Reagent Cluster Anions for Multiple Gas-Phase Covalent Modifications of Peptide and Protein Cations

Multiple gas phase ion/ion covalent modifications of peptide and protein ions are demonstrated using cluster-type reagent anions of N-hydroxysulfosuccinimide acetate (sulfo-NHS acetate) and 2-formyl-benzenesulfonic acid (FBMSA). These reagents are used to selectively modify unprotonated primary amine functionalities of peptides and proteins. Multiple reactive reagent molecules can be present in a single cluster ion, which allows for multiple covalent modifications to be achieved in a single ion/ion encounter and at the ‘cost’ of only a single analyte charge. Multiple derivatizations are demonstrated when the number of available reactive sites on the analyte cation exceeds the number of reagent molecules in the anionic cluster (e.g., data shown here for reactions between the polypeptide [K₁₀ + 3H]³⁺ and the reagent cluster [5R_5Na – Na]^–). This type of gas-phase ion chemistry is also applicable to whole protein ions. Here, ubiquitin was successfully modified using an FBMSA cluster anion which, upon collisional activation, produced fragment ions with various numbers of modifications. Data for the pentamer cluster are included as illustrative of the results obtained for the clusters comprised of two to six reagent molecules.

Electronic shell structure in multiply charged silver clusters

Silver clusters are generated by standard laser vaporization technique and ionized via multiphoton ionization. Time-of-flight mass spectrometry reveals singly, doubly and triply charged clusters, Ag _n ^z+ (z=1,2,3). The spectra show, for all charge states, intensity variations, indicating enhanced stabilities for cluster sizes with closed electronic configurations in accord with the spherical jellium model.     

Fragmentation of clusters induced by collision with a solid surface: comparison of antimony and bismuth cluster ions

Mass-selected antimony cluster ions Sb _n ⁺ (n = 3-12) and bismuth cluster ions Bi _{ntn} ⁺ (n = 3-8) are allowed to collide with the surface of highly oriented pyrolytic graphite at energies up to 350 eV. The resulting fragment ions are analysed in a time-of-flight mass spectrometer. Two main fragmentation channels can be identified. At low impact energies both Sb _n ⁺ and Bi _n ⁺ cluster ions lose neutral tetramer and dimer units upon collision. Above about 150 eV impact energy Sb ₃ ⁺ becomes the predominant fragment ion of all investigated antimony clusters. The enhanced stability of these fragment clusters can be explained in the framework of the polyhedral skeletal electron pair theory. In contrast, Bi _n ⁺ cluster scattering leads to the formation of Bi ₃ ⁺ , Bi ₂ ⁺ and Bi+ with nearly equal abundances, if the collision energy exceeds 75 eV. The integral scattering yield is substantially higher in this case as compared to Sb _n ⁺ clusters.     

Charge Site Mass Spectra: Conformation-Sensitive Components of the Electron Capture Dissociation Spectrum of a Protein

A conventional electron capture dissociation (ECD) spectrum of a protein is uniquely characteristic of the first dimension of its linear structure. This sequence information is indicated by summing the primary c ^m+ and z ^m+? products of cleavage at each of its molecular ion’s inter-residue bonds. For example, the ECD spectra of ubiquitin (M?+?nH)ⁿ⁺ ions, n?=?7–13, provide sequence characterization of 72 of its 75 cleavage sites from 1843 ions in seven c ^(1–7)+ and eight z ^(1–8)+? spectra and their respective complements. Now we find that each of these c/z spectra is itself composed of “charge site (CS)” spectra, the c ^m+ or z ^m+? products of electron capture at a specific protonated basic residue. This charge site has been H-bonded to multiple other residues, producing multiple precursor ion forms; ECD at these residues yields the multiple products of that CS spectrum. Closely similar CS spectra are often formed from a range of charge states of ubiquitin and KIX ions; this indicates a common secondary conformation, but not the conventional α-helicity postulated previously. CS spectra should provide new capabilities for comparing regional conformations of gaseous protein ions and delineating ECD fragmentation pathways.

Fragmentation by electron impact ionization and intracluster reactions of size selected (N2H4) n and (OCS) n clusters

The hydrogen-bonded (N₂H₄) _n clusters and the van der Waals (OCS) _n clusters are size selected in a scattering experiment with a He beam up to the cluster sizen=6. By measuring the angular distributions of the scattered clusters the complete fragmentation pattern of electron impact ionization is obtained. For Hydrazine the two main fragment masses are the protonated species (N₂H₄) _n?1H⁺ and with somewhat weaker intensities also the nominal ion mass (N₂H₄) _n ⁺ . The largest intensity is observed for the monomer ion N₂H ₄ ⁺ to which clusters up ton=5 fragment. For carbonylsulfide, completely different results are obtained. Aside from the fragments of the OCS monomer and the van der Waals cluster fragments (OCS) ₂ ⁺ and (OCS) ₃ ⁺ signals at mass S ₂ ⁺ , S ₃ ⁺ and S₂OCS⁺ are detected. This indicates a fast chemical reaction in the cluster according to: S + OCS → CO + S₂ which occurs for clusters of sizen ≥ 2. Peaks at S ₃ ⁺ and S₂OCS⁺ are seen for the first time forn ≥ 5 according to a further reaction of S₂ in the cluster.     

A diatomics-in-molecules model for singly ionized neon clusters

A minimum-basis diatomics-in-molecules (DIM) model previously developed for singly-ionized argon clusters is applied to neon clusters, Ne _n ⁺ , forn=3, 4,...,22. A search for the global minimum energy of each cluster yields structures with the positive charge localised on a dimer-ion. This appears to be due largely to the linear unsymmetrical configuration which the model finds for Ne ₃ ⁺ . For this reason, the structures of the clusters at their minimum energy are different from those for Ar _n ⁺ computed with the same model. On the other hand, the behaviour of the charge distribution as a function of the geometrical configuration is similar to that for Ar _n ⁺ , as are the overall shapes of the potential energy surfaces. The results are discussed in terms of the charge distributions and the ratios of equilibrium properties of the dimers and dimer-ions which constitute the input to the model.     

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.

Metastable decay of rare gas cluster ions: mechanism and kinetics

Metastable decay of cluster ions has been discovered only recently. It was noted that one has to take this metastable decay into account when using mass spectrometry to probe neutral clusters, because ion abundance anomalies in mass spectra of rare gas and molecular clusters are caused by delayed metastable evaporation of monomers following ion production. Moreover, it was found that(i) the individual metastable reaction rates k depend strongly on cluster size and cluster ion production pathways and that(ii) there exists experimental evidence (k=k(t)) and a theoretical prediction that a given mass selected cluster ion generated by electron impact ionization of a nozzle expansion beam will comprise a range of metastable decay rates. In addition, it was discovered that metastable Ar cluster ions which lose two monomers in the μs time regime decay via sequential decay series Ar _n ⁺ *→Ar _n?1 ⁺ *→Ar _n?2 ⁺ * with cluster sizes 7≤n≤10 andn=3 (similar results were obtained recently in case of N₂ cluster ions). Conversely, the dominant metastable decay channel of Ar ₄ ⁺ * into Ar ₂ ⁺ was found to proceed predominantly via a single step fissioning process.     

High-mass cluster ions of ionic liquids in positive-ion and negative-ion DART-MS and their application for wide-range mass calibrations

Eight ionic liquids (ILs) are subjected to both positive-ion and negative-ion direct analyses in real time (DART) Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry (MS). First, their ability to deliver evenly distributed cluster ion series covering a wide m/z range is explored. Then, one of the ILs exhibiting particularly useful cluster ion series in either ion polarity is applied for mass calibration. Using 1-butyl-3-methylimidazolium tricyanomethide delivers positive cluster ions suitable for mass calibration in the m/z 100–4,000 range and covers the m/z 100–2,000 range in negative-ion DART-MS. The corresponding mass reference lists are provided for either polarity. Furthermore, based on 1-butyl-3-methylimidazolium tricyanomethide, a high-mass record of m/z?>?5,000 for positive-ion DART-MS is presented. The mass calibration procedure is finally validated by application to established standard compounds such as polydimethylsiloxanes, perfluorononanoic acid, and Ultramark 1621, a mixture of hexakis (fluoroalkoxy) phosphazenes. Further proof is presented by consistent exact mass differences between adjacent cluster ions.

More Than Charged Base Loss — Revisiting the Fragmentation of Highly Charged Oligonucleotides

Tandem mass spectrometry is a well-established analytical tool for rapid and reliable characterization of oligonucleotides (ONs) and their gas-phase dissociation channels. The fragmentation mechanisms of native and modified nucleic acids upon different mass spectrometric activation techniques have been studied extensively, resulting in a comprehensive catalogue of backbone fragments. In this study, the fragmentation behavior of highly charged oligodeoxynucleotides (ODNs) comprising up to 15 nucleobases was investigated. It was found that ODNs exhibiting a charge level (ratio of the actual to the total possible charge) of 100% follow significantly altered dissociation pathways compared with low or medium charge levels if a terminal pyrimidine base (3' or 5') is present. The corresponding product ion spectra gave evidence for the extensive loss of a cyanate anion (NCO^–), which frequently coincided with the abstraction of water from the 3'- and 5'-end in the presence of a 3'- and 5'-terminal pyrimidine nucleobase, respectively. Subsequent fragmentation of the M-NCO^– ion by MS³ revealed a so far unreported consecutive excision of a metaphosphate (PO₃ ^–)-ion for the investigated sequences. Introduction of a phosphorothioate group allowed pinpointing of PO₃ ^– loss to the ultimate phosphate group. Several dissociation mechanisms for the release of NCO^– and a metaphosphate ion were proposed and the validity of each mechanism was evaluated by the analysis of backbone- or sugar-modified ONs.

The Collision Cross Sections of Iodide Salt Cluster Ions in Air via Differential Mobility Analysis-Mass Spectrometry

To date, most collision cross section (CCS) predictions have invoked gas molecule impingement-reemission rules in which specular and elastic scattering of spherical gas molecules from rigid polyatomic surfaces are assumed. Although such predictions have been shown to agree well with CCSs measured in helium bath gas, a number of studies reveal that these predictions do not agree with CCSs for ions in diatomic gases, namely, air and molecular nitrogen. To further examine the validity of specular-elastic versus diffuse-inelastic scattering models, we measured the CCSs of positively charged metal iodide cluster ions of the form [MI]_n[M⁺]_z, where M?=?Na, K, Rb, or Cs, n?=?1 – 25, and z?=?1 – 2. Measurements were made in air via differential mobility analysis mass spectrometry (DMA-MS). The CCSs measured are compared with specular-elastic as well as diffuse-inelastic scattering model predictions with candidate ion structures determined from density functional theory. It is found that predictions from diffuse-inelastic collision models agree well (within 5 %) with measurements from sodium iodide cluster ions, while specular-elastic collision model predictions are in better agreement with cesium iodide cluster ion measurements. The agreement with diffuse-inelastic and specular-elastic predictions decreases and increases, respectively, with increasing cation mass. However, even when diffuse-inelastic cluster ion predictions disagree with measurements, the disagreement is of a near-constant factor for all ions, indicating that a simple linear rescaling collapses predictions to measurements. Conversely, rescaling cannot be used to collapse specular-elastic predictions to measurements; hence, although the precise impingement reemission rules remain ambiguous, they are not specular-elastic.

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.

Gas-Phase Fragmentations of Anions Derived from N-Phenyl Benzenesulfonamides

In addition to the well-known SO₂ loss, there are several additional fragmentation pathways that gas-phase anions derived from N-phenyl benzenesulfonamides and its derivatives undergo upon collisional activation. For example, N-phenyl benzenesulfonamide fragments to form an anilide anion (m/z 92) by a mechanism in which a hydrogen atom from the ortho position of the benzenesulfonamide moiety is specifically transferred to the charge center. Moreover, after the initial SO₂ elimination, the product ion formed undergoes primarily, an inter-annular H₂ loss to form a carbazolide anion (m/z 166) because the competing intra-annular H₂ loss is significantly less energetically favorable. Results from tandem mass spectrometric experiments conducted with deuterium-labeled compounds confirmed that the inter-ring mechanism is the preferred pathway. Furthermore, N-phenyl benzenesulfonamide and its derivatives also undergo a phenyl radical loss to form a radical ion with a mass-to-charge ratio of 155, which is in violation of the so-called “even-electron rule.”

Formation of negatively-charged cluster ions in thermal energy collisions with state-selected rydberg atoms

Using crossed atomic, molecular cluster, and cw laser beams in conjunction with mass spectrometric ion detection, we have obtained for the first time results for electron transfer fromstate-selected Rydberg atoms to molecular clusters. We report negative ion mass spectra for (CO₂) _k ^? (4≦k≦25) and (O₂) _k ^? (1≦k≦13) cluster ions, resulting from collisions of Ar** (nd) Rydberg atoms (12≦n≦40) with (CO₂) _m and (O₂) _m clusters at relative velocities around 830 m/s, and, for comparison, positive ion mass spectra due to Ne(3s ³ P _{2, 0}) Penning ionization. For both CO ₂ ^? and O₂-clusters, the negative and the positive ion mass spectra are very different. For (CO₂) _k ^Emphasis>/? cluster ions, the mass spectra show distinct variations with principal quantum number of the Rydberg atom, corresponding to differentn-dependences of the effective rate constant for selected cluster ions, as measured relative to the knownn-dependence for SF ₆ ^? formation in collisions with SF₆. For (O₂) _k ^? cluster ions, on the other hand, the mass spectra are almost independent ofn with ion intensities, which clearly reflect their thermochemical stabilities (O ₄ ^? as dominant species).     

Multiple H 3 + fragment production in single collision of fast H n + clusters with He atoms

The production of H ₃ ⁺ ions resulting from single collisions of mass-selected ionic hydrogen clusters, H _n ⁺ (n=9, 25, 31), with helium at high velocity (1.55 times the Bohr velocity) has been studied. A strong double H ₃ ⁺ ion production resulting from one incident cluster is observed. Moreover, evidence for a triple H ₃ ⁺ fragment production is presented forn=25 and 31. Thus, in this energy range, the collision gives rise to multifragmentation processes. The formation of H ₃ ⁺ ions takes place in the fragmentation of the multicharged cluster resulting from the collision.     

Unblocking the Sink: Improved CID-Based Analysis of Phosphorylated Peptides by Enzymatic Removal of the Basic C-Terminal Residue

A one-step enzymatic reaction for improving the collision-induced dissociation (CID)-based tandem mass spectrometry (MS/MS) analysis of phosphorylated peptides in an ion trap is presented. Carboxypeptidase-B (CBP-B) was used to selectively remove C-terminal arginine or lysine residues from phosphorylated tryptic/Lys-C peptides prior to their MS/MS analysis by CID with a Paul-type ion trap. Removal of this basic C-terminal residue served to limit the extent of gas-phase neutral loss of phosphoric acid (H₃PO₄), favoring the formation of diagnostic b and y ions as determined by an increase in both the number and relative intensities of the sequence-specific product ions. Such differential fragmentation is particularly valuable when the H₃PO₄ elimination is so predominant that localizing the phosphorylation site on the peptide sequence is hindered. Improvement in the quality of tandem mass spectral data generated by CID upon CBP-B treatment resulted in greater confidence both in assignment of the phosphopeptide primary sequence and for pinpointing the site of phosphorylation. Higher Mascot ion scores were also generated, combined with lower expectation values and higher delta scores for improved confidence in site assignment; Ascore values also improved. These results are rationalized in accordance with the accepted mechanisms for the elimination of H₃PO₄ upon low energy CID and insights into the factors dictating the observed dissociation pathways are presented. We anticipate this approach will be of utility in the MS analysis of phosphorylated peptides, especially when alternative electron-driven fragmentation techniques are not available.

A DIM model for homogeneous noble gas ionic clusters

The method of diatomics-in-molecules (DIM) is applied to the calculation of the energy of the homogeneous noble-gas ionic clusters Ar _n ⁺ and Xe _n ⁺ forn=3, 4, ..., 22. The trimers are stable symmetric linear molecules exhibiting chemical binding, a result in agreement both with ab initio calculations and with previous DIM work. The clusters up ton=13 are best described as a trimer ion surrounded by neutrals, whereby the charge distribution changes slightly with increasingn. Both noble gases exhibit a special stability associated with the completion of the first shell of neutral atoms atn=13. Asn increases from 13 to 22, there is a greater delocalization of the positive charge, the central ion tending to become a linear tetramer, symmetric for Xe and unsymmetric for Ar. Energies of the excited electronic states are reported and the possibility of developing simpler DIM models for the clusters and for mixed noble gases is discussed.     

FTMS studies of sputtered metal cluster ions (IV): size-selective effects in the chemistry of Fe n + with NH3 and Pd n + with D2 or C2H4

Fe _n ⁺ and Pd _n ⁺ clusters up ton=19 andn=25, respectively, are produced in an external ion source by sputtering of the respective metal foils with Xe⁺ primary ions at 20 keV. They are transferred to the ICR cell of a home-built Fourier transform mass spectrometer, where they are thermalized to nearly room temperature and stored for several tens of seconds. During this time, their reactions with a gas leaked in at low level are studied. Thus in the presence of ammonia, most Fe _n ⁺ clusters react by simply adsorbing intact NH₃ molecules. Only Fe ₄ ⁺ ions show dehydrogenation/adsorption to Fe₄(NH) _m ⁺ intermediates (m=1, 2) that in a complex scheme go on adsorbing complete NH₃ units. To clarify the reaction scheme, one has to isolate each species in the ion cell, which often requires the ejection of ions very close in mass. This led to the development of a special isolation technique that avoids the use of isotopically pure metal samples. Pd _n ⁺ cluster ions (n=2...9) dehydrogenate C₂H₄ in general to yield Pd _n (C₂H₂)⁺, yet Pd ₆ ⁺ appear totally unreactive. Towards D₂, Pd ₇ ⁺ ions seem inert, whereas Pd ₈ ⁺ adsorb up to two molecules.     

Photofragmentation of mass resolved carbon cluster ions

The results of a detailed study of the photodissociation of carbon cluster ions, C ₃ ⁺ to C ₂₀ ⁺ , are presented and discussed. The experiments were performed using internally cold cluster ions derived from pulsed laser evaporation of a graphite target rod in a helium buffer gas followed by supersonic expansion. The mass selected clusters were photodissociated using 248 nm and 351 nm light from an excimer laser. Photofragment branching ratios, photodissociation cross sections and data on the laser fluence dependence of photodissociation are reported. For almost all initial clusters, C _n ⁺ , the dominant photodissociation pathway was observed to be loss of a C₃ unit to give a C _n?3 ⁺ ion. This observation is interpreted as indicating that dissociation occurs by a statistical unimolecular process rather than by direct photodissociation. The photodissociation was found to be linear with laser fluence forn>5 with 248 nm and 351 nm light; quadratic forn=5 for 248 nm and 351 nm; and linear forn=4 at 248 nm. Dissociation energies for the carbon cluster ions implied by these results are discussed. The photodissociation cross sections were found to change dramatically with cluster size and with the wavelength of the photodissociating light.     

Reactivity of positively charged cobalt cluster ions with CH4, N2, H2, C2H4, and C2H2

Reactivity of positively charged cobalt cluster ions (Co _n ⁺ ,n=2?22), produce by laser vaporization, with various gas samples (CH₄, N₂, H₂, C₂H₄, and C₂H₂) were systematically investigated by using a fast-flow reactor. The reactivity of Co _n ⁺ with the various gas samples is qualitatively consistent with the adsorption rate of the gas to cobalt metal surfaces. Co _n ⁺ highly reacts with C₂H₂ as characterized by the adsorption rate to metal surfaces, and it indicates no size dependence. In contrast, the reactions of Co _n ⁺ with the other gas samples indicate a similar cluster size dependence; atn=4, 5, and 10?15, Co _n ⁺ highly reacts. The difference can be explained by the amount of the activation energy for chemisorption reaction. Compared with neutral cobalt clusters, the size dependence is almost similar except for Co ₄ ⁺ and Co ₅ ⁺ . The reactivity enhancement of Co ₄ ⁺ and Co ₅ ⁺ indicates that the cobalt cluster ions are presumed to have an active site for chemisorption atn=4 and 5, induced by the influence of positive charge.