Tandem mobility mass spectrometry study of electrosprayed tetraheptyl ammonium bromide clusters

Multiply charged electrospray ions from concentrated solutions of Heptyl4N+Br- (designated A+B- hereafter) in formamide are analyzed mass spectrometrically (MS) following mobility selection in ambient air in a differential mobility analyzer (DMA). Most of the sharp mobility peaks seen are identified as (AB)(n)A+ clusters, with 0 < or = n < ot = 5. One anomalously abundant and mobile ion is identified as NH4+(AB)4. Six ions in the (AB)n(A+)2 series are also identified, completing and correcting earlier mobility data for singly and doubly charged ions up to masses of almost 9000 Da. The more mobile of two broad humps seen in the mobility spectrum includes m/z values approximately from 2500 up to 12,000 Da. It is formed primarily by multiply charged (AB)n(A+)z clusters with multiple ammonium bromide adducts. Because of overlapping of many peaks of different m/z and charge state z, only a few individual species can be identified by MS alone in this highly congested region. However, the spectral simplification brought about by mobility selection upstream of the MS reveals a series of broad modulations in m/z space, with all ions resolved in the second, third, ...sixth modulation being in charge states z = 2, 3, ...6, respectively. Extrapolation of this trend beyond the sixth wave fixes the ion charge state (in some cases up to z = 15) and mass (beyond m = 175,000 u). This wavy structure had been previously observed and explained in terms of ion evaporation kinetics from volatile drops, though without mass identification. All observations indicate that the clusters are formed as charged residues, but their charge state is fixed by the Iribarne-Thomson ion evaporation mechanism. Consequently, the measured curve of cluster diameter versus z yields the two parameters governing ion evaporation kinetics. Clusters with z > 1 and electrical mobility Z > 0.495 cm2/V/s are metastable and evaporate a singly charged cluster, probably (AB)2A+, between the DMA and the MS. Plotting the electrical mobilities Z of the clusters in the form (z/Z)1/2 versus m(1/3) (both proportional to cluster diameter) collapse the data for all cluster sizes and charge states into one single straight line for Z below 0.495 cm2/V/s. This linear relation reveals a uniform apparent cluster density of 0.935 g/cm3 and an effective hard-sphere diameter of the air molecules of 0.44 nm. An anomalous mobility increase is observed at diameters below 3 nm.     

Kinetics of small ion evaporation from the charge and mass distribution of multiply charged clusters in electrosprays

The distribution of charge z and radii R in clusters electrosprayed from formamide solutions of tetraheptylammonium bromide was investigated by selecting those within a narrow range of electrical mobilities Z(1) in a first differential mobility analyzer (DMA), reducing their charge to unity by passage through a neutralizing chamber containing a radioactive (alpha) source, and measuring the mobilities Z(z) of the resulting discrete set of singly charged clusters in a second DMA. After correcting for the polarization contribution to cluster drag, the tandem DMA data yield the range of radii present at detectable levels for each charge state up to z = 9. Because small ion evaporation from electrospray drops leads to charge loss when a drop reaches a certain critical radius R(crit)(z), the measured maximum and minimum cluster radii associated with a given z can be used to infer the activation energy Delta for ion evaporation as a function of drop charge and curvature. These results confirm the Iribarne-Thomson ion-evaporation mechanism, and support earlier theoretical expressions for the functional form of Delta(z,R). The different phenomenon of ion evaporation from metastable multiply charged dry clusters is also observed at characteristic times of 1 s. Its activation energy is estimated as approximately 0.3 eV larger than for ion evaporation from the drops. This new process complicates the interpretation of the present measurements in terms of ion evaporation from liquid surfaces, but introduces no radical change in the picture. It helps understand why salt clusters with more than two or three charges are harder to see in mass spectrometers than in mobility studies under ambient conditions. Copyright 2000 John Wiley & Sons, Ltd.     

Capillary electrophoresis--electrospray ionization--mass spectrometry for the characterization of natural organic matter: an evaluation with free flow electrophoresis-off-line flow injection electrospray ionization-mass spectrometry

The separation of Suwannee River natural organic matter (NOM) with capillary zone electrophoresis hyphenated to electrospray ionization-mass spectrometry (CZE-ESI-MS) is presented. The obtained electropherograms and signal distributions are comparable to the mobility distributions obtained with more classical UV detection. A direct comparison of the results was possible with free-flow electrophoresis (FFE), which allows an upscaling of the CZE method and the analysis of the collected fractions in an off-line modus with flow-injection electrospray ionization-mass spectrometry (FI-ESI-MS). The changes of the m/z distributions with mobility are very similar with both methods and show a decrease of the m/z with increasing electrophoretic mobility in the humic hump at alkaline pH; superimposed on this hump a low-molecular-weight fraction migrates at lower mobility. The analysis of benzene carboxylic acids, glycerrhycic acid as well as oligomers of polystyrene sulfonic acid and polyacrylic acid additionally illustrates possible fragmentation, formation of adducts and multiplicity of the charges of the molecules prior to MS detection. These hardly controllable difficulties add a challenge to the interpretation of the obtained m/z distributions of NOM in terms of charge and mass distributions of molecules present in the NOM mixture.     

Impact ionisation spectra from hypervelocity impacts using aliphatic poly(methyl methacrylate) microparticle projectiles

We report impact ionisation spectra from spherical poly(methyl methacrylate) (PMMA) microparticles of 724 nm diameter impacting a rhodium target. These projectiles were coated with an ultrathin (~11 nm) overlayer of polypyrrole, an electrically conducting organic polymer; this enabled the accumulation of sufficient surface charge to allow electrostatic acceleration up to speeds of 4 to 8 km s(-1) using a high-voltage Van de Graaff instrument. A grid above the target (held at 3.33 kV cm(-1) with respect to the target) accelerated the cations that were generated during the hypervelocity impacts, and these ions then drifted to a charge detector. By measuring the collected charge vs. time and assuming only single ionisation events, time-of-flight mass spectra were obtained. Strong signals were observed for cationic species with ions of m/z 41, 65 and 115. There were also minor contributions from cations with masses ranging from m/z 29 to 142. The three major signals are assigned to fragment ions (C(3)H(5)(+), C(4)H(5)O(+)/C(5)H(9)(+) and C(6)H(11)O(2)(+)) which are known to be associated with the decomposition of PMMA. These impact ionisation spectra differ significantly from those reported earlier using polystyrene (PS) microparticles. The aliphatic PMMA microparticles generate small (m/z <100) fragment ions more readily at lower speeds than the predominantly aromatic PS microparticles, where speeds of at least 10 km s(-1) are typically required for substantial yields of low-mass fragment ions. This correlates well with the well-known greater chemical and thermal fragility of PMMA compared to PS. The PMMA microparticles should prove useful synthetic mimics for aliphatic carbonaceous micrometeorites.     

Programmable gate delayed ion mobility spectrometry-mass spectrometry: a study with low concentrations of dipropylene-glycol-monomethyl-ether in air

The concept of using a short ionisation event, in this case a pulsed corona discharge, in conjunction with programmed gate delay is described. This technique is proposed for the selective study of different ionisation processes within the reaction region of an ion mobility spectrometer. The utility of such an approach was tested in a study of the ionisation of dipropylene-glycol-monomethyl-ether (DPM); a compound commonly used to test the operation of ion mobility spectrometers. Dipropylene-glycol-monomethyl-ether at a concentration of 113 microg m(-3) in air, with a water level of 75 mg m(-3) in air, was analysed using a switchable, high resolution ion mobility spectrometer, operating in the positive mode at 40 degrees C at ambient pressure. The ion mobility spectrometer was fitted with a pulsed corona discharge ionisation source, doped with ammonia at a concentration of 1.3 mg m(-3) in the reaction region, and interfaced to a mass spectrometer. Synchronisation of the ionisation event to the operation of the shutter grids for the drift region enabled different parts of the product ion population to be injected into the drift tube, and programming the gate delays produced a map of the gate delay verses drift time response surface. Ammonium bound dipropylene-glycol-monomethyl-ether was observed, [(DPM)NH4]+ (m/z 166) as well as the ammonium bound dimer [(DPM)2NH4]+ (m/z 314), the same as those observed with a 63Ni source. Two other species were also observed, but their molecular identity was not elucidated. One of them m/z 146, also observed with 63Ni, formed ammonium bound ions [(m/z 146)NH4]+ (K0= 1.49 cm2 V(-1) s(-1)), ammonium bound dimer ions [(m/z 146)2NH4]+(K0= 1.18 cm2 V(-1) s(-1)) and a mixed cluster ion with DPM [(m/z 146)(DPM)NH4]+(K0= 1.18 cm2 V(-1) s(-1)); while the other, m/z 88 a decomposition product, formed ammonium bound monomer [(m/z 88)NH4]+(K0= 1.68 cm2 V(-1) s(-1)), dimer ions [(m/z 88)2NH4]+(K0= 1.40 cm2 V(-1) s(-1)) and a mixed cluster ion containing DPM and ammonium, [(DPM)(m/z 88)2NH4]+(K0= 1.40 cm2 V(-1) s(-1)). The assignment of responses to these ions required the additional dimensionality in the data provided from the gate delay studies. The relationships evident in the programmable gate delay data enabled these ions to be differentiated from alternative assignments of possible nitrogen clusters, formed at the interface of the mass spectrometer.     

The analysis of polystyrene and polystyrene aggregates into the mega dalton mass range by cryodetection MALDI TOF MS

Mass spectra of atactic polystyrene were collected into the mega-dalton mass range with a matrix-assisted laser desorption ionization time of flight (MALDI TOF) mass spectrometer, which incorporates a cryodetector comprised of an array of 16 superconducting tunnel junctions (STJ). The STJ cryodetector, theoretically, has no loss in signal response at any mass compared with the reduced signal found at high mass when using a conventional secondary-ionization detector. Since ion detection at high m/z is one of the fundamental limitations of mass spectrometry (MS), the cryodetector was used to explore the high m/z limit of the MALDI TOF technique for the analysis of two polymer types. Mass spectra were collected for polystyrene at Mn 170, 400, 900, and 2000 kDa and polymethyl methacrylate (PMMA) at Mn 62.6 kDa and 153.7 kDa. For polystyrene, the data showed a trend toward increased aggregation and charge state with mass. The Mn 2 MDa polystyrene data revealed a peak at m/z 2.2 MegaTh and a charge state analysis revealed that these ions were primarily polystyrene aggregates with a mass of approximately 4 MDa. This aggregate assignment was possible because the cryodetector response allows for the determination of a charge state up to about four. The contribution of each charge state for a selected peak can be determined in this fashion. This analysis revealed the preferential formation of doubly charged even-numbered aggregates over odd-numbered aggregates for high molecular mass polystyrene. A potential mechanism for the aggregation process for doubly charged species is discussed.     

Translational to vibrational energy conversion during surface-induced dissociation of n-butylbenzene molecular ions colliding at self-assembled monolayer surfaces

Translational to vibrational (T-->V) energy conversion in the course of inelastic collisions of n-butylbenzene molecular ions with thiolate self-assembled monolayer (SAM) gold surfaces is studied to better understand internal energy uptake by the hyperthermal projectile ions. The projectile ion is selected by a mass spectrometer of BE configuration and product ions are analyzed using a quadrupole mass analyzer after kinetic energy selection with an electric sector. The branching ratio for formation of the fragment ions m/z 91 and m/z 92, measured over a range of collision energies, is used to estimate the average internal energy with the aid of calculations based on unimolecular dissociation kinetics [Rice-Ramsperger-Kassel-Marcus (RRKM) theory]. The measured T-->V conversion efficiencies (the fraction of the laboratory kinetic energy converted into internal energy) are 11 approximately 12% for dodecanethiolate SAM (H-SAM) and 19 approximately 20% for 2-perfluorooctylethanethiolate SAM (F-SAM), respectively, over ranges of a few 10s of eV. The values are similar to those reported earlier for other thermometer molecules undergoing surface collisions. Chemical sputtering leading to ionization of the surface is a prominent feature of the surface-induced dissociation (SID) spectra of n-butylbenzene acquired using the H-SAM surface but not the F-SAM surface because of the lower ionization energy of the former.     

Improved sensitivity and mass range in time-of-flight bioaerosol mass spectrometry using an electrostatic ion guide

Bioearosol mass spectrometry (BAMS) analyzes single particles in real time from ambient air, placing strict demands on instrument sensitivity. Modeling of the BAMS reflectron time of flight (TOF) with SIMION revealed design limitations associated with ion transmission and instrument sensitivity at higher masses. Design and implementation of a BAMS linear TOF with electrostatic ion guide and delayed extraction capabilities has greatly increased the sensitivity and mass range relative to the reflectron design. Initial experimental assessment of the new instrument design revealed improved sensitivity at high masses as illustrated when using standard particles of cytochrome C (m/z approximately 12,000), from which the compound's monomer, dimer (m/z approximately 24,000) and trimer (m/z approximately 36,000) were readily detected.     

Paper spray ionization with ion mobility spectrometry at ambient pressure

A paper spray ion source was combined with a drift tube operating at ambient pressure for mobility measurements of ions derived from pharmaceutical solutions. Paper spray ionization with solvent alone resulted in a mixture of ions convolved to a single peak with a reduced mobility of 2.19 cm²/Vs in the mobility spectrum. These were mass-identified principally as m/z 157, (MeOH)₂(HCOOH)₂H⁺ and m/z 129, (MeOH)₄(H₂O)H⁺ while pharmaceuticals with nitrogen bases formed MH⁺ product ions. The duration of response was governed by the volume of liquid added to the paper source and was limited by evaporation of solvent in gas at 58 °C venting the drift tube. Quantitative variation was attributed in part to morphologic changes in the tip of the paper spray source. This was associated with mass flow in the electrical discharge and not due alone to cycles of wetting and drying of the paper. Mobility spectra of chlorpromazine in urine, exhibited a single product ion peak and linear response was 30 to 500 ng with an estimated limit of detection of 1.5 ng. Ion flux could be prolonged by continuous addition of liquid and findings portend a combination of paper spray ionization IMS with paper chromatography.     

Effect of protein stabilization on charge state distribution in positive- and negative-ion electrospray ionization mass spectra

Changes in protein conformation are thought to alter charge state distributions observed in electrospray ionization mass spectra (ESI-MS) of proteins. In most cases, this has been demonstrated by unfolding proteins through acidification of the solution. This methodology changes the properties of the solvent so that changes in the ESI-MS charge envelopes from conformational changes are difficult to separate from the effects of changing solvent on the ionization process. A novel strategy is presented enabling comparison of ESI mass spectra of a folded and partially unfolded protein of the same amino acid sequence subjected to the same experimental protocols and conditions. The N-terminal domain of the Escherichia coli DnaB protein was cyclized by in vivo formation of an amide bond between its N- and C-termini. The properties of this stabilized protein were compared with its linear counterpart. When the linear form was unfolded by decreasing pH, a charge envelope at lower m/z appeared consistent with the presence of a population of unfolded protein. This was observed in both positive-ion and negative-ion ESI mass spectra. Under the same conditions, this low m/z envelope was not present in the ESI mass spectrum of the stable cyclized form. The effects of changing the desolvation temperature in the ionization source of the Q-TOF mass spectrometer were also investigated. Increasing the desolvation temperature had little effect on positive-ion ESI mass spectra, but in negative-ion spectra, a charge envelope at lower m/z appeared, consistent with an increase in the abundance of unfolded protein molecules.     

Photofragmentation of Isoleucine by Vacuum Ultraviolet Photoionization

Vacuum ultraviolet photon-induced ionization and dissociation of isoleucine are investi-gated with synchrotron radiation photoionization mass spectroscopy and theoretical cal-culations. The main fragment ions at m/z=86, 75, 74, 69, 57, 46, 45, 44, 41, 30, 28, and 18 from isoleucine are observed in the mass spectrum at the photon energy of 13 eV. From the photoionization e±ciency curves, appearance energies for the principal fragment ions C₅H₁₂N⁺ (m/z=86)、C₂H₅NO₄⁺ (m/z=75)、C₅H₉⁺ (m/z=69)、C₄H₉⁺(m/z=57), and CH₄N⁺(m/z=30) are determined to be 8.84±0.07, 9.25±0.06, 10.20±0.12, 9.25±0.10, and 11.05±0.07 eV, respectively, and possible formation pathways are established in detail by the calculations at the B3LYP/6-31++G(d, p) levels. These proposed channels include simple bond cleavage reactions as well as reactions involving intermediates and transition structures. The experimental and computational appearance energies or barriers are in good agreement.     

Ion mobility augments the utility of mass spectrometry in the identification of human hemoglobin variants

The global dispersion of hemoglobin variants through population migration has precipitated a need for their identification. A particularly effective mass spectrometry (MS)-based procedure involves analysis of the intact globin chains in diluted blood to detect the variant through mass anomalies, followed by location of the variant amino acid residue by direct analysis of the enzymatically digested globins. Here we demonstrate the use of ion mobility separation in combination with this MS procedure to reduce mass spectral complexity. In one example, the doubly charged tryptic peptide from a low abundance variant (4%) occurred at the same m/z value as a singly and a doubly charged interfering ion. In another example, the singly charged tryptic peptide from an alpha-chain variant (26%) occurred at the same m/z value as a doubly charged interfering ion. Ion mobility was used to separate the variant ions from the interfering ions, thus allowing the variant peptides to be observed and sequenced by tandem mass spectrometry.     

Radial stratification of ions as a function of mass to charge ratio in collisional cooling radio frequency multipoles used as ion guides or ion traps

Collisional cooling in radio frequency (RF) ion guides has been used in mass spectrometry as an intermediate step during the transport of ions from high pressure regions of an ion source into high vacuum regions of a mass analyzer. Such collisional cooling devices are also increasingly used as 'linear', two-dimensional (2D) ion traps for ion storage and accumulation to achieve improved sensitivity and dynamic range. We have used the effective potential approach to study m/z dependent distribution of ions in the devices. Relationships obtained for the ideal 2D multipole demonstrate that after cooling the ion cloud forms concentric cylindrical layers, each of them composed of ions having the same m/z ratio; the higher the m/z, the larger is the radial position occupied by the ions. This behavior results from the fact that the effective RF focusing is stronger for ions of lower m/z, pushing these ions closer to the axis. Radial boundaries of the layers are more distinct for multiply charged ions, compared to singly charged ions having the same m/z and charge density. In the case of sufficiently high ion density and low ion kinetic energy, we show that each m/z layer is separated from its nearest neighbor by a radial gap of low ion density. The radial gaps of low ion population between the layers are formed due to the space charge repulsion. Conditions for establishing the m/z stratified structure include sufficiently high charge density and adequate collisional relaxation. These conditions are likely to occur in collisional RF multipoles operated as ion guides or 2D ion traps for external ion accumulation. When linear ion density increases, the maximum ion cloud radius also increases, and outer layers of high m/z ions approach the multipole rods and may be ejected. This 'overfilling' of the multipole capacity results in a strong discrimination against high m/z ions. A relationship is reported for the maximum linear ion density of a multipole that is not overfilled.     

Protein desolvation in UV matrix-assisted laser desorption/ionization (MALDI)

We describe experiments in MALDI-TOF and MALDI-TOF-TOF showing that the ejection of protein-matrix cluster ions and their partial decay in the source occur in MALDI. The use of radial beam deflection and small size detector in linear mode allows detection of ions with higher time-of-flight and kinetic energy deficit. MALDI-TOF-TOF experiments were carried out by selecting chemical noise ions at m/z higher than that of a free peptide ion. Whatever the selected m/z (up to m/z 300) the molecular peptide ion appeared as the main fragment. The production of protein-matrix clusters and their partial decay in the source was found to increase with the size of the protein (MW from 1000 to 150,000 u), although it decreases with increasing charge state. These effects were observed for different matrices (HCCA and SA) and in a large laser fluence range. Experimental results and calculation highlight that a continuous decay of protein-matrix cluster ions occurs in the source. This decay-desolvation process can account for the high-mass tailing and peak shifting as well as the strong noise/background in the mass spectra of proteins.     

Observation of Na(+)-bound oligomers of quercetin in the gas phase

While developing a liquid chromatography/tandem mass spectrometry method for the analysis of the flavonoid quercitin, it was observed that quercetin (3,3',4',5,7-pentahydroxyflavone) exhibited clustering in both the positive and negative ion mode. Two series of positive ion clusters were observed; the first series corresponds to singly charged [2M + Na](+) at m/z 627.2 to [13M + Na](+) at m/z 3947.5, while the second series corresponds to doubly charged [7M + 2Na](2+) at m/z 1080.4 to [25M + 2Na](2+) at m/z 3798.5. In the negative ion mode, the behavior of quercetin parallels that of apigenin (4',5,7-trihydroxyflavone) in that [M + NO(3)](-), [2M + NO(3)](-), and [3M + NO(3)](-) were observed at m/z 364.1, 666.0, and 968.9, respectively; in addition, quercitin clusters with chloride ions ([2M + Cl](-) at m/z 638.9 and [3M + Cl](-) at m/z 940. 9) were observed. The results of tandem mass spectrometric examination of several cluster ions are reported.     

Two-dimensional separations with electrospray ionization ambient pressure high-resolution ion mobility spectrometry/quadrupole mass spectrometry

The coupling of ion mobility spectrometry (IMS) instruments with mass spectrometers has been described since early in IMS development, most commonly with quadrupole mass analyzers. The recent development of IMS with time-of-flight (TOF) instruments has demonstrated that the time compatibility (IMS milliseconds and TOFMS microseconds) of the two techniques enables rapid two-dimensional separations to be performed, theoretically in the order of seconds for a complete analysis. This study presents a unique way to operate a traditional IMS/QMS system to attain separations similar to those achieved with IMS/TOF. For this new approach, the quadrupole was slowly scanned in the single-ion monitoring mode while IMS spectra were continually embedded in each m/z step. In this way, two-dimensional separations (IMS drift times and m/z) were obtained using the traditional IMS/QMS arrangement. An example of a five amino acid separation (quadrupole scan of 40 m/z values at a rate of approximately 7 steps/min) led to a complete two-dimensional analysis within 6 min, comparable to rapid chromatographic separations with mass spectrometry. Proposed approaches to reduce the analysis time are discussed and a reduction in the analysis time to less than 1 min is feasible when the IMS/QMS separation conditions are optimized.     

Temporal evolution of an electron-free afterglow in the pulsed plasma polymerisation of acrylic acid

By use of time and energy-resolved mass spectrometry, negative ions with masses ranging from m/z = 1-287 amu have been observed in the afterglow of a low-pressure (10 mTorr) pulsed acrylic acid polymerizing plasma. The most intense peaks, seen at m/z = 71, 143, 215, and 287, are assigned to the dehydrogenated oligomer of the form [nM-H](-) for n = 1, 2, 3, and 4, respectively. The results strongly suggest that both m/z = 71 and 143 ions are produced in the on period of the pulse cycle (0.1 ms duration), with higher masses m/z = 215 and 287 being produced by neutral ion chemistry in the off period (up to 40 ms in duration). The increase in the intensity of the [3M-H](-) and [4M-H](-) peaks in the off period is accompanied by a rapid fall in the concentration of [M-H]- ions and electrons, the latter decreasing from approximately 10(15) m(-3) to zero within 150 micros. Deep into the afterglow, Langmuir probe measurements show that the charge species only consist of positive and negative ions, present at equal concentrations in excess of approximately 10(14) m(-3) even after 10 ms that is, the plasma is wholly electron free. To describe the growth of large negative ions a number of possible ion-neutral chemical pathways have been postulated, and a calculation of the ambipolar diffusion rates to the walls suggests that, in the off period, the positive and negative ion contribution to the deposition rate is small ( approximately 1%) compared to the net total deposition rate. However, the observations do indicate that it may be necessary to update models of film growth in the pulsed plasma polymerization of acrylic acid to account for negative ions.     

Combining low and high mass ion accumulation for enhancing shotgun proteome analysis by accurate mass measurement

A simple procedure is described that increases sensitivity and dynamic range for the analysis of a proteome batch digest by FT-ICR mass spectrometry. Ions at the low and high mass ranges are preferentially collected using two different sets of tuning conditions. By combing data collected using tuning conditions that favor low mass (m/z < 2000) and high mass (m/z > 2000) ions, 277 proteins are identified for a whole cell lysate of Methanococcus maripaludis in a single HPLC-MALDI FT-ICR mass spectrometry experiment, a 70% improvement compared with previous analyses using a wide mass range acquisition. This procedure improves the detection of low abundance ions and thereby increases the range of proteins that are observed. Because the observed mass range is effectively narrower for each spectrum, mass calibration is more accurate than for the standard method that provides a wide range of masses. The trap plate potential on the analyzer cell may be set to a higher value than used for wide mass range measurements, increasing the ion capacity of the analyzer cell and extending the dynamic range, while still maintaining mass accuracy.     

Strategies for determination of insulin with tandem electrospray mass spectrometry: implications for other analyte proteins?

Using human insulin (MW 5808 Da) as a model compound, the possible strategies towards optimization of sensitivity and selectivity of measurement by electrospray ionization with a standard triple quadrupole mass spectrometer were investigated. For measurement in selected ion-monitoring (SIM) mode, these strategies involved systematic variation of instrumental parameters and spray pH. In this investigation four different operating modes were used corresponding to positive/negative ionization modes with acidic/basic sprays and pH reversed (hereafter termed 'wrong-way-round' operation); the cone voltage was optimized for each mode of operation. When collision-activated dissociation (CAD) is employed, two additional operation modes are possible: namely, low collision energies (10-35 eV, CAD-l) for the generation of sequence-specific fragments and high collision energies (>80 eV, CAD-h) for the generation of nonspecific fragments. Overall, this results in twelve different modes of operation. Loop-injection of aqueous insulin standards were run for each of the twelve operating modes and measurements made for five different charge states (n = 2-6) observable with our instrument that has an upper mass limit of m/z 4000. The signal/noise (S/N) ratio was optimized for each charge state, resulting in 60 measurements. The best S/N ratios (20 000) were achieved under positive SIM conditions with charge state 6 (m/z 969) and under 'wrong-way-round' negative SIM conditions with charge state 3 (m/z 1935). Lower S/N ratios were observed under positive CAD-h conditions with charge state 5 (m/z 1163, S/N 15 000) and positive CAD-l conditions with charge state 6 (m/z 969, S/N 10 000). All other operating modes gave maximum S/N ratios of 4000. For measurement of insulin standards, the results obtained show SIM to give the best S/N ratio. However, for samples in complex matrices, our general experience suggests CAD to be the preferable operating mode. Consequently, for the development of a quantitative method for proteins in general, it might be advocated that all of the twelve operating modes and all relevant charge states be investigated to find the optimum S/N ratio.     

COMPLX: a computer algorithm for the detection of protein-ligand and other macromolecular complexes in mass spectra

A new algorithm has been designed and tested to identify protein, or any other macromolecular, complexes that have been widely reported in mass spectral data. The program takes advantage of the appearance of multiply charged ions that are common to both electrospray ionization and, to a lesser extent, matrix-assisted laser desorption/ionization (MALDI) mass spectra. The algorithm, known as COMPLX for the COMposition of Protein-Ligand compleXes, is capable of identifying complexes for any protein or macromolecule with a binding partner of molecular mass up to 100 000 Da. It does so by identifying ion pairs present in a mass spectrum that, when they share a common charge, have an m/z value difference that is an integer fraction of a ligand or binding partner molecular mass. Several additional criteria must be met in order for the result to be ranked in the output file including that all m/z values for ions of the protein or complex have progressively lower values as their assigned charge increases, the difference between the m/z values for adjacent charge states (z, z + 1) decrease as the assigned charge state increases, and the ratio of any two m/z values assigned to a protein or complex is equal to the inverse ratio of their charge. The entries that satisfy these criteria are then ranked according to the appearance of ions in the mass spectrum associated with the binding partner, the length of a continuous series of charges across any set of ions for a protein and complex and the lowest error recorded for the molecular mass of the ligand or binding partner. A diverse range of hypothetical and experimental mass spectral data were used to implement and test the program, including those recorded for antibody-peptide, protein-peptide and protein-heme complexes. Spectra of increasing complexity, in terms of the number of ions input, were also successfully analysed in which the number of input m/z values far exceeds the few associated with a macromolecular complex. Thus the program will be of value in a future goal of proteomics, where mass spectrometry already plays a central role, for the direct analysis of protein and other associations within biological extracts.