Analysis of saturated hydrocarbons by using chemical ionization combined with laser-induced acoustic desorption/Fourier transform ion cyclotron resonance mass spectrometry

Laser-induced acoustic desorption (LIAD), combined with chemical ionization by the cyclopentadienyl cobalt radical cation (CpCo.+), is demonstrated to facilitate the analysis of saturated hydrocarbons by Fourier transform ion cyclotron resonance mass spectrometry. The LIAD/CpCo.+ method produces unique pseudomolecular ions for alkanes from C(24)H(50) to C(50)H(102). These alkanes were tested individually and in artificial mixtures of up to seven components. Only one product ion, [R + CpCo - 2H(2)].+, was detected for each alkane (R). The product ions' relative abundances correspond to the relative molar concentration of each alkane in mixtures. These findings provide a solid groundwork for the future application of this method for hydrocarbon polymer analyses.     

FTMS structure elucidation of natural products: application to muraymycin antibiotics using ESI multi-CHEF SORI-CID FTMS(n), the top-down/bottom-up approach,and HPLC ESI capillary-skimmer CID FTMS

The molecular formulas for the structures and substructures of muraymycin antibiotics A1 (C52H90N14O19, MW 1214) and B1 (C49H83N11O18, MW 1113) were determined using electrospray ionization (ESI) Fourier transform mass spectrometry (FTMS). The muraymycin A1 and B1 structures were elucidated by utilizing capillary-skimmer fragmentation with up to five stages of mass spectrometry (MS5). Multi-CHEF, a multiple ion isolation method, was used at each stage of MS(n) to isolate a parent ion and up to four reference ions, for exact-mass calibration. The parent ions were fragmented by SORI-CID and the product ions internally calibrated with average absolute mass errors less than 1 ppm at each stage in the fragmentation processes. Using the top-down/bottom-up approach, the molecular formulas for the antibiotics were determined by summing the elemental formulas of the neutral losses, obtained by measuring the mass differences (<500 Da) between the genetically related sequential parent ion masses in the MS(n) spectra, with the unique elemental formula of the lowest parent ion mass (<500 Da). The structures of 12 additional compounds in the muraymycin complex were elucidated using HPLC ESI capillary-skimmer CID FTMS by correlating their fragmentation patterns with those of muraymycins A1 and B1. Sequential neutral losses of an aminosugar, a valine, a uridine, and an ester fatty acid from the muraymycin parent ions provided diagnostic fragments for characterization.     

Multiple ionization mass spectrometry strategy used to reveal the complexity of metabolomics

A multiple ionization mass spectrometry strategy is presented based on the analysis of human serum extracts. Chromatographic separation was interfaced inline with the atmospheric pressure ionization techniques electrospray ionization (ESI) and atmospheric pressure chemical ionization (APCI) in both positive (+) and negative (-) ionization modes. Furthermore, surface-based matrix-assisted laser desorption/ionization (MALDI) and desorption ionization on silicon (DIOS) mass spectrometry were also integrated with the separation through fraction collection and offline mass spectrometry. Processing of raw data using the XCMS software resulted in time-aligned ion features, which are defined as a unique m/z at a unique retention time. The ion feature lists obtained through LC-MS with ESI and APCI interfaces in both +/- ionization modes were compared, and unique ion tables were generated. Nonredundant, unique ion features, were defined as mass numbers for which no mass numbers corresponding to [M + H](+), [M - H](-), or [M + Na](+) were observed in the other ionization methods at the same retention time. Analysis of the extracted serum using ESI for both (+) and (-) ions resulted in >90% additional unique ions being detected in the (-) ESI mode. Complementing the ESI analysis with APCI resulted in an additional approximately 20% increase in unique ions. Finally, ESI/APCI ionization was combined with fraction collection and offline-MALDI and DIOS mass spectrometry. The parts of the total ion current chromatograms in the LC-MS acquired data corresponding to collected fractions were summed, and m/z lists were compiled and compared to the m/z lists obtained from the DIOS/MALDI spectra. It was observed that, for each fraction, DIOS accounted for approximately 50% of the unique ions detected. These results suggest that true global metabolomics will require multiple ionization technologies to address the inherent metabolite diversity and therefore the complexity in and of metabolomics studies.     

Laser-induced acoustic desorption/fourier transform ion cyclotron resonance mass spectrometry for petroleum distillate analysis

Laser-induced acoustic desorption (LIAD) coupled with a 3-T Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR) allows the simultaneous analysis of both the nonpolar and polar components in petroleum distillates. The LIAD/FT-ICR method was validated by examining model compounds representative of the various classes of polar and nonpolar hydrocarbons commonly found in petroleum. LIAD successfully desorbs all the compounds as intact neutral molecules into the FT-ICR. Electron ionization (EI) at low energies (10 eV) and chemical ionization using cyclopentadienyl cobalt radical cation (CpCo*+) were employed to ionize the desorbed molecules. The EI experiments lead to extensive fragmentation of many of the hydrocarbon compounds studied. However, the CpCo*+ ion ionizes all the hydrocarbon compounds by producing only pseudomolecular ions without other fragmentation, with the exception of one compound (*CH3 loss occurs). Examination of two different petroleum distillate samples revealed hundreds of compounds. The most abundant components have an even molecular weight; i.e., they are likely to contain no (or possibly an even number of) nitrogen atoms.     

Characterization of laser-induced acoustic desorption coupled with a Fourier transform ion cyclotron resonance mass spectrometer

Several experimental factors have been investigated that influence the efficiency of desorption and subsequent chemical ionization of nonvolatile, thermally labile molecules during laser-induced acoustic desorption/Fourier transform ion cyclotron resonance mass spectrometry (LIAD/FT-ICR) experiments. The experiments were performed by using two specially designed LIAD probes of different outer diameters (1/2 and 7/8 in.) and designs. Several improvements to the design of the "first generation" (1/2 in.) LIAD probe are presented. The larger diameter (7/8 in.) probe provides a larger surface area for desorption than the smaller diameter probe. Further, it was designed to desorb molecules on-axis with the magnetic field of the instrument. This is in contrast to the smaller probe for which desorption occurs 1.3 mm off-axis. This improved alignment, which provides better overlap between the desorbed molecules and trapped reagent ions, results in a substantial increase in the sensitivity of LIAD analyses. The thickness of the sample layer deposited on the irradiated metal foil and the number of laser shots fired on the backside of the foil were found to have a significant effect on the overall signal and the relative abundances of the ions formed in the experiment. Evaporation of a tetrapeptide, Val-Ala-Ala-Phe (VAAF), from Ag, Al, Au, Cu, Fe, and Ti foils, followed by protonation by protonated pyridine, revealed that the titanium foil provides the greatest signal. The importance of the laser power density was examined by desorbing a low MW polymer, polyisobutenyl succinic anhydride, at power densities ranging from 5.40 x 10(8) to 9.00 x 10(8) W/cm(2) at the backside of the foil. Higher laser power densities resulted in greater signals and an improved distribution for the higher molecular weight oligomers.     

Analysis of polyethylene by using cyclopentadienyl cobalt chemical ionization combined with laser-induced acoustic desorption/fourier transform ion cyclotron resonance mass spectrometry

A new mass spectrometric method has been developed for the analysis of low molecular weight polyethylene (PE). Laser-induced acoustic desorption (LIAD), combined with chemical ionization by the cyclopentadienyl cobalt radical cation (CpCo.+) in a Fourier transform ion cyclotron resonance mass spectrometer, produces predominantly a quasimolecular ion, (R + CpCo - 2H2).+, for each PE oligomer (R). An examination of artificial alkane mixtures revealed no mass bias for alkanes of differing molecular weights. However, the success of the LIAD/CpCo.+ CI technique depends greatly upon the LIAD sample preparation method used. Several sample preparation methods were evaluated, and pneumatically assisted spin coating was concluded to provide the best mass spectra as a result of its ability to provide uniform PE coverage on the LIAD foils. The molecular weight distributions measured for several low molecular weight PE samples (200-655) were found to be in good agreement with manufacturers' values as determined by gel permeation chromatography.     

Laser desorption and matrix-assisted laser desorption/ionization mass spectrometry of 29-kDa Au:SR cluster compounds

Positive and negative ions generated by laser-based ionization methods from three gold:thiolate cluster compounds are mass analyzed by time-of-flight mass spectrometry. The three compounds have similar inorganic core masses ( approximately 29 kDa, approximately 145 Au atoms) but different n-alkanethiolate ligands associated with each cluster compound (Au:SR, R = butane, hexane, dodecane). Irradiation of neat films (laser desorption/ionization) and films generated by dilution of the cluster compounds in an organic acid matrix (matrix-assisted laser desorption/ionization) with a nitrogen laser (337 nm) produced distinct ion abundances that are relevant to different structural aspects of the cluster compound. Laser desorption/ionization of neat Au:SR compound films produces ions consistent with the inorganic core mass (i.e., devoid of original hydrocarbon content). Matrix-assisted laser desorption/ionization produces either ions with m/z values consistent with the core mass of the cluster compounds or ions with m/z values consistent with the approximate molecular weight of the cluster compounds, depending on ionization conditions. The ion abundances, and ionization conditions under which they are detected, provide insight into desorption/ionization processes for these unique cluster compounds as well as other analytes typically studied by matrix-assisted laser desorption/ionization.     

Analysis of lipids: metal oxide laser ionization mass spectrometry

Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) has been used for lipid analysis; however, one of the drawbacks of this technique is matrix interference peaks at low masses. Metal oxide surfaces are described here for direct, matrix-free analysis of small (MW < 1000 Da) lipid compounds, without interferences in the resulting spectra from traditional matrix background peaks. Spectra from lipid standards produced protonated and sodiated molecular ions. More complex mixtures including vegetable oil shortening and lipid extracts from bacterial and algal sources provided similar results. Mechanistic insight into the mode of ionization from surface spectroscopy, negative ion mass spectrometry, and stable isotope studies is also presented. The metal oxide system is compared to other reported matrix-free systems.     

MALDI ion trap mass spectrometer with charge detector for large biomolecule detection

Up to now, all commercial matrix-assisted laser desorption/ionization (MALDI) mass spectrometers still can not efficiently analyze very large biomolecules. In this work, we report the development of a novel MALDI ion trap mass spectrometer which can enrich biomolecular ions to enhance the detection sensitivity. A charge detector was installed to measure the large ions directly. With this design, we report the first measurement of IgM with the mass-to-charge ratio (m/z) at 980?000. In addition, quantitative measurements of the number of ions can be obtained. A step function frequency scan was first developed to get a clear signal in the m/z range from 200,000 to 1,000,000.     

Experimental investigations of the internal energy of molecules evaporated via laser-induced acoustic desorption into a Fourier transform ion cyclotron resonance mass spectrometer

The internal energy of neutral gas-phase organic and biomolecules, evaporated by means of laser-induced acoustic desorption (LIAD) into a Fourier transform ion cyclotron resonance mass spectrometer, was investigated through several experimental approaches. The desorbed molecules were demonstrated not to undergo degradation during the desorption process by collecting LIAD-evaporated molecules and subjecting them to analysis by electrospray ionization/quadrupole ion trap mass spectrometry. Previously established gas-phase basicity values were remeasured for LIAD-evaporated organic molecules and biomolecules with the use of the bracketing method. No endothermic reactions were observed. The remeasured basicity values are in close agreement with the values reported in the literature. The amount of internal energy deposited during LIAD is concluded to be less than a few kilocalories per mole. Chemical ionization with a series of proton-transfer reagents was employed to obtain a breakdown curve for a protonated dipeptide, Val-Pro, evaporated by LIAD. Comparison of this breakdown curve with a previously published analogous curve obtained by using substrate-assisted laser desorption (SALD) to evaporate the peptide suggests that the molecules evaporated via LIAD have a similar internal energy as those evaporated via SALD.     

Desorption and ionization mechanisms in desorption atmospheric pressure photoionization

The factors influencing desorption and ionization in newly developed desorption atmospheric pressure photoionization-mass spectrometry (DAPPI-MS) were studied. Redirecting the DAPPI spray was observed to further improve the versatility of the technique: for dilute samples, parallel spray with increased analyte signal was found to be the best suited, while for more concentrated samples, the orthogonal spray with less risk for contamination is recommended. The suitability of various spray solvents and sampling surface materials was tested for a variety of analytes with different polarities and molecular weights. As in atmospheric pressure photoionization, the analytes formed [M + H](+), [M - H](-), M(+*), M(-*), [M - H + O](-), or [M - 2H + 2O](-) ions depending on the analyte, spray solvent, and ionization mode. In positive ion mode, anisole and toluene as spray solvents promoted the formation of M(+*) ions and were therefore best suited for the analysis of nonpolar compounds (anthracene, benzo[a]pyrene, and tetracyclone). Acetone and hexane were optimal spray solvents for polar compounds (MDMA, testosterone, and verapamil) since they produced intensive [M + H](+) ion peaks of the analytes. In negative ion mode, the type of spray solvent affected the signal intensity, but not the ion composition. M(-*) ions were formed from 1,4-dinitrobenzene, and [M - H + O](-) and [M - 2H + 2O](-) ions from 1,4-naphthoquinone, whereas acidic compounds (naphthoic acid and paracetamol) formed [M - H](-) ions. The tested sampling surfaces included various materials with different thermal conductivities. The materials with low thermal conductivity, i.e., polymers like poly(methyl methacrylate) and poly(tetrafluoroethylene) (Teflon) were found to be the best, since they enable localized heating of the sampling surface, which was found to be essential for efficient analyte desorption. Nevertheless, the sampling surface material did not affect the ionization mechanisms.     

Ultrahigh Mass Accuracy in Isotope-Selective Collision-Induced Dissociation Using Correlated Sweep Excitation and Sustained Off-Resonance Irradiation: A Fourier Transform Ion Cyclotron Resonance Mass Spectrometry Case Study on the [M + 2H](2+) Ion of Bradykinin

Using electrospray ionization with a 9.4 T Fourier transform mass spectrometer, fragment ion spectra were acquired for a single isotopomer of doubly protonated bradykinin (molecular mass, 1059.6 Da). Correlated sweep excitation methods were applied to mass-select the single isotopomer (m/z = 530.8). Sustained off-resonance irradiation was used to activate and fragment the ions. The accuracy (in terms of m/z) in detection of the fragment ions was on average 1.2 ppm, making the assignments unambiguous. The methods employed would be generally applicable to ions in the mass range of approximately 50 Da to 50 kDa.     

Atmospheric pressure laser-induced acoustic desorption chemical ionization mass spectrometry for analysis of saturated hydrocarbons

We present atmospheric pressure laser-induced acoustic desorption chemical ionization (AP/LIAD-CI) with O(2) carrier/reagent gas as a powerful new approach for the analysis of saturated hydrocarbon mixtures. Nonthermal sample vaporization with subsequent chemical ionization generates abundant ion signals for straight-chain, branched, and cycloalkanes with minimal or no fragmentation. [M - H](+) is the dominant species for straight-chain and branched alkanes. For cycloalkanes, M(+?) species dominate the mass spectrum at lower capillary temperature (<100 °C) and [M - H](+) at higher temperature (>200 °C). The mass spectrum for a straight-chain alkane mixture (C(21)-C(40)) shows comparable ionization efficiency for all components. AP/LIAD-CI produces molecular weight distributions similar to those for gel permeation chromatography for polyethylene polymers, Polywax 500 and Polywax 655. Coupling of the technique to Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS) for the analysis of complex hydrocarbon mixtures provides unparalleled mass resolution and accuracy to facilitate unambiguous elemental composition assignments, e.g., 1754 peaks (rms error = 175 ppb) corresponding to a paraffin series (C(12)-C(49), double-bond equivalents, DBE = 0) and higher DBE series corresponding to cycloparaffins containing one to eight rings. Isoabundance-contoured plots of DBE versus carbon number highlight steranes (DBE = 4) of carbon number C(27)-C(30) and hopanes of C(29)-C(35) (DBE = 5), with sterane-to-hopane ratio in good agreement with field ionization (FI) mass spectrometry analysis, but performed at atmospheric pressure. The overall speciation of nonpolar, aliphatic hydrocarbon base oil species offers a promising diagnostic probe to characterize crude oil and its products.     

Electrospray ionization mass spectrometry of tetracycline, oxytetracycline, chlorotetracycline, minocycline, and methacycline

The effects of mobile-phase additives and analyte concentration on electrospray ionization mass spectra of a series of tetracyclines were investigated in both positive and negative ion modes. Only [M + H](+) and [M - H](-) ions were observed. The greatest sensitivity as [M + H](+) ions was obtained with 1% acetic acid and the greatest sensitivity as [M - H](-) ions was obtained using 50 mM ammonium hydroxide. Sensitivities in the positive ion mode were greater than those in the negative ion mode. The sensitivity as [M + H](+) showed no systematic variation with pH; however, the sensitivity as [M - H](-) did increase with increasing pH. A larger linear range was observed for [M - H](-) than for [M + H](+) ions. Both [M + Na](+) and [M + H](+) ions were observed with 0.5 mM sodium acetate and sodium iodide, but no adduct ions were observed with ammonium acetate. Some M(2)H(+) ions were observed at higher concentrations. Cluster ions, Na(NaOAc)(n)(+) or Na(NaI)(n)(+), but no sample ions were observed using 5 mM salts. The data suggest that mechanisms in addition to solution ionization are involved in the formation of the ESI sample ions. The utility of mobile phases containing 1% HOAc or 50 mM NH(4)OH was demonstrated for chromatographic separations.     

Scrubbing ions with molecules: kinetic studies of chemical noise reduction in mass spectrometry using ion-molecule reactions with dimethyl disulfide

The kinetics and product distributions of the reactions of dimethyl disulfide (DMDS) have been investigated with a group of chemical background ions commonly observed in atmospheric pressure ionization (API) mass spectrometry (MS) in order to assess the value of this molecule in filtering (or "scrubbing") these ions by changing their mass/charge (m/z) ratio. The measurements were taken with a novel electrospray ionization/selected ion flow tube/QqQ tandem mass spectrometer. The background ions studied include those with m/z 42 (protonated acetonitrile, ACN), 83 (protonated ACN dimer), 99 (protonated phosphoric acid), 117 (water cluster of m/z 99), 131 (methanol cluster of m/z 99), 149 (protonated phthalic anhydride, formed from the phthalates), and 327 (protonated triphenyl phosphate). In addition, reactions of DMDS have been studied with two model analytes--protonated caffeine and doubly protonated bradykinin--in order to assess the selectivity of DMDS reactivity. All the measurements were taken at 295 +/- 2 K in helium buffer gas at a pressure of 0.35 +/- 0.01 Torr. DMDS was observed to react efficiently with m/z 42 (ACNH+), 149 (from phthalates), and 99 (protonated phosphoric acid), with k/kc=0.91, 0.47, and 0.38, respectively. Only proton transfer was observed with ACNH+, followed by the secondary reaction of [DMDSH]+ with DMDS to yield [CH3S-S(CH3)-SCH3]+. Ligation of DMDS was the dominant primary channel observed for the reaction of the m/z 149 background ion; however, some proton transfer also was observed. Both of these primary product ions react further with DMDS to yield [CH3S-S(CH3)-SCH3]+, the structure of which we have determined computationally using DFT calculations. Only the sequential ligation with two DMDS molecules was observed for the reaction of the m/z 99 ion. Reactions of DMDS with m/z 117 [H3PO4 + H + H2O]+ and m/z 131 [H3PO4 + H + MeOH]+ were observed to proceed with k/kc=0.71 and 0.058, respectively. Ligand substitution of DMDS for H2O predominated ( approximately 94%) over DMDS ligation ( approximately 6%) in the reaction with m/z 117, while only DMDS ligation was observed for the reaction of m/z 131 with DMDS. In contrast, the reactions of DMDS with ions of m/z 83 (protonated dimer of ACN) and 327 (protonated triphenyl phosphate) were extremely inefficient, with k/kc=0.0042 and 0.0079, respectively. The higher reactivity of DMDS toward ACNH+ (m/z 42) compared to (ACN)2H+ (m/z 83) is attributed to the lower proton affinity of the unsolvated ACN. The reactivity of DMDS toward the two model analyte ions studied-protonated caffeine and doubly protonated bradykinin-was negligible, with k/kc=0.0073 and 0.010, for the respective reactions. These results suggest that, under appropriate reagent pressure conditions, DMDS can be an appropriate reagent for chemically filtering out many common API-MS background ions, without significantly affecting the observed intensity of analyte peaks.     

Molecular weight distributions of asphaltenes and deasphaltened oils studied by laser desorption ionization and ion mobility mass spectrometry

Laser desorption ionization (LDI) and ion mobility mass spectrometry (IM-MS) are applied to study molecular weight distribution and cross sections of petroleum asphaltene (ASPH) and deasphaltened oils (DAO). Ion mobility data confirmed the presence of gas-phase aggregation in LDI experiments. Most of the molecules with MW > 3000 g/mol in LDI result from gas-phase aggregation. Two-dimensional (2D) IM-MS trend lines are compared with model polymer systems to confirm the order of cross sections (polywax > polystyrene > DAO > ASPH > fullerenes), and these data illustrate that ASPH has a more condensed average structure than DAO.     

Atmospheric pressure laser-induced acoustic desorption chemical ionization fourier transform ion cyclotron resonance mass spectrometry for the analysis of complex mixtures

We present a novel nonresonant laser-based matrix-free atmospheric pressure ionization technique, atmospheric pressure laser-induced acoustic desorption chemical ionization (AP/LIAD-CI). The technique decouples analyte desorption from subsequent ionization by reagent ions generated from a corona discharge initiated in ambient air or in the presence of vaporized toluene as a CI dopant at room temperature. Analyte desorption is initiated by a shock wave induced in a titanium foil coated with electrosprayed sample, irradiated from the rear side by high-energy laser pulses. The technique enables facile and independent optimization of the analyte desorption, ionization, and sampling events, for coupling to any mass analyzer with an AP interface. Moreover, the generated analyte ions are efficiently thermalized by collisions with atmospheric gases, thereby reducing fragmentation. We have coupled AP/LIAD-CI to ultrahigh-resolution FT-ICR MS to generate predominantly [M + H](+) or M(+?) ions to resolve and identify thousands of elemental compositions from organic mixtures as complex as petroleum crude oil distillates. Finally, we have optimized the AP/LIAD CI process and investigated ionization mechanisms by systematic variation of placement of the sample, placement of the corona discharge needle, discharge current, gas flow rate, and inclusion of toluene as a dopant.     

Studies on thermal decomposition mechanism of CL-20 by pyrolysis gas chromatography-mass spectrometry (Py-GC/MS)

The thermal decomposition study of CL-20 (hexanitrohexaazaisowurtzitane) using pyrolysis GC/MS was carried out mainly by electron impact (EI) mode. Chemical ionization (CI) mode was used for further confirmation of identified species. Mass spectrum of CL-20 decomposition products predominantly revealed fragments with m/z 81 and 96 corresponding to C(4)H(5)N(2)(+) and C(4)H(4)N(2)O(+) ions, respectively. The total ion chromatogram (TIC) of CL-20 pyrolysis shows peak within first 2 min due to the presence of low molecular weight gases. Peaks corresponding to several other products were also observed including the atmospheric gases. Cyanogen formation (C(2)N(2), m/z 52) observed to be enriched at the scan number 300-500. The low molecular mass range decomposition products formed by cleavage of C-N ring structure were found in majority. Additional structural information was sought by employing chemical ionization mode. The data generated during this study was instrumented in determining decomposition pathways of CL-20.     

Laser-driven acoustic desorption of organic molecules from back-irradiated solid foils

Laser-induced acoustic desorption (LIAD) from thin metal foils is a promising technique for gentle and efficient volatilization of intact organic molecules from surfaces of solid substrates. Using the single-photon ionization method combined with time-of-flight mass spectrometry, we have examined the neutral component of the desorbed flux in LIAD and compared it to that from direct laser desorption. These basic studies of LIAD, conducted for molecules of various organic dyes (rhodamine B, fluorescein, anthracene, coumarin, BBQ), have demonstrated detection of intact parent molecules of the analyte even at its surface concentrations corresponding to a submonolayer coating. In some cases (rhodamine B, fluorescein, BBQ), the parent molecular ion peak was accompanied by a few fragmentation peaks of comparable intensity, whereas for others, only peaks corresponding to intact parent molecules were detected. At all measured desorbing laser intensities (from 100 to 500 MW/cm2), the total amount of desorbed parent molecules depended exponentially on the laser intensity. Translational velocities of the desorbed intact molecules, determined for the first time in this work, were of the order of hundreds of meters per second, less than what has been observed in our experiments for direct laser desorption, but substantially greater than the possible perpendicular velocity of the substrate foil surface due to laser-generated acoustic waves. Moreover, these velocities did not depend on the desorbing laser intensity, which implies the presence of a more sophisticated mechanism of energy transfer than direct mechanical or thermal coupling between the laser pulse and the adsorbed molecules. Also, the total flux of desorbed intact molecules as a function of the total number of desorbing laser pulses, striking the same point on the target, decayed following a power law rather than an exponential function, as would have been predicted by the shake-off model. To summarize, the results of our experiments indicate that the LIAD phenomenon cannot be described in terms of simple mechanical shake-off or direct laser desorption. Rather, they suggest that multistep energy-transfer processes are involved. Two possible (and not mutually exclusive) qualitative mechanisms of LIAD that are based on formation of nonequilibrium energy states in the adsorbate-substrate system are proposed and discussed.     

Analysis of protein phosphorylation by hypothesis-driven multiple-stage mass spectrometry

We describe a strategy, which we term hypothesis-driven multiple-stage mass spectrometry (HMS-MS), for the sensitive detection and identification of phosphopeptides derived from enzymatic digests of phosphoproteins. In this strategy, we postulate that any or all of the potential sites of phosphorylation in a given protein may be phosphorylated. Using this assumption, we calculate the m/z values of all the corresponding singly charged phosphopeptide ions that could, in theory, be produced by the enzyme employed for proteolysis. We test ions at these m/z values for the presence of phosphoserine or phosphothreonine residues using tandem mass spectrometry (MS(2)) in a vacuum MALDI ion trap mass spectrometer, where the neutral loss of the elements of H(3)PO(4) (98 Da) provides a sensitive assay for the presence of phosphopeptides. Subsequent MS(3) analysis of the (M + H - 98)(+) peaks allows us to confirm or reject the hypotheses that the putative phosphopeptides are present in the sample. HMS-MS was successfully applied to the detection and identification of phosphopeptides from substrates of the Saccharomyces cerevisiae cyclin-dependent kinase (Cdk) Cdc28, phosphorylated in vitro (Ipl1) and in vivo (Orc6), basing hypothesis formation on the minimal Cdk consensus phosphorylation motif Ser/Thr-Pro. The method was also used to find in vitro phosphopeptides from a domain of the Drosophila melanogaster protein PERIOD, hypothesizing possible phosphorylations of all Ser/Thr residues without assuming a consensus motif. Our results demonstrate that HMS-MS is a sensitive, highly specific tool for systematically surveying proteins for Ser/Thr phosphorylation, and represents a significant step toward our goal of comprehensive phosphorylation mapping.