic product synthesized byTraube andSchwarz from mesityl oxide and guanidine has not been 4.4.6-trimethyl-4.5-dihydro-2-pyrimidinamine (1), but a mixture containing the 4.4.6-trimethyl-3.4-dihydro-2(1H)-pyrimidinimine (resp. an isomeric pyrimidinamine)2 a (resp.2 b, 2 c) and the dimeric 4.4′-methylenedi[2(1H)-pyrimidinimine] (resp. an isomeric methylenedipyrimidinamine)3 a (resp.3 b, 2 c) and the dimerisation reaction were studied in a series of experiments. The product of the reaction of guanidine and phorone is not the guanidinopropylpyrimidine8 ⁴, but the 4.4′-spirobi[2(1H)-pyrimidinimine] (resp. a spirobipyrimidinamine)11 a (resp.11 b, 11 c). No determination was possible on the basis of NMR whether the condensation products of guanidine—in solutions ofDMSO-d₆—are pyrimidinimines (2 a, 3 a, 11 a) or pyrimidinamines (2 b resp.2 c, 3 b resp.3 c, 11 b resp.11 c) or mixtures of the isomeric compounds. The NMR-and mass spectra of2 a (resp.2 b, 2 c),3 a (resp.3 b, 3 c),11 a (resp.11 b, 11 c) and their derivates are discussed.     

Electron Capture Dissociation Studies of the Fragmentation Patterns of Doubly Protonated and Mixed Protonated-Sodiated Peptoids

The fragmentation patterns of a group of doubly protonated ([P + 2H]²⁺) and mixed protonated-sodiated ([P + H + Na]²⁺) peptide-mimicking oligomers, known as peptoids, have been studied using electron capturing dissociation (ECD) tandem mass spectrometry techniques. For all the peptoids studied, the primary backbone fragmentation occurred at the N-C_α bonds. The N-terminal fragment ions, the C-ions (protonated) and the C′-ions (sodiated) were observed universally for all the peptoids regardless of the types of charge carrier. The C-terminal ions varied depending on the type of charge carrier. The doubly protonated peptoids with at least one basic residue located at a position other than the N-terminus fragmented by producing the Z^?-series of ions. In addition, most doubly protonated peptoids also produced the Y-series of ions with notable abundances. The mixed protonated-sodiated peptoids fragmented by yielding the Z^?′-series of ions in addition to the C′-series. Chelation between the sodium cation and the amide groups of the peptoid chain might be an important factor that could stabilize both the N-terminal and the C-terminal fragment ions. Regardless of the types of the charge carrier, one notable fragmentation for all the peptoids was the elimination of a benzylic radical from the odd-electron positive ions of the protonated peptoids ([P + 2H]^?+) and the sodiated peptoids ([P + H + Na]^?+). The study showed potential utility of using the ECD technique for sequencing of peptoid libraries generated by combinatorial chemistry.

Interleaved Distance-of-Flight Mass Spectrometry: A Simple Method to Improve the Instrument Duty Factor

Distance-of-flight mass spectrometry (DOFMS) is a velocity-based, spatially dispersive MS technique in which ions are detected simultaneously along the plane of a spatially selective detector. In DOFMS, ions fly though the instrument and mass separate over a set period of time. The single flight time at which all ions are measured defines the specific m/z values that are detectable; the range of m/z values is dictated by the length of the spatially selective detector. However, because each packet of ions is detected at a single flight time, multiple groups of ions can fly through the instrument concurrently and be detected at a single detector. In this way, DOFMS experiments can be interleaved to perform several mass separation experiments within a single DOF repetition period. Interleaved operation allows the orthogonal acceleration region to be operated at a repetition rate higher than the reciprocal of the flight time, which improves the duty factor of the technique. In this paper, we consider the fundamental parameters of interleaved DOFMS and report first results.

Activated Ion ETD Performed in a Modified Collision Cell on a Hybrid QLT-Oribtrap Mass Spectrometer

We describe the implementation and characterization of activated ion electron transfer dissociation (AI-ETD) on a hybrid QLT-Orbitrap mass spectrometer. AI-ETD was performed using a collision cell that was modified to enable ETD reactions, in addition to normal collisional activation. The instrument manifold was modified to enable irradiation of ions along the axis of this modified cell with IR photons from a CO₂ laser. Laser power settings were optimized for both charge (z) and mass to charge (m/z) and the instrument control firmware was updated to allow for automated adjustments to the level of irradiation. This implementation of AI-ETD yielded 1.6-fold more unique identifications than ETD in an nLC-MS/MS analysis of tryptic yeast peptides. Furthermore, we investigated the application of AI-ETD on large scale analysis of phosphopeptides, where laser power aids ETD, but can produce b- and y-type ions because of the phosphoryl moiety’s high IR adsorption. nLC-MS/MS analysis of phosphopeptides derived from human embryonic stem cells using AI-ETD yielded 2.4-fold more unique identifications than ETD alone, demonstrating a promising advance in ETD sequencing of PTM containing peptides.

Fragmentation Reactions of Methionine-Containing Protonated Octapeptides and Fragment Ions Therefrom: An Energy-Resolved Study

The fragmentation reactions of the MH⁺ ions as well as the b₇, a₇, and a₇* ions derived therefrom have been studied in detail for the octapeptides MAAAAAAA, AAMAAAAA, AAAAMAAA, and AAAAAAMA. Ionization was by electrospray using a QqToF mass spectrometer, which allowed a study of the evolution of the fragmentation channels as a function of the collision energy. Not surprisingly, the product ion mass spectra for the b₇ ions are independent of the original precursor sequence, indicating macrocyclization and reopening to the same mixture of protonated oxazolones prior to fragmentation. The results show that this sequence scrambling results in a distinct preference to place the Met residue in the C-terminal position of the protonated oxazolones. The a₇ and a₇* ions also produce product ion mass spectra independent of the original peptide sequence. The results for the a₇ ions indicate that fragmentation occurs primarily from an amide structure analogous to that observed for a₄ ions (Bythell et al. in J Am Chem Soc 132:14766–14779, 2010). Clearly, the rearrangement reaction they have proposed applies equally well to a_n ions as large as a₇. The major fragmentation modes of the MH⁺ ions at low collision energies produce b₇, b_6, and b₅ ions. As the collision energy is increased further fragmentation of these primary products produces, in part, non-direct sequence ions, which become prominent at lower m/z values, particularly for the peptides with the Met residue near the N-terminus.

Improved DFT-Based Interpretation of ESI-MS of Aqueous Metal Cations

We present results showing that our recently developed density functional theory (DFT)-based speciation model of the aqueous Al³⁺ system has the potential to improve the interpretations of ESI-MS studies of aqueous metal cation hydrolytic speciation. The main advantages of our method are that (1) it allows for the calculation of the relative abundance of a given species which may be directly assigned to the signal intensity in a mass spectrum; (2) in cases where species with identical m?z ratios may coexist, the assignment can be unambiguously assigned based on their theoretical relative abundances. As a demonstration of its application, we study four pairs of monomer and dimer aqueous Al³⁺ species, each with identical m/z ratio. For some of these pairs our method predicts that the dominant species changes from the monomer to the dimer species under varying pH conditions.